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 Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer 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 CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample pox qox pox_cutoff isArtifactMode oxoGCut CTD-2012J19.3 0 broad.mit.edu 37 5 1602656 1602656 + RNA SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:1602656G>A ENST00000605200.1 + 0 622 RP11-43F13.1_ENST00000507841.1_RNA acagagacggggggagaggga 0.458000 5 92 0 0 1 0 0 SMAD4 4089 broad.mit.edu 37 18 48575671 48575671 + Nonsense_Mutation SNP C C G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr18:48575671C>G ENST00000342988.3 + 4 969 c.431C>G c.(430-432)tCa>tGa p.S144* SMAD4_ENST00000398417.2_Nonsense_Mutation_p.S144*|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000452201.2_Nonsense_Mutation_p.S144*|SMAD4_ENST00000588745.1_Nonsense_Mutation_p.S144* NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 144 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?(36)|p.S144*(5)|p.?(4) NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1) 454 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) TAAGATCTCTCAGGATTAACA 0.294000 30 49 0 0 1 0 0 AGAP10 728127 broad.mit.edu 37 10 47207813 47207813 + Splice_Site SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:47207813T>C ENST00000355232.3 - 5 3482 c.471_splice c.e5+1 p.H157_splice AGAP10_ENST00000413193.2_Splice_Site_p.H228_splice|RP11-144G6.12_ENST00000605970.1_RNA|AGAP10_ENST00000452145.2_Splice_Site_p.H132_splice ArfGAP with GTPase domain, ankyrin repeat and PH domain 10 p.H228R(20) endometrium(5)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1) 12 TTTACTTACATGGTTTGTACA 0.294000 5 77 0 0 1 0 0 LAMB2 3913 broad.mit.edu 37 3 49166233 49166233 + Missense_Mutation SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:49166233C>T ENST00000418109.1 - 15 1915 c.1751G>A c.(1750-1752)cGc>cAc p.R584H LAMB2_ENST00000305544.4_Missense_Mutation_p.R584H NM_002292.3 NP_002283.3 P55268 LAMB2_HUMAN laminin, beta 2 (laminin S) 584 Laminin IV type B. cell adhesion laminin-11 complex|laminin-3 complex structural molecule activity p.R584H(1) NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 61 BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245) GGTCACCAGGCGCTCCACCAC 0.617000 124 270 0 0 1 0 0 KDM3B 51780 broad.mit.edu 37 5 137756544 137756544 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:137756544G>A ENST00000314358.5 + 15 4065 c.3865G>A c.(3865-3867)Gaa>Aaa p.E1289K KDM3B_ENST00000394866.1_Missense_Mutation_p.E945K|KDM3B_ENST00000542866.1_Missense_Mutation_p.E321K NM_016604.3 NP_057688.2 Q7LBC6 KDM3B_HUMAN lysine (K)-specific demethylase 3B 1289 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3) 65 CAACAAAACCGAAGGGTCTAG 0.547000 10 354 0 0 1 0 0 PDZRN3 23024 broad.mit.edu 37 3 73438996 73438996 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:73438996G>A ENST00000263666.4 - 7 1501 c.1387C>T c.(1387-1389)Cgc>Tgc p.R463C PDZRN3_ENST00000466348.1_5'UTR|PDZRN3_ENST00000479530.1_Missense_Mutation_p.R180C|PDZRN3_ENST00000535920.1_Missense_Mutation_p.R185C|PDZRN3_ENST00000462146.2_Missense_Mutation_p.R120C|PDZRN3_ENST00000466780.1_Missense_Mutation_p.R120C NM_015009.1 NP_055824.1 Q9UPQ7 PZRN3_HUMAN PDZ domain containing ring finger 3 463 PDZ 2. ubiquitin-protein ligase activity|zinc ion binding breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1) 69 Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236) BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134) TCTCGGATGCGCCCATCCTTG 0.468000 102 250 0 0 1 0 0 TP53 7157 broad.mit.edu 37 17 7579358 7579358 + Missense_Mutation SNP C C A rs11540654 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:7579358C>A ENST00000420246.2 - 4 461 c.329G>T c.(328-330)cGt>cTt p.R110L TP53_ENST00000269305.4_Missense_Mutation_p.R110L|TP53_ENST00000445888.2_Missense_Mutation_p.R110L|TP53_ENST00000359597.4_Missense_Mutation_p.R110L|TP53_ENST00000413465.2_Missense_Mutation_p.R110L|TP53_ENST00000455263.2_Missense_Mutation_p.R110L NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 110 Interaction with HIPK1 (By similarity).|Interaction with WWOX. R -> C (in sporadic cancers; somatic mutation).|R -> G (in a sporadic cancer; somatic mutation).|R -> H (in sporadic cancers; somatic mutation).|R -> L (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation; dbSNP:rs11540654).|R -> S (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|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|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 repressor activity|ubiquitin protein ligase binding|zinc ion binding p.R110L(36)|p.R110P(9)|p.0?(8)|p.G59fs*23(3)|p.R110fs*13(2)|p.F109_R110delFR(2)|p.R110H(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y107fs*44(1)|p.R110fs*39(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y107fs*38(1)|p.Y103_L111>L(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 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) GAAGCCCAGACGGAAACCGTA 0.612000 111 """Mis, N, F""" """breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types""" """breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types""" Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 124 167 3.6033e-41 4.07173e-41 1 1 0 POM121L9P 0 broad.mit.edu 37 22 24659591 24659591 + RNA SNP A A G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:24659591A>G ENST00000414583.2 + 0 3116 NR_003714.1 ACTCACTGACATCGAAGGCTG 0.632000 8 132 0 0 1 0 0 PCDHGB6 0 broad.mit.edu 37 5 140788898 140788898 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:140788898G>A ENST00000520790.1 + 1 1129 c.1129G>A c.(1129-1131)Gga>Aga p.G377R PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA8_ENST00000398604.2_Intron NM_018926.2|NM_032100.1 NP_061749.1|NP_115271.1 breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2) 48 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TCTGGATTTCGGAGGAAATGG 0.413000 53 171 0 0 1 0 0 CACNA1A 773 broad.mit.edu 37 19 13445253 13445253 + Silent SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:13445253C>T ENST00000360228.5 - 8 1136 c.1137G>A c.(1135-1137)ctG>ctA p.L379L CACNA1A_ENST00000573710.2_Silent_p.L379L NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2 NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2 O00555 CAC1A_HUMAN calcium channel, voltage-dependent, P/Q type, alpha 1A subunit 379 cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion cytoplasm|nucleus syntaxin binding breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1) 42 OV - Ovarian serous cystadenocarcinoma(19;5.07e-21) Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230) GTTGCCGCCTCAGCTTCAGAA 0.517000 130 278 0 0 1 0 0 SPTBN4 57731 broad.mit.edu 37 19 41063285 41063285 + Silent SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:41063285T>C ENST00000352632.3 + 26 5732 c.5646T>C c.(5644-5646)caT>caC p.H1882H SPTBN4_ENST00000595535.1_Silent_p.H1882H|SPTBN4_ENST00000338932.3_Silent_p.H1882H|SPTBN4_ENST00000598249.1_Silent_p.H1882H|SPTBN4_ENST00000392025.1_Silent_p.H625H|SPTBN4_ENST00000392023.1_Silent_p.H558H Q9H254 SPTN4_HUMAN spectrin, beta, non-erythrocytic 4 1882 actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport cytosol|nuclear matrix|PML body|spectrin actin binding|ankyrin binding|structural constituent of cytoskeleton breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1) 73 Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384) CCTTTGAGCATGACCTGCAGC 0.667000 134 267 0 0 1 0 0 PCDHA4 0 broad.mit.edu 37 5 140188477 140188477 + Missense_Mutation SNP C C T rs13189658 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:140188477C>T ENST00000530339.1 + 1 1705 c.1705C>T c.(1705-1707)Cgg>Tgg p.R569W PCDHA4_ENST00000356878.4_Missense_Mutation_p.R569W|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.R569W|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron NM_018907.2 NP_061730.1 breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 78 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCTAGCGCCTCGGGCGGGTGG 0.687000 179 341 0 0 1 0 0 TUBB8P7 0 broad.mit.edu 37 16 90162513 90162513 + RNA SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:90162513T>C ENST00000564451.1 + 0 1866 TUBB8P7_ENST00000567960.1_RNA p.N415N(2) GCAACATGAATGACCTGGTGT 0.537000 12 588 0 0 1 0 0 WNT7B 7477 broad.mit.edu 37 22 46327243 46327243 + Missense_Mutation SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:46327243C>T ENST00000339464.4 - 3 679 c.305G>A c.(304-306)cGt>cAt p.R102H WNT7B_ENST00000409496.3_Missense_Mutation_p.R106H|WNT7B_ENST00000410058.1_Missense_Mutation_p.R102H|WNT7B_ENST00000410089.1_Missense_Mutation_p.R86H NM_058238.2 NP_478679.1 P56706 WNT7B_HUMAN wingless-type MMTV integration site family, member 7B 102 activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway extracellular space|plasma membrane|proteinaceous extracellular matrix extracellular matrix structural constituent|frizzled binding|signal transducer activity endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1) 19 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247) GGCAGCCTCACGGCTCCCTGC 0.701000 59 62 0 0 1 0 0 PRPS1 5631 broad.mit.edu 37 X 106890883 106890883 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:106890883G>A ENST00000372435.4 + 6 874 c.752G>A c.(751-753)gGa>gAa p.G251E PRPS1_ENST00000372418.1_Missense_Mutation_p.G151E|PRPS1_ENST00000372428.4_Missense_Mutation_p.G184E|PRPS1_ENST00000543248.1_Missense_Mutation_p.G251E NM_002764.3 NP_002755.1 P60891 PRPS1_HUMAN phosphoribosyl pyrophosphate synthetase 1 251 5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process cytosol ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1) 23 TTGACTCATGGAATCTTCTCC 0.443000 42 727 0 0 1 0 0 SLCO1C1 53919 broad.mit.edu 37 12 20854386 20854386 + Silent SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:20854386T>C ENST00000381552.1 + 3 632 c.264T>C c.(262-264)ttT>ttC p.F88F SLCO1C1_ENST00000540354.1_Silent_p.F88F|SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000266509.2_Silent_p.F88F|SLCO1C1_ENST00000545604.1_Silent_p.F88F Q9NYB5 SO1C1_HUMAN solute carrier organic anion transporter family, member 1C1 88 sodium-independent organic anion transport integral to membrane|plasma membrane thyroid hormone transmembrane transporter activity NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1) 60 Esophageal squamous(101;0.149) ATGGTAGTTTTGAAATTGGTA 0.418000 175 309 0 0 1 0 0 AMZ2P1 0 broad.mit.edu 37 17 62968690 62968690 + RNA SNP A A G rs138671696 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:62968690A>G ENST00000430983.1 - 0 1554 NR_026903.1 AAAATTCCACAAGTCTCTTGG 0.373000 9 415 0 0 1 0 0 SGSM3 27352 broad.mit.edu 37 22 40802489 40802489 + Silent SNP G G A rs143556388 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:40802489G>A ENST00000248929.9 + 10 1197 c.1008G>A c.(1006-1008)acG>acA p.T336T SGSM3_ENST00000454798.2_Silent_p.T269T NM_015705.4 NP_056520.2 Q96HU1 SGSM3_HUMAN small G protein signaling modulator 3 336 cell cycle arrest|Rap protein signal transduction cytoplasm Rab GTPase activator activity|Rab GTPase binding cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6) 19 TCTTCAACACGCTATCGGATA 0.627000 4 120 0 0 1 0 0 AC008103.5 0 broad.mit.edu 37 22 18844888 18844888 + RNA SNP A A G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:18844888A>G ENST00000412938.1 + 0 3138 GCTCACGGAAATACAGCTTCA 0.587000 14 368 0 0 1 0 0 VPS29 51699 broad.mit.edu 37 12 110933972 110933972 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:110933972G>A ENST00000549578.1 - 2 105 c.40C>T c.(40-42)Cgg>Tgg p.R14W VPS29_ENST00000447578.2_5'UTR|VPS29_ENST00000549970.1_5'UTR|VPS29_ENST00000360579.7_Missense_Mutation_p.R18W|VPS29_ENST00000546588.1_Missense_Mutation_p.R46W|VPS29_ENST00000552130.2_5'UTR NM_016226.3 NP_057310.1 Q9UBQ0 VPS29_HUMAN vacuolar protein sorting 29 homolog (S. cerevisiae) 14 protein transport endosome membrane metal ion binding|phosphoserine phosphatase activity kidney(1)|large_intestine(1)|lung(1)|prostate(1) 4 CTGTTGCACCGGTGTGGGATG 0.398000 103 260 0 0 1 0 0 TRIM73 0 broad.mit.edu 37 7 75028266 75028266 + Missense_Mutation SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:75028266C>T ENST00000323819.3 + 2 249 c.49C>T c.(49-51)Ccc>Tcc p.P17S TRIM73_ENST00000450434.1_Intron|TRIM73_ENST00000430211.1_Missense_Mutation_p.P17S|TRIM73_ENST00000447409.2_Missense_Mutation_p.P17S|TRIM73_ENST00000437796.1_Missense_Mutation_p.P17S|TRIM73_ENST00000463766.1_3'UTR NM_198924.2 NP_944606.2 Q86UV6 TRI74_HUMAN tripartite motif containing 73 17 intracellular zinc ion binding endometrium(1)|large_intestine(1)|lung(1)|pancreas(1) 4 GCTTCAGTGTCCCATCTGCCT 0.602000 106 439 0 0 1 0 0 SLCO1B3 28234 broad.mit.edu 37 12 21011409 21011409 + Missense_Mutation SNP G G C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:21011409G>C ENST00000381545.3 + 5 482 c.263G>C c.(262-264)gGa>gCa p.G88A SLCO1B3_ENST00000261196.2_Missense_Mutation_p.G88A|LST3_ENST00000540229.1_Missense_Mutation_p.G88A|LST3_ENST00000381541.3_Missense_Mutation_p.G88A|SLCO1B3_ENST00000545880.1_3'UTR|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.G88A|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.G88A NM_019844.3 NP_062818.1 Q9NPD5 SO1B3_HUMAN solute carrier organic anion transporter family, member 1B3 88 bile acid metabolic process|sodium-independent organic anion transport basolateral plasma membrane|cytoplasm|integral to plasma membrane bile acid transmembrane transporter activity|organic anion transmembrane transporter activity breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2) 63 Esophageal squamous(101;0.149) AGTTACTTTGGATCTAAACTA 0.308000 10 215 0 0 1 0 0 GUSBP1 0 broad.mit.edu 37 5 21491513 21491513 + RNA SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:21491513G>A ENST00000607545.1 + 0 179 NR_027026.1 AAACAAAGTCGTGGACAACCA 0.547000 11 265 0 0 1 0 0 UGGT2 55757 broad.mit.edu 37 13 96651510 96651510 + Missense_Mutation SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr13:96651510T>C ENST00000376747.3 - 6 782 c.712A>G c.(712-714)Att>Gtt p.I238V UGGT2_ENST00000376714.3_Missense_Mutation_p.I238V|UGGT2_ENST00000397618.3_Missense_Mutation_p.I238V|UGGT2_ENST00000376712.4_Missense_Mutation_p.I238V|UGGT2_ENST00000467305.1_5'UTR NM_020121.3 NP_064506.3 Q9NYU1 UGGG2_HUMAN UDP-glucose glycoprotein glucosyltransferase 2 238 post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine endoplasmic reticulum lumen|ER-Golgi intermediate compartment UDP-glucose:glycoprotein glucosyltransferase activity NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2) 60 GTACTCTTAATTGCTAGCTCC 0.348000 171 378 0 0 1 0 0 TUBB8P7 0 broad.mit.edu 37 16 90162462 90162462 + RNA SNP A A G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:90162462A>G ENST00000564451.1 + 0 1815 TUBB8P7_ENST00000567960.1_RNA p.T398T(1) ACTGGTACACAGGCGAGGGCA 0.522000 15 491 0 0 1 0 0 RP11-156P1.3 0 broad.mit.edu 37 17 45128812 45128812 + RNA SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:45128812C>T ENST00000575173.1 - 0 418 AGTCCTGTTTCTGTGTGGATT 0.373000 8 165 0 0 1 0 0 RP11-798G7.5 0 broad.mit.edu 37 17 43587730 43587730 + RNA SNP A A C rs142536398 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:43587730A>C ENST00000253803.2 + 0 267 LRRC37A4P_ENST00000579913.1_RNA GTATTGATTCATTTTATTCAT 0.343000 7 281 0 0 1 0 0 TSSC2 0 broad.mit.edu 37 11 3427845 3427845 + RNA SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:3427845C>T ENST00000529482.1 + 0 962 CTTCAAGTGGCAGGAGCAGAA 0.587000 7 221 0 0 1 0 0 ZFHX3 463 broad.mit.edu 37 16 72821615 72821615 + Silent SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:72821615G>A ENST00000268489.5 - 10 11232 c.10560C>T c.(10558-10560)ggC>ggT p.G3520G AC004943.1_ENST00000584072.1_RNA|ZFHX3_ENST00000397992.5_Silent_p.G2606G NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 3520 Poly-Gly. 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 NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) cgccgccgccgccaccgccgc 0.706000 12 218 0 0 1 0 0 AC024560.3 0 broad.mit.edu 37 3 197348634 197348634 + RNA SNP G G C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:197348634G>C ENST00000418868.1 - 0 625 NR_003266.2 CAGCAGCACCGATGGGCCTGC 0.542000 19 370 0 0 1 0 0 SERPINB5 5268 broad.mit.edu 37 18 61156680 61156680 + Missense_Mutation SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr18:61156680T>C ENST00000382771.4 + 4 699 c.407T>C c.(406-408)aTt>aCt p.I136T SERPINB5_ENST00000489441.1_Missense_Mutation_p.I136T NM_002639.4 NP_002630.2 P36952 SPB5_HUMAN serpin peptidase inhibitor, clade B (ovalbumin), member 5 136 cellular component movement|regulation of proteolysis cytoplasm|extracellular space protein binding|serine-type endopeptidase inhibitor activity kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1) 12 AACAACTCAATTAAGGATCTC 0.388000 92 91 0 0 1 0 0 VTN 7448 broad.mit.edu 37 17 26696428 26696428 + Missense_Mutation SNP T T C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:26696428T>C ENST00000226218.4 - 4 1169 c.551A>G c.(550-552)gAc>gGc p.D184G SEBOX_ENST00000536498.1_5'UTR|SARM1_ENST00000379061.4_Intron|CTB-96E2.3_ENST00000591482.1_RNA|TMEM199_ENST00000509083.1_Intron NM_000638.3 NP_000629.3 P04004 VTNC_HUMAN vitronectin 184 Hemopexin-like 1. cell adhesion mediated by integrin|immune response|negative regulation of endopeptidase activity|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein binding|positive regulation of receptor-mediated endocytosis|positive regulation of smooth muscle cell migration|positive regulation of vascular endothelial growth factor receptor signaling pathway|smooth muscle cell-matrix adhesion alphav-beta3 integrin-vitronectin complex|extracellular space heparin binding|integrin binding|scavenger receptor activity kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1) 13 all_lung(13;0.000533)|Lung NSC(42;0.00171) UCEC - Uterine corpus endometrioid carcinoma (53;0.153) Urokinase(DB00013) TGCCTTTTCGTCCAGTTCATA 0.617000 8 293 0 0 1 0 0 RP11-156P1.3 0 broad.mit.edu 37 17 45128792 45128792 + RNA SNP G G T rs143713325 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:45128792G>T ENST00000575173.1 - 0 418 AATTCAGGTTGTCAGAATGCA 0.373000 8 199 0.000274275 0.000276724 1 1 0 CCT6P1 0 broad.mit.edu 37 7 65222986 65222986 + RNA SNP G G T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:65222986G>T ENST00000442266.1 + 0 578 GAATTCTGGCGTTTTTTACAA 0.289000 6 78 0.000157383 0.000160219 1 1 0 KRT16P2 0 broad.mit.edu 37 17 16735618 16735618 + RNA SNP G G A rs645134 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:16735618G>A ENST00000579062.1 - 0 270 TACCAGTCACGGATCTTCACT 0.582000 14 561 0 0 1 0 0 KRTAP1-5 83895 broad.mit.edu 37 17 39183145 39183145 + Missense_Mutation SNP A A G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:39183145A>G ENST00000361883.5 - 1 309 c.263T>C c.(262-264)aTc>aCc p.I88T NM_031957.1 NP_114163.1 Q9BYS1 KRA15_HUMAN keratin associated protein 1-5 88 15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP]. keratin filament p.I88T(11) central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2) 17 Breast(137;0.00043) STAD - Stomach adenocarcinoma(17;0.000371) GCAGGAGCTGATCTGGCAGCA 0.632000 15 228 0 0 1 0 0 ULK4 54986 broad.mit.edu 37 3 41795926 41795926 + Missense_Mutation SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:41795926C>T ENST00000301831.4 - 22 2710 c.2248G>A c.(2248-2250)Gca>Aca p.A750T NM_017886.2 NP_060356.2 Q96C45 ULK4_HUMAN unc-51 like kinase 4 750 ATP binding|protein serine/threonine kinase activity breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1) 22 KIRC - Kidney renal clear cell carcinoma(284;0.214) AAGGCTTTTGCTCTAATGCAT 0.358000 10 328 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414340 20414340 + Silent SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr9:20414340G>A ENST00000380338.4 - 5 790 c.504C>T c.(502-504)agC>agT p.S168S MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 168 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding p.S168S(5) central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) tgctgctgctgctactgctgc 0.537000 T MLL ALL 24 463 0 0 1 0 0 TACC2 10579 broad.mit.edu 37 10 123844650 123844650 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:123844650G>A ENST00000369005.1 + 4 2975 c.2635G>A c.(2635-2637)Gtg>Atg p.V879M TACC2_ENST00000453444.2_Missense_Mutation_p.V879M|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.V879M|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.V879M|TACC2_ENST00000334433.3_Missense_Mutation_p.V879M NM_206862.2 NP_996744.2 O95359 TACC2_HUMAN transforming, acidic coiled-coil containing protein 2 879 microtubule organizing center|nucleus nuclear hormone receptor binding NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3) 83 all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197) CCATGTACCTGTGGAACCTCA 0.517000 96 216 0 0 1 0 0 SPARC 6678 broad.mit.edu 37 5 151045924 151045924 + Silent SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:151045924G>A ENST00000231061.4 - 8 1045 c.732C>T c.(730-732)gaC>gaT p.D244D NM_003118.3 NP_003109.1 P09486 SPRC_HUMAN secreted protein, acidic, cysteine-rich (osteonectin) 244 ossification|platelet activation|platelet degranulation|signal transduction basement membrane|extracellular space|platelet alpha granule lumen calcium ion binding|collagen binding p.D244D(1) central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1) 15 Medulloblastoma(196;0.109)|all_hematologic(541;0.122) Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) OV - Ovarian serous cystadenocarcinoma(192;0.00118) Becaplermin(DB00102) GGTCTTACCCGTCAATGGGGT 0.572000 63 229 0 0 1 0 0 WTAP 9589 broad.mit.edu 37 6 160174521 160174521 + Missense_Mutation SNP G G A rs112093927 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:160174521G>A ENST00000358372.4 + 7 2239 c.482G>A c.(481-483)tGt>tAt p.C161Y SOD2_ENST00000546087.1_Intron NM_001270531.1|NM_004906.4 NP_001257460.1|NP_004897.2 Q15007 FL2D_HUMAN Wilms tumor 1 associated protein 161 cell cycle|mRNA processing|RNA splicing nuclear membrane|nucleolus central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1) 18 Breast(66;0.000776)|Ovarian(120;0.0303) OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06) ATGGCGAAGTGTCGAATGCTT 0.423000 93 124 0 0 1 0 0 FLRT2 23768 broad.mit.edu 37 14 86089482 86089482 + Missense_Mutation SNP C C A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr14:86089482C>A ENST00000330753.4 + 2 2391 c.1624C>A c.(1624-1626)Ctg>Atg p.L542M FLRT2_ENST00000554746.1_Missense_Mutation_p.L542M NM_013231.4 NP_037363.1 O43155 FLRT2_HUMAN fibronectin leucine rich transmembrane protein 2 542 cell adhesion integral to plasma membrane|proteinaceous extracellular matrix protein binding, bridging|receptor signaling protein activity NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 73 BRCA - Breast invasive adenocarcinoma(234;0.0319) CTCCCCCTTTCTGCTGGCGGG 0.587000 223 471 1.45647e-77 1.6794e-77 1 1 0 ADNP 23394 broad.mit.edu 37 20 49510730 49510730 + Missense_Mutation SNP T T A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr20:49510730T>A ENST00000396029.3 - 5 1088 c.521A>T c.(520-522)gAt>gTt p.D174V ADNP_ENST00000396032.3_Missense_Mutation_p.D174V|ADNP_ENST00000349014.3_Missense_Mutation_p.D174V|ADNP_ENST00000371602.4_Missense_Mutation_p.D174V NM_015339.2 NP_056154.1 Q9H2P0 ADNP_HUMAN activity-dependent neuroprotector homeobox 174 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2) 39 ATAAAGAGGATCTCGGTAAGT 0.398000 270 611 0 0 1 0 0 OPCML 4978 broad.mit.edu 37 11 132307162 132307162 + Silent SNP G G A rs143650226 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:132307162G>A ENST00000331898.7 - 4 1196 c.618C>T c.(616-618)aaC>aaT p.N206N OPCML_ENST00000541867.1_Silent_p.N206N|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000374778.4_Silent_p.N165N|OPCML_ENST00000524381.1_Silent_p.N199N NM_002545.3 NP_002536.1 Q14982 OPCM_HUMAN opioid binding protein/cell adhesion molecule-like 206 Ig-like C2-type 2. cell adhesion|neuron recognition anchored to membrane|integral to plasma membrane opioid receptor activity endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8) 47 all_hematologic(175;0.019) all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129) all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012) CAGCGACATCGTTCAACGCGC 0.552000 117 246 0 0 1 0 0 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:25398284C>A ENST00000311936.3 - 2 226 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000256078.4_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V NM_004985.3 NP_004976.2 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog 12 G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation). 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 p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57) 25349 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) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis """pancreatic, colorectal, lung, thyroid, AML, others""" Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) 15 75 1.67942e-08 1.77359e-08 1 1 0 GPR115 221393 broad.mit.edu 37 6 47682152 47682152 + Missense_Mutation SNP A A T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:47682152A>T ENST00000283303.2 + 6 1429 c.1171A>T c.(1171-1173)Atg>Ttg p.M391L GPR115_ENST00000327753.3_Missense_Mutation_p.M391L|GPR115_ENST00000371220.1_Missense_Mutation_p.M448L NM_153838.3 NP_722580.3 Q8IZF3 GP115_HUMAN G protein-coupled receptor 115 391 GPS. neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2) 52 TTCCATTCTCATGTCCTCCAA 0.463000 88 175 0 0 1 0 0 LINC00264 0 broad.mit.edu 37 10 26880266 26880266 + RNA SNP G G A rs138111133 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:26880266G>A ENST00000412114.1 + 0 501 NR_026793.1 ACCAAGCCCAGTGGACAGATG 0.443000 7 232 0 0 1 0 0 FRG1B 0 broad.mit.edu 37 20 29625955 29625955 + Nonsense_Mutation SNP A A T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr20:29625955A>T ENST00000278882.3 + 5 579 c.199A>T c.(199-201)Aga>Tga p.R67* FRG1B_ENST00000358464.4_Nonsense_Mutation_p.R67*|FRG1B_ENST00000439954.2_Nonsense_Mutation_p.R72* endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 AATTGGACCAAGAGAACAATG 0.338000 13 437 0 0 1 0 0 CENPJ 55835 broad.mit.edu 37 13 25480645 25480645 + Missense_Mutation SNP C C A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr13:25480645C>A ENST00000381884.4 - 7 1716 c.1531G>T c.(1531-1533)Gat>Tat p.D511Y CENPJ_ENST00000545981.1_Missense_Mutation_p.D511Y NM_018451.4 NP_060921.3 Q9HC77 CENPJ_HUMAN centromere protein J 511 cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization centriole|cytosol|gamma-tubulin small complex|microtubule protein domain specific binding|tubulin binding endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 Lung SC(185;0.0225)|Breast(139;0.0602) all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139) CAGCCAGTATCGCAAGGTTTT 0.458000 194 401 3.14452e-69 3.58921e-69 1 1 0 POM121L9P 0 broad.mit.edu 37 22 24659593 24659593 + RNA SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:24659593C>T ENST00000414583.2 + 0 3118 NR_003714.1 TCACTGACATCGAAGGCTGCC 0.632000 8 132 0 0 1 0 0 LINC00969 0 broad.mit.edu 37 3 195404651 195404651 + RNA SNP C C G rs1996904 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:195404651C>G ENST00000445430.1 + 0 1508 TGTCACGAATCTTGACAAATT 0.418000 5 132 0 0 1 0 0 CADM1 23705 broad.mit.edu 37 11 115080343 115080343 + Silent SNP G G T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:115080343G>T ENST00000537058.1 - 8 1049 c.1029C>A c.(1027-1029)acC>acA p.T343T CADM1_ENST00000331581.6_Silent_p.T343T|CADM1_ENST00000452722.2_Silent_p.T343T|CADM1_ENST00000542447.2_Intron|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000536727.1_Intron Q9BY67 CADM1_HUMAN cell adhesion molecule 1 343 PPTTIPPPTTTTTTTTTTTTTILTIIT -> TTATTEPAVH GLTQLPNSAEELDSEDLS (in Ref. 3; BAC11657). adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity basolateral plasma membrane|cell-cell junction|integral to membrane PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding p.T343T(5) cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1) 32 all_hematologic(175;0.0628) all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237) BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303) tggtggtggtggttgttgtgg 0.433000 12 305 3.07112e-06 3.15488e-06 1 1 0 SYNJ2 8871 broad.mit.edu 37 6 158490618 158490618 + Missense_Mutation SNP C C G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:158490618C>G ENST00000355585.4 + 14 1928 c.1853C>G c.(1852-1854)tCt>tGt p.S618C SYNJ2_ENST00000367122.2_Missense_Mutation_p.S618C|SYNJ2_ENST00000367121.3_Missense_Mutation_p.S618C NM_001178088.1|NM_003898.3 NP_001171559.1|NP_003889.1 O15056 SYNJ2_HUMAN synaptojanin 2 618 nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 46 OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05) ATCTCACGCTCTCATAGATAC 0.453000 72 81 0 0 1 0 0 KIAA1244 57221 broad.mit.edu 37 6 138528250 138528250 + Missense_Mutation SNP C C T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:138528250C>T ENST00000251691.4 + 3 375 c.209C>T c.(208-210)gCa>gTa p.A70V NM_020340.4 NP_065073.3 Q5TH69 BIG3_HUMAN KIAA1244 70 regulation of ARF protein signal transduction cytoplasm|integral to membrane ARF guanyl-nucleotide exchange factor activity NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2) 44 Breast(32;0.135) OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259) CATGCTTTGGCAGGGATGCAG 0.443000 3 37 0 0 1 0 0 MYO9A 4649 broad.mit.edu 37 15 72208758 72208758 + Missense_Mutation SNP G G C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr15:72208758G>C ENST00000356056.5 - 19 3110 c.2638C>G c.(2638-2640)Cat>Gat p.H880D MYO9A_ENST00000444904.1_Missense_Mutation_p.H861D|MYO9A_ENST00000566885.1_Missense_Mutation_p.H500D|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Missense_Mutation_p.H880D|MYO9A_ENST00000564571.1_Missense_Mutation_p.H880D NM_006901.3 NP_008832.2 B2RTY4 MYO9A_HUMAN myosin IXA 880 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception cytosol|integral to membrane|unconventional myosin complex actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 88 TTGTGTAAATGAAGAAGAGAC 0.353000 97 152 0 0 1 0 0 PMS2CL 0 broad.mit.edu 37 7 6776941 6776941 + RNA SNP A A G TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:6776941A>G ENST00000486256.1 + 0 1068 NR_002217.1 AGCACTTCAGATGCCATCTCT 0.542000 11 356 0 0 1 0 0 CELSR3 1951 broad.mit.edu 37 3 48680455 48680455 + Missense_Mutation SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:48680455G>A ENST00000544264.1 - 30 8646 c.8366C>T c.(8365-8367)cCa>cTa p.P2789L CELSR3_ENST00000164024.4_Missense_Mutation_p.P2784L Q9NYQ7 CELR3_HUMAN cadherin, EGF LAG seven-pass G-type receptor 3 2784 homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway integral to membrane|plasma membrane calcium ion binding|G-protein coupled receptor activity|protein binding NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5) 83 BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619) CAGACAGGCTGGCATCCAGGC 0.637000 112 229 0 0 1 0 0 AGAP10 728127 broad.mit.edu 37 10 47207828 47207828 + Missense_Mutation SNP C C A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:47207828C>A ENST00000355232.3 - 5 3467 c.455G>T c.(454-456)aGc>aTc p.S152I AGAP10_ENST00000413193.2_Missense_Mutation_p.S223I|RP11-144G6.12_ENST00000605970.1_RNA|AGAP10_ENST00000452145.2_Missense_Mutation_p.S127I ArfGAP with GTPase domain, ankyrin repeat and PH domain 10 p.S223I(4) endometrium(5)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1) 12 TGTACAGTTGCTTCTTCTTAT 0.264000 4 76 1 1 1 1 0 ZNF513 130557 broad.mit.edu 37 2 27601875 27601875 + Silent SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:27601875G>A ENST00000323703.6 - 3 456 c.258C>T c.(256-258)gaC>gaT p.D86D ZNF513_ENST00000407879.1_Silent_p.D24D NM_144631.5 NP_653232.3 Q8N8E2 ZN513_HUMAN zinc finger protein 513 86 Gly-rich. regulation of transcription, DNA-dependent|response to stimulus|retina development in camera-type eye|transcription, DNA-dependent|visual perception nucleus transcription regulatory region DNA binding|zinc ion binding endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2) 17 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CAGACTCATCGTCGCTCAGCC 0.622000 9 194 0 0 1 0 0 IGFALS 3483 broad.mit.edu 37 16 1842049 1842049 + Silent SNP G G A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:1842049G>A ENST00000415638.3 - 2 563 c.484C>T c.(484-486)Ctg>Ttg p.L162L IGFALS_ENST00000215539.3_Silent_p.L124L|IGFALS_ENST00000568221.1_3'UTR NM_001146006.1|NM_004970.2 NP_001139478.1|NP_004961.1 P35858 ALS_HUMAN insulin-like growth factor binding protein, acid labile subunit 124 cell adhesion|signal transduction soluble fraction insulin-like growth factor binding endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 8 AGGTGGCACAGGTTCTCTAGG 0.692000 29 61 0 0 1 0 0 RP11-798G7.5 0 broad.mit.edu 37 17 43587569 43587569 + RNA SNP G G C rs149697015 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:43587569G>C ENST00000253803.2 + 0 267 LRRC37A4P_ENST00000579913.1_RNA aactccgtctgaaaagaaaag 0.443000 8 255 0 0 1 0 0 PLEKHG5 57449 broad.mit.edu 37 1 6536011 6536013 + In_Frame_Del DEL CTC CTC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:6536011_6536013delCTC ENST00000377748.1 - 4 855_857 c.358_360delGAG c.(358-360)del p.E120del PLEKHG5_ENST00000544978.1_In_Frame_Del_p.E43del|PLEKHG5_ENST00000377732.1_In_Frame_Del_p.E80del|PLEKHG5_ENST00000535355.1_In_Frame_Del_p.E112del|PLEKHG5_ENST00000377725.1_In_Frame_Del_p.E43del|PLEKHG5_ENST00000537245.1_In_Frame_Del_p.E122del|PLEKHG5_ENST00000400915.3_In_Frame_Del_p.E99del|PLEKHG5_ENST00000377728.3_In_Frame_Del_p.E43del|PLEKHG5_ENST00000340850.5_In_Frame_Del_p.E43del|PLEKHG5_ENST00000400913.1_In_Frame_Del_p.E43del|PLEKHG5_ENST00000377737.2_In_Frame_Del_p.E43del|PLEKHG5_ENST00000377740.3_In_Frame_Del_p.E120del NM_198681.3 NP_941374.2 O94827 PKHG5_HUMAN pleckstrin homology domain containing, family G (with RhoGef domain) member 5 99 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) CCACAGAGCTCTCCTCCTCCTCC 0.631 OREG0013041 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 16 707 --- --- --- --- PHF13 148479 broad.mit.edu 37 1 6680069 6680071 + In_Frame_Del DEL GAA GAA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:6680069_6680071delGAA ENST00000377648.4 + 3 730_732 c.348_350delGAA c.(346-351)ctg>ct p.LK116del PHF13_ENST00000495385.1_Intron NM_153812.2 NP_722519.2 Q86YI8 PHF13_HUMAN PHD finger protein 13 116 cell division|chromatin modification|mitotic chromosome condensation nucleoplasm chromatin binding|methylated histone residue binding|zinc ion binding endometrium(3)|large_intestine(1)|lung(3) 7 Ovarian(185;0.0212)|all_lung(157;0.154) all_cancers(23;1.46e-33)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443) Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0642) cggacaagctgaagaagaagaag 0.576 15 509 --- --- --- --- VAMP3 9341 broad.mit.edu 37 1 7838212 7838214 + In_Frame_Del DEL TCA TCA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:7838212_7838214delTCA ENST00000054666.6 + 4 381_383 c.266_268delTCA c.(265-270)ttc>t p.FI89del VAMP3_ENST00000470357.1_In_Frame_Del_p.FI61del NM_004781.3 NP_004772.1 Q15836 VAMP3_HUMAN vesicle-associated membrane protein 3 89 cellular membrane fusion|positive regulation of receptor recycling|protein complex assembly|protein transport|retrograde transport, endosome to Golgi|substrate adhesion-dependent cell spreading|vesicle docking involved in exocytosis cell junction|clathrin-coated vesicle|integral to membrane|recycling endosome|synapse|synaptosome protein binding breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3) 6 Ovarian(185;0.0634)|all_lung(157;0.178) all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|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;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642) CTGGTTATCTTCATCATCATCAT 0.365 8 1254 --- --- --- --- CLSTN1 22883 broad.mit.edu 37 1 9790640 9790642 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:9790640_9790642delCCT ENST00000377298.4 - 19 3662_3664 c.2870_2872delAGG c.(2869-2874)ggg>g p.EG957del CLSTN1_ENST00000361311.4_In_Frame_Del_p.EG947del|CLSTN1_ENST00000377288.3_In_Frame_Del_p.EG938del|CLSTN1_ENST00000477264.1_5'UTR NM_001009566.1 NP_001009566.1 O94985 CSTN1_HUMAN calsyntenin 1 957 Glu-rich (highly acidic). homophilic cell adhesion cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane calcium ion binding breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 36 all_lung(157;0.222) all_lung(284;4.03e-05)|Lung NSC(185;6.93e-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;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419) CCCTGCTCCCCCTCCTCCTCCTC 0.645 11 626 --- --- --- --- MFN2 9927 broad.mit.edu 37 1 12052736 12052736 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:12052736delT ENST00000235329.5 + 4 622 c.300delT c.(298-300)gcfs p.A100fs MFN2_ENST00000444836.1_Frame_Shift_Del_p.A100fs NM_014874.3 NP_055689.1 O95140 MFN2_HUMAN mitofusin 2 100 blood coagulation|mitochondrial fusion|mitochondrial membrane organization|mitochondrion localization|negative regulation of Ras protein signal transduction|negative regulation of smooth muscle cell proliferation|protein targeting to mitochondrion cytosol|integral to membrane|intrinsic to mitochondrial outer membrane GTP binding|GTPase activity|ubiquitin protein ligase binding endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2) 20 Ovarian(185;0.249) Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656) TGAAAGTGGCTTTTTTTGGCC 0.537 8 1334 --- --- --- --- CROCCP3 0 broad.mit.edu 37 1 16810034 16810034 + RNA DEL C C - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:16810034delC ENST00000263511.4 - 0 1804 NR_023386.1 GCCTCCAGAGCCCACCTACTC 0.657 25 45 --- --- --- --- ZBTB40 9923 broad.mit.edu 37 1 22838561 22838563 + In_Frame_Del DEL AAG AAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:22838561_22838563delAAG ENST00000404138.1 + 12 2906_2908 c.2395_2397delAAG c.(2395-2397)del p.K803del ZBTB40_ENST00000374651.4_In_Frame_Del_p.K691del|ZBTB40_ENST00000375647.4_In_Frame_Del_p.K803del NM_001083621.1 NP_001077090.1 Q9NUA8 ZBT40_HUMAN zinc finger and BTB domain containing 40 803 bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 26 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;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216) CGATGCCCCCAAGAAGAAGAAGA 0.517 23 464 --- --- --- --- TCEB3 6924 broad.mit.edu 37 1 24078404 24078404 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:24078404delA ENST00000418390.2 + 4 1658 c.1387delA c.(1387-1389)aafs p.K464fs NM_003198.2 NP_003189.2 Q14241 ELOA1_HUMAN transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A) 464 positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction integral to membrane DNA binding p.N439fs*19(1) breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1) 19 Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187) TAAAGGACTTAAAAAAAATGA 0.413 OREG0013232 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 7 1039 --- --- --- --- PHACTR4 65979 broad.mit.edu 37 1 28785730 28785730 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:28785730delA ENST00000373839.3 + 3 412 c.151delA c.(151-153)aafs p.K53fs PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Frame_Shift_Del_p.K63fs NM_001048183.1 NP_001041648.1 Q8IZ21 PHAR4_HUMAN phosphatase and actin regulator 4 53 actin binding|protein phosphatase inhibitor activity p.S64fs*12(3) NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1) 32 Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261) OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649) GAAATGGAGGAAAAAAAAAAG 0.393 21 357 --- --- --- --- C1orf94 84970 broad.mit.edu 37 1 34666398 34666398 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:34666398delA ENST00000488417.1 + 3 1155 c.1035delA c.(1033-1035)ccfs p.P345fs C1orf94_ENST00000373374.3_Frame_Shift_Del_p.P155fs NM_001134734.1 NP_001128206.1 Q6P1W5 CA094_HUMAN chromosome 1 open reading frame 94 155 protein binding central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2) 32 Myeloproliferative disorder(586;0.0393) CCAAGGAGCCAAAAAAGGGTC 0.572 8 500 --- --- --- --- TMCO2 127391 broad.mit.edu 37 1 40713708 40713709 + Frame_Shift_Del DEL TC TC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:40713708_40713709delTC ENST00000372766.3 + 1 136_137 c.43_44delTC c.(43-45)tfs p.S15fs TMCO2_ENST00000468258.1_Intron NM_001008740.3 NP_001008740.1 Q7Z6W1 TMCO2_HUMAN transmembrane and coiled-coil domains 2 15 integral to membrane kidney(1)|large_intestine(3)|lung(1)|ovary(1) 6 Lung NSC(20;4.38e-06)|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;6.3e-18) CCTCTTAGAGTCTCTCTCTCTC 0.406 8 1055 --- --- --- --- LPAR3 23566 broad.mit.edu 37 1 85331664 85331665 + Frame_Shift_Ins INS - - A rs76299065 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:85331664_85331665insA ENST00000440886.1 - 1 177_178 c.139_140insT c.(139-141)taafs p.*47fs LPAR3_ENST00000370611.3_Frame_Shift_Ins_p.*47fs|LPAR3_ENST00000491034.1_5'UTR Q9UBY5 LPAR3_HUMAN lysophosphatidic acid receptor 3 47 G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission integral to plasma membrane|intracellular membrane-bounded organelle central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1) 24 CAGAGAATTAGAAAAAAAAATA 0.401 11 646 --- --- --- --- CDC7 8317 broad.mit.edu 37 1 91967356 91967357 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:91967356_91967357insA ENST00000428239.1 + 2 342_343 c.83_84insA c.(82-84)taafs p.*28fs CDC7_ENST00000430031.2_Frame_Shift_Ins_p.*28fs|CDC7_ENST00000234626.6_Frame_Shift_Ins_p.*28fs|CDC7_ENST00000497611.1_3'UTR NM_001134420.1 NP_001127892.1 O00311 CDC7_HUMAN cell division cycle 7 28 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 breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2) 23 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) GAAGGCTCTTTAAAAAAAAACG 0.406 16 571 --- --- --- --- EVI5 7813 broad.mit.edu 37 1 93159366 93159366 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:93159366delT ENST00000370331.1 - 9 1231 c.1222delA c.(1222-1224)tgfs p.M408fs EVI5_ENST00000540033.1_Frame_Shift_Del_p.M408fs|EVI5_ENST00000543509.1_Frame_Shift_Del_p.M408fs NM_005665.4 NP_005656.4 O60447 EVI5_HUMAN ecotropic viral integration site 5 408 Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.|Targeting to the centrosomes. cell cycle|cell division|cell proliferation|multicellular organismal development microtubule organizing center|nucleus|spindle protein binding|Rab GTPase activator activity breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1) 38 all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203) Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211) TACTTTTTCATTTTTTTTGAA 0.318 7 466 --- --- --- --- CCDC18 343099 broad.mit.edu 37 1 93667515 93667516 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:93667515_93667516insA ENST00000343253.7 + 7 1267_1268 c.765_766insA c.(763-768)taaaaafs p.*K255fs CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000401026.3_Frame_Shift_Ins_p.*K255fs|CCDC18_ENST00000338949.4_Frame_Shift_Ins_p.*K54fs|CCDC18_ENST00000557479.1_Frame_Shift_Ins_p.*K373fs Q5T9S5 CCD18_HUMAN coiled-coil domain containing 18 255 p.V377fs*15(1) breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 42 all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203) all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967) TCCAACAATATAAAAAAAAAGT 0.317 9 179 --- --- --- --- NOTCH2 4853 broad.mit.edu 37 1 120612003 120612004 + Frame_Shift_Del DEL GG GG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:120612003_120612004delGG ENST00000256646.2 - 1 236_237 c.17_18delCC c.(16-18)cfs p.P6fs NM_024408.3 NP_077719.2 Q04721 NOTC2_HUMAN notch 2 6 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 p.P6fs*27(2) breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 158 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) ACAGCAGAGCGGGGCGCAGGGC 0.762 """N, F, Mis""" """marginal zone lymphoma, DLBCL""" Alagille Syndrome 28 79 --- --- --- --- RP11-343N15.1 0 broad.mit.edu 37 1 121137698 121137699 + RNA INS - - TT rs57730437 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:121137698_121137699insTT ENST00000437515.1 - 0 329 CTACTTACATCTTTTTGTCTTT 0.441 22 156 --- --- --- --- RP11-343N15.1 0 broad.mit.edu 37 1 121137791 121137793 + RNA DEL CCA CCA - rs28552466 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:121137791_121137793delCCA ENST00000437515.1 - 0 329 ATTTCGCCCTCCACCGCCGCCGC 0.631 28 51 --- --- --- --- TCHH 7062 broad.mit.edu 37 1 152082957 152082959 + In_Frame_Del DEL CTC CTC - rs143222885 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:152082957_152082959delCTC ENST00000368804.1 - 2 2733_2735 c.2734_2736delGAG c.(2734-2736)del p.E912del NM_007113.2 NP_009044.2 Q07283 TRHY_HUMAN trichohyalin 912 10 X 30 AA tandem repeats. keratinization cytoskeleton calcium ion binding NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4) 105 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) CTCTCTGTAGCTCCTCCTCCTCC 0.586 20 1106 --- --- --- --- FLG2 388698 broad.mit.edu 37 1 152324558 152324559 + Frame_Shift_Del DEL TG TG - rs140875805 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:152324558_152324559delTG ENST00000388718.5 - 3 5775_5776 c.5703_5704delCA c.(5701-5706)cagcfs p.HS1901fs FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA NM_001014342.2 NP_001014364.1 Q5D862 FILA2_HUMAN filaggrin family member 2 1901 calcium ion binding|structural molecule activity p.H1901fs*30(1) NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5) 188 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) CTGGCTTGGCTGTGTGTGTGTC 0.515 19 1449 --- --- --- --- HAX1 10456 broad.mit.edu 37 1 154245864 154245866 + In_Frame_Del DEL GAA GAA - rs11556342 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:154245864_154245866delGAA ENST00000328703.7 + 2 319_321 c.106_108delGAA c.(106-108)del p.E40del HAX1_ENST00000483970.2_In_Frame_Del_p.E40del|HAX1_ENST00000532105.1_Intron|HAX1_ENST00000457918.2_Intron NM_006118.3 NP_006109.2 O00165 HAX1_HUMAN HCLS1 associated protein X-1 40 Asp/Glu-rich (highly acidic).|Required for localization in mitochondria (By similarity). actin cytoskeleton|cytoplasmic membrane-bounded vesicle|lamellipodium|mitochondrion|nuclear membrane|sarcoplasmic reticulum|soluble fraction interleukin-1 binding|protein N-terminus binding cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1) 15 all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877) LUSC - Lung squamous cell carcinoma(543;0.185) TGATGATGAGGAAGAAGAAGAAG 0.522 Kostmann syndrome 7 346 --- --- --- --- LMX1A 4009 broad.mit.edu 37 1 165177332 165177334 + In_Frame_Del DEL TGC TGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:165177332_165177334delTGC ENST00000342310.3 - 7 1165_1167 c.783_785delGCA c.(781-786)caa>ca p.QQ261del LMX1A_ENST00000294816.2_In_Frame_Del_p.QQ261del|LMX1A_ENST00000489443.2_5'UTR|LMX1A_ENST00000367893.4_In_Frame_Del_p.QQ261del NM_177398.3 NP_796372.1 Q8TE12 LMX1A_HUMAN LIM homeobox transcription factor 1, alpha 261 Gln-rich.|Poly-Gln. nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4) 35 all_hematologic(923;0.248) CTGCTGATCTTGCTGCTGCTGCT 0.567 7 151 --- --- --- --- CACNA1E 777 broad.mit.edu 37 1 181680102 181680103 + Frame_Shift_Del DEL AG AG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:181680102_181680103delAG ENST00000526775.1 + 8 1233_1234 c.1068_1069delAG c.(1066-1071)aaagfs p.KE356fs CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.KE307fs|CACNA1E_ENST00000367573.2_Frame_Shift_Del_p.KE356fs|CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.KE356fs|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.KE307fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.KE356fs NM_001205294.1 NP_001192223.1 Q15878 CAC1E_HUMAN calcium channel, voltage-dependent, R type, alpha 1E subunit 356 energy reserve metabolic process|membrane depolarization|synaptic transmission voltage-gated calcium channel complex voltage-gated calcium channel activity NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 204 AATTTGCCAAAGAGAGAGAGAG 0.510 14 443 --- --- --- --- APOBEC4 403314 broad.mit.edu 37 1 183616826 183616828 + In_Frame_Del DEL TTC TTC - rs141411396 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:183616826_183616828delTTC ENST00000308641.4 - 2 1360_1362 c.1089_1091delGAA c.(1087-1092)aaa>aa p.KK363del RGL1_ENST00000536277.1_Intron|RGL1_ENST00000367531.1_Intron|RGL1_ENST00000304685.3_Intron|APOBEC4_ENST00000481562.1_5'UTR NM_203454.2 NP_982279.1 Q8WW27 ABEC4_HUMAN apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative) 363 mRNA processing hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1) 21 TTTCTTCCCTTTCTTCTTCTTCT 0.419 7 885 --- --- --- --- ZC3H11A 9877 broad.mit.edu 37 1 203786224 203786225 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:203786224_203786225insT ENST00000545588.1 + 2 3853_3854 c.26_27insT c.(25-27)tttfs p.F9fs ZC3H11A_ENST00000367214.1_Frame_Shift_Ins_p.F9fs|ZC3H11A_ENST00000367212.3_Frame_Shift_Ins_p.F9fs|ZC3H11A_ENST00000332127.4_Frame_Shift_Ins_p.F9fs|ZC3H11A_ENST00000367210.1_Frame_Shift_Ins_p.F9fs NM_001271675.1 NP_001258604.1 O75152 ZC11A_HUMAN zinc finger CCCH-type containing 11A 9 nucleic acid binding|protein binding|zinc ion binding central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 32 all_cancers(21;0.0904)|all_epithelial(62;0.234) BRCA - Breast invasive adenocarcinoma(75;0.109) GAAGACTGCTATTTTTTTTTCT 0.371 14 437 --- --- --- --- PTPN14 5784 broad.mit.edu 37 1 214557049 214557051 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr1:214557049_214557051delCCT ENST00000366956.5 - 13 2341_2343 c.2147_2149delAGG c.(2146-2151)gct>g p.EA716del PTPN14_ENST00000543945.1_3'UTR NM_005401.4 NP_005392.2 Q15678 PTN14_HUMAN protein tyrosine phosphatase, non-receptor type 14 716 Poly-Glu. lymphangiogenesis cytoplasm|cytoskeleton protein tyrosine phosphatase activity|receptor tyrosine kinase binding p.E716delE(1) NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155) GATTCTGGAGCCTCCTCCTCCTC 0.626 12 326 --- --- --- --- ATP6V1C2 245973 broad.mit.edu 37 2 10917819 10917820 + Frame_Shift_Del DEL AG AG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:10917819_10917820delAG ENST00000272238.4 + 11 1043_1044 c.934_935delAG c.(934-936)afs p.R312fs ATP6V1C2_ENST00000381661.3_Intron NM_001039362.1 NP_001034451.1 Q8NEY4 VATC2_HUMAN ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2 312 ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport cytosol|proton-transporting V-type ATPase, V1 domain endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 19 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152) GCAGACCGACAGAGAGAGAGAG 0.604 10 540 --- --- --- --- RTN4 57142 broad.mit.edu 37 2 55253745 55253746 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:55253745_55253746insT ENST00000337526.6 - 3 1732_1733 c.1489_1490insA c.(1489-1491)agafs p.R497fs RTN4_ENST00000357732.4_Intron|RTN4_ENST00000357376.3_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000354474.6_Frame_Shift_Ins_p.R265fs|RTN4_ENST00000404909.1_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000405240.1_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000394611.2_Frame_Shift_Ins_p.R291fs NM_020532.4 NP_065393.1 Q9NQC3 RTN4_HUMAN reticulon 4 497 apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane protein binding NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1) 36 CTTTTCTTCTATTTTTTTTTCA 0.381 10 535 --- --- --- --- AC105399.2 0 broad.mit.edu 37 2 78020197 78020200 + RNA DEL TCCT TCCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:78020197_78020200delTCCT ENST00000422418.1 + 0 402_405 ATACTAAAAATCCTaaaaaaaaaa 0.319 13 39 --- --- --- --- SLC9B1P2 0 broad.mit.edu 37 2 92081531 92081532 + RNA INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:92081531_92081532insA ENST00000606405.1 - 0 167 GGGCACACAATAAAAAAAAAAC 0.342 7 132 --- --- --- --- FAHD2CP 0 broad.mit.edu 37 2 96687233 96687234 + RNA DEL AG AG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:96687233_96687234delAG ENST00000607780.1 + 0 1061 TGAAAAGCAAAGAGAGCAAGGG 0.559 12 57 --- --- --- --- ITPRIPL1 150771 broad.mit.edu 37 2 96992793 96992795 + In_Frame_Del DEL GAG GAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:96992793_96992795delGAG ENST00000361124.4 + 1 859_861 c.448_450delGAG c.(448-450)del p.E155del ITPRIPL1_ENST00000542887.1_In_Frame_Del_p.E139del|ITPRIPL1_ENST00000439118.2_In_Frame_Del_p.E147del|ITPRIPL1_ENST00000536814.1_In_Frame_Del_p.E139del NM_178495.5 NP_848590.3 Q6GPH6 IPIL1_HUMAN inositol 1,4,5-trisphosphate receptor interacting protein-like 1 147 integral to membrane breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 TTCCAGCAGTGAGGAGGAGGAGG 0.532 11 359 --- --- --- --- CIR1 9541 broad.mit.edu 37 2 175213712 175213713 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:175213712_175213713insT ENST00000342016.3 - 10 957_958 c.865_866insA c.(865-867)acafs p.T289fs CIR1_ENST00000362053.5_3'UTR NM_004882.3 NP_004873.3 Q86X95 CIR1_HUMAN corepressor interacting with RBPJ, 1 289 Lys/Ser-rich. mRNA processing|negative regulation of transcription, DNA-dependent|RNA splicing nuclear speck protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1) 15 cttcctttgtatttttttttct 0.381 10 324 --- --- --- --- SLC11A1 6556 broad.mit.edu 37 2 219252307 219252307 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:219252307delT ENST00000233202.6 + 7 931 c.591delT c.(589-591)gcfs p.A197fs SLC11A1_ENST00000539932.1_Frame_Shift_Del_p.A79fs NM_000578.3 NP_000569.3 P49279 NRAM1_HUMAN solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1 197 activation of protein kinase activity|antigen processing and presentation of peptide antigen|cadmium ion transmembrane transport|cellular cadmium ion homeostasis|cellular iron ion homeostasis|defense response to Gram-negative bacterium|defense response to protozoan|divalent metal ion export|inflammatory response|interleukin-2 production|interleukin-3 production|iron ion transport|L-arginine import|macrophage activation|MHC class II biosynthetic process|mRNA stabilization|multicellular organismal iron ion homeostasis|negative regulation of cytokine production|nitrite transport|phagocytosis|positive regulation of dendritic cell antigen processing and presentation|positive regulation of interferon-gamma production|positive regulation of phagocytosis|positive regulation of T-helper 1 type immune response|positive regulation of transcription from RNA polymerase II promoter|respiratory burst|response to interferon-gamma|response to lipopolysaccharide|T cell cytokine production|T cell proliferation involved in immune response|vacuolar acidification|wound healing integral to plasma membrane|late endosome membrane|lysosome|phagocytic vesicle membrane|tertiary granule membrane manganese ion transmembrane transporter activity|metal ion:hydrogen antiporter activity|protein homodimerization activity NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1) 19 Renal(207;0.0474) Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942) AGCTGGAAGCTTTTTTTGGAC 0.448 11 2318 --- --- --- --- TTLL4 9654 broad.mit.edu 37 2 219602773 219602773 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr2:219602773delA ENST00000392102.1 + 3 714 c.374delA c.(373-375)cafs p.Q125fs TTLL4_ENST00000258398.4_Frame_Shift_Del_p.Q125fs|TTLL4_ENST00000442769.1_Frame_Shift_Del_p.Q125fs|TTLL4_ENST00000457313.1_5'UTR NM_014640.4 NP_055455.3 Q14679 TTLL4_HUMAN tubulin tyrosine ligase-like family, member 4 125 protein polyglutamylation cilium|microtubule basal body ATP binding|tubulin binding|tubulin-tyrosine ligase activity endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2) 39 Renal(207;0.0915) Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101) AGCTATAGGCAAAAACCGTAC 0.532 7 758 --- --- --- --- TATDN2 9797 broad.mit.edu 37 3 10291121 10291123 + In_Frame_Del DEL CTC CTC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:10291121_10291123delCTC ENST00000287652.4 + 2 1288_1290 c.237_239delCTC c.(235-240)aac>aa p.NS79del TATDN2_ENST00000448281.2_In_Frame_Del_p.NS79del|RP11-438J1.1_ENST00000450534.1_In_Frame_Del_p.NS22del NM_014760.3 NP_055575.3 Q93075 TATD2_HUMAN TatD DNase domain containing 2 79 nucleus endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2) 28 GCAGAAATAACTCCTCCTCCTCC 0.635 8 1243 --- --- --- --- TMEM40 55287 broad.mit.edu 37 3 12790198 12790200 + In_Frame_Del DEL GAG GAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:12790198_12790200delGAG ENST00000314124.7 - 3 521_523 c.165_167delCTC c.(163-168)tct>tc p.SS69del TMEM40_ENST00000264728.8_In_Frame_Del_p.SS69del|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000435218.2_In_Frame_Del_p.SS69del|TMEM40_ENST00000431022.2_In_Frame_Del_p.SS85del NM_018306.2 NP_060776.2 Q8WWA1 TMM40_HUMAN transmembrane protein 40 69 Ser-rich. integral to membrane breast(1)|large_intestine(3)|lung(5)|urinary_tract(1) 10 tgaggaggaagaggaggaggagg 0.419 7 875 --- --- --- --- ANO10 55129 broad.mit.edu 37 3 43647213 43647213 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:43647213delT ENST00000292246.3 - 2 302 c.132delA c.(130-132)aafs p.K44fs ANO10_ENST00000396091.3_Frame_Shift_Del_p.K44fs|ANO10_ENST00000414522.2_Frame_Shift_Del_p.K44fs|ANO10_ENST00000451430.2_Frame_Shift_Del_p.K44fs|ANO10_ENST00000350459.4_Frame_Shift_Del_p.K44fs NM_018075.3 NP_060545.3 Q9NW15 ANO10_HUMAN anoctamin 10 44 cell death chloride channel complex chloride channel activity NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3) 29 CACCTCCATCTTTTTTTTTAG 0.408 10 325 --- --- --- --- QRICH1 54870 broad.mit.edu 37 3 49094314 49094316 + In_Frame_Del DEL TGC TGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:49094314_49094316delTGC ENST00000395443.2 - 3 1789_1791 c.1317_1319delGCA c.(1315-1320)caa>ca p.QQ439del QRICH1_ENST00000479449.1_5'UTR|QRICH1_ENST00000424300.1_In_Frame_Del_p.QQ439del|QRICH1_ENST00000357496.2_In_Frame_Del_p.QQ439del NM_198880.1 NP_942581.1 Q2TAL8 QRIC1_HUMAN glutamine-rich 1 439 Gln-rich. breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1) 25 BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258) AACTTGGAgttgctgctgctgct 0.562 7 425 --- --- --- --- CACNA1D 776 broad.mit.edu 37 3 53804484 53804484 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:53804484delT ENST00000288139.3 + 33 4127 c.4009delT c.(4009-4011)ttfs p.F1338fs CACNA1D_ENST00000540742.1_Frame_Shift_Del_p.F210fs|CACNA1D_ENST00000422281.2_Frame_Shift_Del_p.F1303fs|CACNA1D_ENST00000350061.5_Frame_Shift_Del_p.F1318fs NM_000720.2 NP_000711.1 Q01668 CAC1D_HUMAN calcium channel, voltage-dependent, L type, alpha 1D subunit 1318 axon guidance|energy reserve metabolic process|regulation of insulin secretion voltage-gated calcium channel complex voltage-gated calcium channel activity breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 90 BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613) Verapamil(DB00661) CTCCATCACCTTTTTCCGTCT 0.443 7 531 --- --- --- --- ERC2 26059 broad.mit.edu 37 3 55733470 55733472 + In_Frame_Del DEL TGG TGG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:55733470_55733472delTGG ENST00000288221.6 - 16 3036_3038 c.2781_2783delCCA c.(2779-2784)cat>ca p.HH931del NM_015576.1 NP_056391.1 O15083 ERC2_HUMAN ELKS/RAB6-interacting/CAST family member 2 931 Poly-His. cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome protein binding breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1) 31 KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219) gtggtggtgatggtggtggtggt 0.502 9 1055 --- --- --- --- MAGI1 9223 broad.mit.edu 37 3 65372850 65372851 + Frame_Shift_Del DEL TC TC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:65372850_65372851delTC ENST00000330909.8 - 15 2466_2467 c.2467_2468delGA c.(2467-2469)afs p.E823fs MAGI1_ENST00000497477.2_Intron|MAGI1_ENST00000483466.1_Frame_Shift_Del_p.E823fs|MAGI1_ENST00000402939.2_Intron NM_015520.1 NP_056335.1 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ domain containing 1 823 PDZ 4. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5) 51 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) GGAATTGATTTCTCTCTCTCTC 0.401 10 310 --- --- --- --- TRMT10C 54931 broad.mit.edu 37 3 101284009 101284009 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:101284009delA ENST00000309922.6 + 2 538 c.384delA c.(382-384)gcfs p.A128fs NM_017819.2 NP_060289.2 tRNA methyltransferase 10 homolog C (S. cerevisiae) CTAACACAGCaaaaaaaaaat 0.343 14 214 --- --- --- --- GOLIM4 27333 broad.mit.edu 37 3 167747642 167747644 + In_Frame_Del DEL CTG CTG - rs61743912 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:167747642_167747644delCTG ENST00000470487.1 - 10 2046_2048 c.1357_1359delCAG c.(1357-1359)del p.Q453del GOLIM4_ENST00000309027.4_In_Frame_Del_p.Q425del NM_014498.3 NP_055313.1 O00461 GOLI4_HUMAN golgi integral membrane protein 4 453 Gln-rich.|Glu-rich. transport cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 CTCTTGCCACctgctgctgctgc 0.640 9 330 --- --- --- --- LINC00969 0 broad.mit.edu 37 3 195400639 195400641 + RNA DEL GTG GTG - rs145880653 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:195400639_195400641delGTG ENST00000445430.1 + 0 1284 AGGTGGGCTTGTGGAGGAATGGG 0.552 9 112 --- --- --- --- LINC00969 0 broad.mit.edu 37 3 195400918 195400919 + RNA INS - - T rs55992531 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr3:195400918_195400919insT ENST00000445430.1 + 0 1454 AGTCttttttctttttttttga 0.525 28 66 --- --- --- --- TMEM175 84286 broad.mit.edu 37 4 946206 946207 + Frame_Shift_Del DEL TG TG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:946206_946207delTG ENST00000264771.4 + 7 615_616 c.430_431delTG c.(430-432)tfs p.C144fs TMEM175_ENST00000515740.1_Frame_Shift_Del_p.C28fs|TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000508204.1_Frame_Shift_Del_p.C62fs NM_032326.2 NP_115702.1 Q9BSA9 TM175_HUMAN transmembrane protein 175 144 integral to membrane NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3) 14 OV - Ovarian serous cystadenocarcinoma(23;0.0158) CTTCTTGTTCTGTGTGTGTGTG 0.515 9 910 --- --- --- --- PROM1 8842 broad.mit.edu 37 4 15995680 15995680 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:15995680delT ENST00000505450.1 - 15 2282 c.1670delA c.(1669-1671)atfs p.N557fs PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000510224.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000447510.2_Frame_Shift_Del_p.N566fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs NM_001145848.1 NP_001139320.1 O43490 PROM1_HUMAN prominin 1 566 camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane beta-actinin binding|cadherin binding breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2) 35 AGTGCCTCTATTTTTTTTGCA 0.428 8 487 --- --- --- --- KLB 152831 broad.mit.edu 37 4 39448946 39448946 + Frame_Shift_Del DEL G G - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:39448946delG ENST00000257408.4 + 4 2697 c.2600delG c.(2599-2601)tgfs p.W867fs NM_175737.3 NP_783864.1 Q86Z14 KLOTB_HUMAN klotho beta 867 Glycosyl hydrolase-1 2. carbohydrate metabolic process integral to membrane|plasma membrane cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6) 29 GTGATTCCCTGGGGGGTGCGC 0.647 8 690 --- --- --- --- GABRG1 2565 broad.mit.edu 37 4 46060358 46060358 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:46060358delA ENST00000295452.4 - 7 959 c.792delT c.(790-792)ttfs p.F264fs NM_173536.3 NP_775807.2 Q8N1C3 GBRG1_HUMAN gamma-aminobutyric acid (GABA) A receptor, gamma 1 264 gamma-aminobutyric acid signaling pathway cell junction|chloride channel complex|postsynaptic membrane chloride channel activity|extracellular ligand-gated ion channel activity p.F264fs*3(1) breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 76 Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23) TGCTCAGGTCAAAAAAAATTG 0.294 10 310 --- --- --- --- UTP3 57050 broad.mit.edu 37 4 71554620 71554622 + In_Frame_Del DEL GAG GAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:71554620_71554622delGAG ENST00000254803.2 + 1 425_427 c.226_228delGAG c.(226-228)del p.E81del NM_020368.2 NP_065101.1 Q9NQZ2 SAS10_HUMAN UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae) 81 Glu-rich. brain development|chromatin modification|gene silencing nucleolus endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4) 18 Lung(101;0.235) ggaggatggcgaggaggaggagg 0.567 13 213 --- --- --- --- PRDM8 56978 broad.mit.edu 37 4 81123250 81123252 + In_Frame_Del DEL CAG CAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:81123250_81123252delCAG ENST00000339711.4 + 10 1865_1867 c.634_636delCAG c.(634-636)del p.Q217del PRDM8_ENST00000415738.2_In_Frame_Del_p.Q217del|PRDM8_ENST00000504452.1_In_Frame_Del_p.Q217del NM_020226.3 NP_064611.3 Q9NQV8 PRDM8_HUMAN PR domain containing 8 217 Gly-rich.|Poly-Gln. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2) 10 tggcaaagaccagcagcagcagc 0.655 OREG0016246 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 12 384 --- --- --- --- PKD2 5311 broad.mit.edu 37 4 88986559 88986559 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:88986559delA ENST00000237596.2 + 11 2218 c.2152delA c.(2152-2154)aafs p.K719fs PKD2_ENST00000508588.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000502363.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000511337.1_3'UTR NM_000297.3 NP_000288.1 Q13563 PKD2_HUMAN polycystic kidney disease 2 (autosomal dominant) 719 EF-hand domain. basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1) 36 Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221) OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237) ACTAAAACTGAAAAAAAATAC 0.383 8 587 --- --- --- --- NAP1L5 266812 broad.mit.edu 37 4 89618431 89618433 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:89618431_89618433delCCT ENST00000323061.5 - 1 953_955 c.473_475delAGG c.(472-477)gct>g p.EA158del HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron NM_153757.2 NP_715638.1 Q96NT1 NP1L5_HUMAN nucleosome assembly protein 1-like 5 158 Glu-rich. nucleosome assembly nucleus protein binding endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1) 7 OV - Ovarian serous cystadenocarcinoma(123;0.000181) TCTGCCGCAGcctcctcctcctc 0.626 9 803 --- --- --- --- NAP1L5 266812 broad.mit.edu 37 4 89618484 89618486 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:89618484_89618486delTCC ENST00000323061.5 - 1 900_902 c.420_422delGGA c.(418-423)gaa>ga p.EE142del HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron NM_153757.2 NP_715638.1 Q96NT1 NP1L5_HUMAN nucleosome assembly protein 1-like 5 142 Glu-rich. nucleosome assembly nucleus protein binding endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1) 7 OV - Ovarian serous cystadenocarcinoma(123;0.000181) gtactcctcttcctcctcctcct 0.606 8 535 --- --- --- --- NPNT 255743 broad.mit.edu 37 4 106863682 106863684 + In_Frame_Del DEL CCA CCA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:106863682_106863684delCCA ENST00000379987.2 + 8 1198_1200 c.982_984delCCA c.(982-984)del p.P333del NPNT_ENST00000305572.8_In_Frame_Del_p.P333del|NPNT_ENST00000506666.1_In_Frame_Del_p.P363del|NPNT_ENST00000453617.2_In_Frame_Del_p.P350del|NPNT_ENST00000427316.2_In_Frame_Del_p.P363del|NPNT_ENST00000514622.1_In_Frame_Del_p.P333del NM_001033047.2 NP_001028219.1 Q6UXI9 NPNT_HUMAN nephronectin 333 Pro-rich. cell differentiation membrane calcium ion binding kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1) 21 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;5.41e-07) AATTCCTACTCCACCACCACCAC 0.522 7 396 --- --- --- --- MAML3 55534 broad.mit.edu 37 4 140811064 140811069 + In_Frame_Del DEL TGCTGC TGCTGC - rs71855026 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:140811064_140811069delTGCTGC ENST00000509479.2 - 2 2377_2382 c.1521_1526delGCAGCA c.(1519-1527)caa>ca p.QQQ507del MAML3_ENST00000398940.1_Splice_Site_p.37_splice|MAML3_ENST00000327122.5_In_Frame_Del_p.QQQ351del NM_018717.4 NP_061187.2 Q96JK9 MAML3_HUMAN mastermind-like 3 (Drosophila) 506 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2) 25 all_hematologic(180;0.162) TGAGtgctgttgctgctgctgctgct 0.515 40 436 --- --- --- --- FGA 2243 broad.mit.edu 37 4 155505987 155505988 + Splice_Site INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:155505987_155505988insA ENST00000302053.3 - 6 1970 c.e6-2 NM_000508.3 NP_000499.1 P02671 FIBA_HUMAN fibrinogen alpha chain platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen eukaryotic cell surface binding|protein binding, bridging|receptor binding NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6) 73 all_hematologic(180;0.215) Renal(120;0.0458) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031) CATCACAGTCTAAAAAAAAAAT 0.366 8 237 --- --- --- --- DDX60 55601 broad.mit.edu 37 4 169182016 169182016 + Splice_Site DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:169182016delA ENST00000393743.3 - 25 3689 c.3398_splice c.e25+1 p.L1133_splice DDX60_ENST00000505393.1_5'UTR NM_017631.5 NP_060101.3 Q8IY21 DDX60_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 60 1133 ATP binding|ATP-dependent helicase activity|RNA binding breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4) 63 Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132) GBM - Glioblastoma multiforme(119;0.0485) AATAACTTACAAAAAAAATAG 0.383 7 407 --- --- --- --- HMGB2 3148 broad.mit.edu 37 4 174253277 174253279 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:174253277_174253279delTCC ENST00000296503.5 - 5 1455_1457 c.582_584delGGA c.(580-585)gaa>ga p.EE196del HMGB2_ENST00000438704.2_In_Frame_Del_p.EE196del|HMGB2_ENST00000446922.2_In_Frame_Del_p.EE196del P26583 HMGB2_HUMAN high mobility group box 2 196 Asp/Glu-rich (acidic). base-excision repair, DNA ligation|cell chemotaxis|cellular response to lipopolysaccharide|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|negative regulation of transcription, DNA-dependent|nucleosome assembly|phosphatidylinositol-mediated signaling|positive regulation of DNA binding|positive regulation of endothelial cell proliferation|positive regulation of erythrocyte differentiation|positive regulation of megakaryocyte differentiation|positive regulation of nuclease activity|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination condensed chromosome|extracellular space|nucleolus|nucleoplasm|perinuclear region of cytoplasm|protein complex chemoattractant activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding|transcription regulatory region DNA binding p.E194E(1) endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3) 14 Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122) all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249) atcttcttcttcctcctcctcct 0.468 7 456 --- --- --- --- FRG1 2483 broad.mit.edu 37 4 190873437 190873439 + In_Frame_Del DEL AAG AAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr4:190873437_190873439delAAG ENST00000226798.4 + 3 476_478 c.254_256delAAG c.(253-258)aaa>a p.KE85del FRG1_ENST00000514482.1_3'UTR NM_004477.2 NP_004468.1 Q14331 FRG1_HUMAN FSHD region gene 1 85 rRNA processing Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1) 32 all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147) all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161) GCTCCACACAAAGAAGGTTTGTG 0.414 7 727 --- --- --- --- PAPD7 11044 broad.mit.edu 37 5 6755013 6755014 + Frame_Shift_Del DEL AC AC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:6755013_6755014delAC ENST00000230859.6 + 13 1713_1714 c.1584_1585delAC c.(1582-1587)aaacfs p.KH528fs NM_001171805.1|NM_001171806.1|NM_006999.4 NP_001165276.1|NP_001165277.1|NP_008930.1 Q5XG87 PAPD7_HUMAN PAP associated domain containing 7 528 cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion nucleus DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 27 GGAGGAAAAAACACACACACAC 0.653 9 254 --- --- --- --- DNAH5 1767 broad.mit.edu 37 5 13919383 13919383 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:13919383delT ENST00000265104.4 - 7 981 c.877delA c.(877-879)gafs p.R293fs NM_001369.2 NP_001360.1 Q8TE73 DYH5_HUMAN dynein, axonemal, heavy chain 5 293 Stem (By similarity). microtubule-based movement cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8) 378 Lung NSC(4;0.00476) TTGGAGAGTCTTTTTTTCCAG 0.517 Kartagener syndrome 10 1401 --- --- --- --- PDZD2 23037 broad.mit.edu 37 5 32090059 32090061 + In_Frame_Del DEL TCC TCC - rs61744453 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:32090059_32090061delTCC ENST00000438447.1 + 20 6893_6895 c.6505_6507delTCC c.(6505-6507)del p.S2173del PDZD2_ENST00000282493.3_In_Frame_Del_p.S2173del O15018 PDZD2_HUMAN PDZ domain containing 2 2173 Ser-rich. cell adhesion cell-cell junction|endoplasmic reticulum|extracellular region|nucleus NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1) 148 AAAACTGGCGTCCTCCTCCTCCT 0.527 8 802 --- --- --- --- SLC22A4 6583 broad.mit.edu 37 5 131676327 131676327 + Frame_Shift_Del DEL T T - rs72552721 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:131676327delT ENST00000200652.3 + 9 1688 c.1514delT c.(1513-1515)ctfs p.L505fs AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000437091.1_RNA NM_003059.2 NP_003050.2 Q9H015 S22A4_HUMAN solute carrier family 22 (organic cation/zwitterion transporter), member 4 505 body fluid secretion|sodium ion transport apical plasma membrane|integral to plasma membrane|mitochondrion ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity p.E509fs*1(1) endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1) 16 all_cancers(142;0.0752)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) L-Carnitine(DB00583) ATCCTCACCCTTTTTTTCCCT 0.418 11 1026 --- --- --- --- PCDHA9 0 broad.mit.edu 37 5 140230589 140230590 + Frame_Shift_Ins INS - - T rs17844337 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:140230589_140230590insT ENST00000378122.3 + 1 3233_3234 c.2509_2510insT c.(2509-2511)tttfs p.F837fs PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron NM_014005.3 NP_054724.1 breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 59 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AATCCAGCAGATTTTTTTTCTG 0.282 8 1061 --- --- --- --- PCDHB4 0 broad.mit.edu 37 5 140502486 140502487 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:140502486_140502487insA ENST00000194152.1 + 1 906_907 c.906_907insA c.(904-909)ttaaaafs p.LK302fs NM_018938.2 NP_061761.1 Q9Y5E5 PCDB4_HUMAN 302 Cadherin 3. calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton calcium ion binding p.K305fs*12(1) autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1) 67 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) AAATACTGTTGAAAAAAAAATT 0.366 10 773 --- --- --- --- TIMD4 91937 broad.mit.edu 37 5 156378745 156378747 + In_Frame_Del DEL TTG TTG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr5:156378745_156378747delTTG ENST00000274532.2 - 3 511_513 c.455_457delCAA c.(454-459)agc>a p.TS152del TIMD4_ENST00000407087.3_In_Frame_Del_p.TS152del NM_138379.2 NP_612388.2 Q96H15 TIMD4_HUMAN T-cell immunoglobulin and mucin domain containing 4 152 Thr-rich. integral to membrane NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2) 37 Renal(175;0.00488) Medulloblastoma(196;0.0523)|all_neural(177;0.21) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) GTGGTGGGGCTTGTTGTTGTTGT 0.537 8 1307 --- --- --- --- RIOK1 83732 broad.mit.edu 37 6 7393450 7393452 + In_Frame_Del DEL GAC GAC - rs2274212 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:7393450_7393452delGAC ENST00000379834.2 + 2 697_699 c.190_192delGAC c.(190-192)del p.D69del NM_031480.2|NM_153005.1 NP_113668.2|NP_694550.1 Q9BRS2 RIOK1_HUMAN RIO kinase 1 69 ATP binding|protein serine/threonine kinase activity p.D57G(1) cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 19 Ovarian(93;0.0418) ggagggttatgacgatgatgatg 0.433 9 340 --- --- --- --- FAM8A1 51439 broad.mit.edu 37 6 17605243 17605248 + In_Frame_Del DEL TTAGTT TTAGTT - rs143076391 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:17605243_17605248delTTAGTT ENST00000259963.3 + 3 995_1000 c.940_945delTTAGTT c.(940-945)del p.LV314del NM_016255.2 NP_057339.1 Q9UBU6 FA8A1_HUMAN family with sequence similarity 8, member A1 314 RDD. integral to membrane endometrium(1)|large_intestine(2)|lung(3) 6 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.143) all cancers(50;0.176)|Epithelial(50;0.204) ATACAGATTATTAGTTTGTTTCTATG 0.301 72 251 --- --- --- --- SLC17A2 10246 broad.mit.edu 37 6 25921520 25921520 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:25921520delT ENST00000377850.3 - 4 885 c.361delA c.(361-363)tgfs p.M121fs SLC17A2_ENST00000265425.3_Frame_Shift_Del_p.M121fs|SLC17A2_ENST00000360488.3_Frame_Shift_Del_p.M121fs O00624 NPT3_HUMAN solute carrier family 17, member 2 121 phosphate metabolic process integral to plasma membrane|membrane fraction sodium:phosphate symporter activity p.M121fs*7(1) endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1) 31 GCACCAAGCATTTTTTTTGCT 0.453 11 445 --- --- --- --- TRIM26 7726 broad.mit.edu 37 6 30157254 30157254 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:30157254delT ENST00000454678.2 - 8 1281 c.845delA c.(844-846)agfs p.K282fs TRIM26_ENST00000453195.1_Frame_Shift_Del_p.K282fs|TRIM26_ENST00000437089.1_Frame_Shift_Del_p.K282fs NM_003449.4 NP_003440.1 Q12899 TRI26_HUMAN tripartite motif containing 26 282 DNA binding|zinc ion binding p.K282fs*16(1) lung(1)|ovary(2) 3 TTCTCCGGTCTTTTTTTTAAC 0.483 7 458 --- --- --- --- MDFI 4188 broad.mit.edu 37 6 41621169 41621171 + In_Frame_Del DEL CTG CTG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:41621169_41621171delCTG ENST00000373050.4 + 4 601_603 c.414_416delCTG c.(412-417)ctc>ct p.LC138del Q99750 MDFI_HUMAN MyoD family inhibitor 199 cytoplasmic sequestering of transcription factor|dorsal/ventral axis specification|negative regulation of DNA binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of Wnt receptor signaling pathway cytoplasm|nucleus endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|prostate(2)|skin(1)|urinary_tract(1) 8 Ovarian(28;0.0327)|Colorectal(47;0.121) Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138) ACTCGTGCCTCTGCTGCTGCTGC 0.655 10 609 --- --- --- --- PHIP 55023 broad.mit.edu 37 6 79655961 79655961 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:79655961delT ENST00000275034.4 - 38 4554 c.4387delA c.(4387-4389)ggfs p.R1463fs PHIP_ENST00000479165.1_5'UTR NM_017934.5 NP_060404.3 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 1463 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 NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3) 68 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) TTTAAGATCCTTTTTTTCCTT 0.358 8 703 --- --- --- --- C6orf165 154313 broad.mit.edu 37 6 88144700 88144700 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:88144700delA ENST00000507897.1 + 11 1506 c.1423delA c.(1423-1425)aafs p.K476fs C6ORF165_ENST00000369562.4_Frame_Shift_Del_p.K476fs Q8IYR0 CF165_HUMAN chromosome 6 open reading frame 165 476 NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575) BRCA - Breast invasive adenocarcinoma(108;0.0419) AGAAAAGGCCAAAAAAAATAC 0.269 8 286 --- --- --- --- GABRR1 2569 broad.mit.edu 37 6 89891719 89891721 + In_Frame_Del DEL AAG AAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:89891719_89891721delAAG ENST00000435811.1 - 7 1255_1257 c.801_803delCTT c.(799-804)ttg>tt p.FL267del GABRR1_ENST00000454853.2_In_Frame_Del_p.FL284del|GABRR1_ENST00000369451.3_In_Frame_Del_p.FL197del NM_001256703.1 NP_001243632.1 P24046 GBRR1_HUMAN gamma-aminobutyric acid (GABA) A receptor, rho 1 284 gamma-aminobutyric acid signaling pathway|synaptic transmission cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1) 35 all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114) BRCA - Breast invasive adenocarcinoma(108;0.00917) Picrotoxin(DB00466) AGTTTGGAGCAAGAAGAAGAAGA 0.522 8 467 --- --- --- --- OLIG3 167826 broad.mit.edu 37 6 137815210 137815212 + In_Frame_Del DEL TGG TGG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr6:137815210_137815212delTGG ENST00000367734.2 - 1 319_321 c.96_98delCCA c.(94-99)cag>ca p.HQ32del NM_175747.2 NP_786923.1 Q7RTU3 OLIG3_HUMAN oligodendrocyte transcription factor 3 32 Poly-His. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding p.Q33K(1) endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1) 11 Breast(32;0.165)|Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447) ACGGCTCTCCtggtggtggtggt 0.596 8 373 --- --- --- --- PMS2CL 0 broad.mit.edu 37 7 6759413 6759413 + RNA DEL G G - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:6759413delG ENST00000486256.1 + 0 346 NR_002217.1 TGTGCCTCCCGGGGGGGAGGT 0.567 7 292 --- --- --- --- NEUROD6 63974 broad.mit.edu 37 7 31378634 31378635 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:31378634_31378635insT ENST00000297142.3 - 2 570_571 c.248_249insA c.(247-249)aacfs p.N83fs NM_022728.2 NP_073565.2 Q96NK8 NDF6_HUMAN neuronal differentiation 6 83 cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 32 GCTTTGTTGTCTTTTTTTTCCT 0.520 13 1236 --- --- --- --- POU6F2 11281 broad.mit.edu 37 7 39379288 39379290 + In_Frame_Del DEL CAG CAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:39379288_39379290delCAG ENST00000518318.2 + 5 601_603 c.559_561delCAG c.(559-561)del p.Q196del POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000403058.1_In_Frame_Del_p.Q196del|POU6F2_ENST00000559001.1_In_Frame_Del_p.Q188del P78424 PO6F2_HUMAN POU class 6 homeobox 2 196 Gln-rich. Q -> QQ (in Ref. 1; AAB49727/AAB49728). central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 42 gctccagctccagcagcagcagc 0.616 10 162 --- --- --- --- OGDH 4967 broad.mit.edu 37 7 44684936 44684936 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:44684936delT ENST00000222673.5 + 3 275 c.233delT c.(232-234)atfs p.I78fs OGDH_ENST00000439616.2_Intron|OGDH_ENST00000543843.1_Frame_Shift_Del_p.I18fs|OGDH_ENST00000443864.2_Frame_Shift_Del_p.I78fs|OGDH_ENST00000444676.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000447398.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000449767.1_Frame_Shift_Del_p.I78fs NM_002541.3 NP_002532.2 Q02218 ODO1_HUMAN oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) 78 glycolysis|lysine catabolic process|tricarboxylic acid cycle mitochondrial matrix|mitochondrial membrane oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding p.R81fs*19(1) breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4) 36 NADH(DB00157) TCATGGGACATTTTTTTTCGC 0.577 15 970 --- --- --- --- LMTK2 22853 broad.mit.edu 37 7 97820131 97820132 + Frame_Shift_Del DEL AG AG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:97820131_97820132delAG ENST00000297293.5 + 10 1383_1384 c.1090_1091delAG c.(1090-1092)afs p.R364fs NM_014916.3 NP_055731.2 Q8IWU2 LMTK2_HUMAN lemur tyrosine kinase 2 364 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 NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3) 59 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) CCAAGTCATTAGAGAGAGAGAC 0.495 10 1231 --- --- --- --- SRRT 51593 broad.mit.edu 37 7 100479332 100479332 + Frame_Shift_Del DEL G G - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:100479332delG ENST00000388793.4 + 4 524 c.304delG c.(304-306)ggfs p.G106fs SRRT_ENST00000347433.4_Frame_Shift_Del_p.G106fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.G106fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.G106fs NM_001128852.1|NM_015908.5 NP_001122324.1|NP_056992.4 Q9BXP5 SRRT_HUMAN serrate RNA effector molecule homolog (Arabidopsis) 106 G -> GG (in Ref. 3; CAB46374). cell proliferation|primary miRNA processing|response to arsenic-containing substance cytoplasm|nucleoplasm protein binding p.G104fs*45(1) breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 40 GCCCTATGCTGGGGGGGGTGG 0.607 7 285 --- --- --- --- FOXP2 93986 broad.mit.edu 37 7 114269971 114269973 + In_Frame_Del DEL CAA CAA - rs149757187 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:114269971_114269973delCAA ENST00000393500.3 + 11 1103_1105 c.283_285delCAA c.(283-285)del p.Q116del FOXP2_ENST00000393491.3_In_Frame_Del_p.Q99del|FOXP2_ENST00000390668.3_In_Frame_Del_p.Q215del|FOXP2_ENST00000360232.4_In_Frame_Del_p.Q191del|FOXP2_ENST00000393498.2_In_Frame_Del_p.Q171del|FOXP2_ENST00000350908.4_In_Frame_Del_p.Q191del|FOXP2_ENST00000378237.3_In_Frame_Del_p.Q191del|FOXP2_ENST00000408937.3_In_Frame_Del_p.Q216del|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393494.2_In_Frame_Del_p.Q191del|FOXP2_ENST00000393489.3_In_Frame_Del_p.Q99del|FOXP2_ENST00000403559.4_In_Frame_Del_p.Q208del O15409 FOXP2_HUMAN forkhead box P2 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 p.Q195Q(1) breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 52 acagcagcagcaacaacaacaac 0.502 8 257 --- --- --- --- WASL 8976 broad.mit.edu 37 7 123329091 123329094 + Splice_Site DEL TCTA TCTA - rs142849943 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr7:123329091_123329094delTCTA ENST00000223023.4 - 10 1789 c.e10+1 NM_003941.2 NP_003932.3 O00401 WASL_HUMAN Wiskott-Aldrich syndrome-like actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent actin cytoskeleton|cytosol|nucleolus|plasma membrane actin binding|small GTPase regulator activity endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 29 tctctctctctctACCTGAAGAAT 0.426 7 1197 --- --- --- --- UNC5D 137970 broad.mit.edu 37 8 35608248 35608248 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr8:35608248delT ENST00000287272.2 + 12 1897 c.1877delT c.(1876-1878)gtfs p.V626fs UNC5D_ENST00000420357.1_Frame_Shift_Del_p.V628fs|UNC5D_ENST00000404895.2_Frame_Shift_Del_p.V695fs|UNC5D_ENST00000416672.1_Frame_Shift_Del_p.V700fs|UNC5D_ENST00000449677.1_Frame_Shift_Del_p.V271fs|UNC5D_ENST00000453357.2_Frame_Shift_Del_p.V690fs Q6UXZ4 UNC5D_HUMAN unc-5 homolog D (C. elegans) 695 ZU5. apoptosis|axon guidance integral to membrane receptor activity NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2) 112 READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723) AAGGTGGCGGTTTTTGGCTGC 0.488 8 724 --- --- --- --- TOX 9760 broad.mit.edu 37 8 59750796 59750798 + In_Frame_Del DEL CTT CTT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr8:59750796_59750798delCTT ENST00000361421.1 - 5 986_988 c.766_768delAAG c.(766-768)del p.K256del NM_014729.2 NP_055544.1 O94900 TOX_HUMAN thymocyte selection-associated high mobility group box 256 nucleus DNA binding endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1) 33 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) CATTGGGATCCTTCTTCTTCTTC 0.453 7 801 --- --- --- --- PREX2 80243 broad.mit.edu 37 8 68992720 68992721 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr8:68992720_68992721insT ENST00000288368.4 + 16 1962_1963 c.1685_1686insT c.(1684-1686)cttfs p.L562fs PREX2_ENST00000529398.1_3'UTR NM_024870.2|NM_025170.4 NP_079146.2|NP_079446.3 Q70Z35 PREX2_HUMAN phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 562 DEP 2. G-protein coupled receptor protein signaling pathway|intracellular signal transduction intracellular protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2) 178 CTACTTTTCCGTTTTTTTTCGG 0.332 8 259 --- --- --- --- TP53INP1 0 broad.mit.edu 37 8 95952409 95952411 + In_Frame_Del DEL TCT TCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr8:95952409_95952411delTCT ENST00000342697.4 - 3 557_559 c.150_152delAGA c.(148-153)gag>ga p.EE50del TP53INP1_ENST00000378776.4_In_Frame_Del_p.EE50del|TP53INP1_ENST00000448464.2_In_Frame_Del_p.EE50del|NDUFAF6_ENST00000396113.1_Intron NM_033285.3 NP_150601.1 Q96A56 T53I1_HUMAN tumor protein p53 inducible nuclear protein 1 50 Glu-rich. apoptosis PML body p.E50E(1) kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1) 9 Breast(36;8.75e-07) GATGTCCTCCTCTTCTTCTTCTT 0.458 10 255 --- --- --- --- PABPC1 26986 broad.mit.edu 37 8 101724994 101724995 + Frame_Shift_Ins INS - - A rs140822921 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr8:101724994_101724995insA ENST00000318607.5 - 6 1889_1890 c.761_762insT c.(760-762)agafs p.R254fs PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Frame_Shift_Ins_p.R209fs|PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.R222fs NM_002568.3 NP_002559.2 P11940 PABP1_HUMAN poly(A) binding protein, cytoplasmic 1 254 CSDE1-binding.|RRM 3. mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation catalytic step 2 spliceosome|cytosol nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 40 all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125) Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206) CATTGAGCTCCTTTCCGTTCAT 0.371 17 312 --- --- --- --- ZNF572 137209 broad.mit.edu 37 8 125987892 125987893 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr8:125987892_125987893insA ENST00000319286.5 + 2 164_165 c.10_11insA c.(10-12)aaafs p.K4fs NM_152412.2 NP_689625.2 Q7Z3I7 ZN572_HUMAN zinc finger protein 572 4 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding p.E4Q(1) endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3) 31 Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205) GATGGAGCAAGAAAAAAAACTG 0.396 HNSCC(60;0.17) 9 335 --- --- --- --- PTPLAD2 401494 broad.mit.edu 37 9 21007045 21007046 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr9:21007045_21007046insT ENST00000495827.1 - 7 734_735 c.689_690insA c.(688-690)aaafs p.K230fs PTPLAD2_ENST00000513293.2_Frame_Shift_Ins_p.K230fs NM_001010915.3 NP_001010915.2 Q5VWC8 HACD4_HUMAN protein tyrosine phosphatase-like A domain containing 2 230 Poly-Lys. fatty acid biosynthetic process endoplasmic reticulum membrane|integral to membrane lyase activity breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1) 10 Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10) TTCACATCTTCTTTTTTTTAAT 0.371 9 411 --- --- --- --- TMEM2 23670 broad.mit.edu 37 9 74300311 74300312 + Splice_Site INS - - A rs72019397 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr9:74300311_74300312insA ENST00000377044.4 - 24 4495 c.e24-2 TMEM2_ENST00000377066.5_Splice_Site|TMEM2_ENST00000396272.3_Splice_Site NM_001135820.1|NM_013390.2 NP_001129292.1|NP_037522.1 Q9UHN6 TMEM2_HUMAN transmembrane protein 2 integral to membrane central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2) 56 all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255) GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16) TGGTACTCCCTaaaaaaaaaaa 0.371 41 117 --- --- --- --- ECM2 1842 broad.mit.edu 37 9 95277146 95277148 + In_Frame_Del DEL TCC TCC - rs137929518 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr9:95277146_95277148delTCC ENST00000344604.5 - 4 968_970 c.819_821delGGA c.(817-822)gat>ga p.ED273del ECM2_ENST00000444490.2_In_Frame_Del_p.ED251del|CENPP_ENST00000375587.3_Intron NM_001197295.1|NM_001393.3 NP_001184224.1|NP_001384.1 O94769 ECM2_HUMAN extracellular matrix protein 2, female organ and adipocyte specific 273 Poly-Glu. cell-matrix adhesion integrin binding breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 27 ctcctcctcatcctcctcctcct 0.606 16 770 --- --- --- --- CEL 1056 broad.mit.edu 37 9 135941982 135941982 + Frame_Shift_Del DEL G G - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr9:135941982delG ENST00000372080.4 + 5 629 c.613delG c.(613-615)ggfs p.G206fs CEL_ENST00000351304.7_Frame_Shift_Del_p.G203fs NM_001807.3 NP_001798.2 P19835 CEL_HUMAN carboxyl ester lipase 203 cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification cytosol|extracellular space acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1) 20 OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196) CGCGGCCTTCGGGGGGGACCC 0.642 8 1020 --- --- --- --- TUBBP5 0 broad.mit.edu 37 9 141070013 141070014 + RNA INS - - GCG rs76591329 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr9:141070013_141070014insGCG ENST00000503395.1 + 0 1132 CTCCTGGGAACGCGGCCCTCCC 0.728 7 174 --- --- --- --- DNAJC1 64215 broad.mit.edu 37 10 22208818 22208818 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:22208818delT ENST00000376980.3 - 5 868 c.578delA c.(577-579)agfs p.K193fs NM_022365.3 NP_071760.2 Q96KC8 DNJC1_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 1 193 negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2) 21 Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262) GCTGCCAGTCTTTTTTTTCTT 0.303 7 688 --- --- --- --- PCDH15 65217 broad.mit.edu 37 10 55587198 55587200 + In_Frame_Del DEL GGC GGC - rs12246234 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:55587198_55587200delGGC ENST00000373965.2 - 33 4735_4737 c.4341_4343delGCC c.(4339-4344)cct>cc p.PP1449del PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000414778.1_In_Frame_Del_p.PP1444del|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395433.1_In_Frame_Del_p.PP1417del|PCDH15_ENST00000395432.2_In_Frame_Del_p.PP1402del|PCDH15_ENST00000395438.1_In_Frame_Del_p.PP1442del|PCDH15_ENST00000395430.1_In_Frame_Del_p.PP1439del|PCDH15_ENST00000437009.1_In_Frame_Del_p.PP1371del|PCDH15_ENST00000409834.1_In_Frame_Del_p.PP1053del|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000320301.6_In_Frame_Del_p.PP1442del|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000361849.3_In_Frame_Del_p.PP1442del|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395445.1_In_Frame_Del_p.PP1449del NM_001142771.1|NM_001142772.1 NP_001136243.1|NP_001136244.1 Q96QU1 PCD15_HUMAN protocadherin-related 15 1442 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 NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1) 237 Melanoma(3;0.117)|Lung SC(717;0.238) ACCTggcggaggcggcggcggcg 0.571 HNSCC(58;0.16) 8 553 --- --- --- --- ANK3 288 broad.mit.edu 37 10 61828745 61828747 + In_Frame_Del DEL GTG GTG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:61828745_61828747delGTG ENST00000280772.1 - 37 12083_12085 c.11892_11894delCAC c.(11890-11895)act>ac p.TT3964del ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron NM_020987.3 NP_066267.2 Q12955 ANK3_HUMAN ankyrin 3, node of Ranvier (ankyrin G) 3964 Thr-rich. establishment of protein localization|signal transduction basolateral plasma membrane|cytoplasm|cytoskeleton protein binding NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7) 196 ggtggtggcagtggtggtggtgg 0.498 8 682 --- --- --- --- RTKN2 219790 broad.mit.edu 37 10 63958149 63958149 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:63958149delT ENST00000373789.3 - 12 1444 c.1348delA c.(1348-1350)ttfs p.I450fs RTKN2_ENST00000395265.1_Frame_Shift_Del_p.I471fs|RTKN2_ENST00000315289.2_Frame_Shift_Del_p.I252fs NM_145307.2 NP_660350.2 Q8IZC4 RTKN2_HUMAN rhotekin 2 450 signal transduction intracellular p.I450fs*67(1) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 21 Prostate(12;0.0297)|all_hematologic(501;0.215) GTCTCTTCAATTTTTTTTTGT 0.333 8 380 --- --- --- --- CCAR1 55749 broad.mit.edu 37 10 70509285 70509286 + Frame_Shift_Del DEL GA GA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:70509285_70509286delGA ENST00000265872.6 + 10 1080_1081 c.961_962delGA c.(961-963)gfs p.E321fs CCAR1_ENST00000535016.1_Frame_Shift_Del_p.E306fs|CCAR1_ENST00000543719.1_Frame_Shift_Del_p.E306fs NM_018237.2 NP_060707.2 Q8IX12 CCAR1_HUMAN cell division cycle and apoptosis regulator 1 321 Arg-rich. apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleoplasm|perinuclear region of cytoplasm calcium ion binding|nucleic acid binding|protein binding NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3) 56 TTTCAGTCGTGAGAGAGAGAGA 0.391 9 234 --- --- --- --- ZMIZ1 57178 broad.mit.edu 37 10 81072446 81072446 + Frame_Shift_Del DEL C C - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:81072446delC ENST00000334512.5 + 25 3716 c.3144delC c.(3142-3144)gafs p.D1048fs ZMIZ1_ENST00000446377.2_Frame_Shift_Del_p.D114fs NM_020338.3 NP_065071.1 Q9ULJ6 ZMIZ1_HUMAN zinc finger, MIZ-type containing 1 1048 transcription, DNA-dependent cytoplasm|nuclear speck zinc ion binding breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1) 30 all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985) Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229) CTTATCTGGACCCCCCCGACC 0.557 7 1404 --- --- --- --- ABCC2 1244 broad.mit.edu 37 10 101558978 101558979 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:101558978_101558979insA ENST00000370449.4 + 8 995_996 c.882_883insA c.(880-885)aaaaaafs p.KK294fs NM_000392.3 NP_000383.1 Q92887 MRP2_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 2 294 apical plasma membrane|integral to plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity p.K294N(1) NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 67 Colorectal(252;0.234) Epithelial(162;2.77e-10)|all cancers(201;2.47e-08) Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138) ATGTTGAAAAGAAAAAAAAGAA 0.441 9 963 --- --- --- --- LZTS2 84445 broad.mit.edu 37 10 102763415 102763417 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:102763415_102763417delCCT ENST00000370220.1 + 2 3623_3625 c.560_562delCCT c.(559-564)gcc>g p.AS187del LZTS2_ENST00000370223.3_In_Frame_Del_p.AS187del Q9BRK4 LZTS2_HUMAN leucine zipper, putative tumor suppressor 2 187 Required for centrosomal localization (By similarity). cell division|mitosis|Wnt receptor signaling pathway membrane|microtubule|microtubule organizing center breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 22 Epithelial(162;7.3e-09)|all cancers(201;3.72e-07) GGGGGCCCTGcctcctcctcctc 0.650 12 1149 --- --- --- --- GRK5 2869 broad.mit.edu 37 10 121189900 121189900 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:121189900delA ENST00000392870.2 + 7 876 c.547delA c.(547-549)aafs p.K183fs GRK5_ENST00000369108.3_Frame_Shift_Del_p.K78fs NM_005308.2 NP_005299.1 P34947 GRK5_HUMAN G protein-coupled receptor kinase 5 183 N-terminal. 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 endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1) 27 Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249) all cancers(201;0.0227) ACCGGTGACCAAAAACACTTT 0.483 7 576 --- --- --- --- TACC2 10579 broad.mit.edu 37 10 123970380 123970380 + Frame_Shift_Del DEL C C - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr10:123970380delC ENST00000369005.1 + 9 6780 c.6440delC c.(6439-6441)acfs p.T2147fs TACC2_ENST00000360561.3_Frame_Shift_Del_p.T225fs|TACC2_ENST00000453444.2_Frame_Shift_Del_p.T2151fs|TACC2_ENST00000368999.1_Frame_Shift_Del_p.T225fs|TACC2_ENST00000513429.1_Frame_Shift_Del_p.T293fs|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000369004.3_Frame_Shift_Del_p.T225fs|TACC2_ENST00000260733.3_Frame_Shift_Del_p.T225fs|TACC2_ENST00000515273.1_Frame_Shift_Del_p.T2151fs|TACC2_ENST00000334433.3_Frame_Shift_Del_p.T2147fs|TACC2_ENST00000515603.1_Frame_Shift_Del_p.T2102fs|TACC2_ENST00000358010.1_Frame_Shift_Del_p.T293fs NM_206862.2 NP_996744.2 O95359 TACC2_HUMAN transforming, acidic coiled-coil containing protein 2 2147 microtubule organizing center|nucleus nuclear hormone receptor binding NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3) 83 all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197) CCCACAGAGACCCCCCCAGTG 0.522 7 1084 --- --- --- --- KRTAP5-5 439915 broad.mit.edu 37 11 1651191 1651199 + In_Frame_Del DEL GGCTGTGGA GGCTGTGGA - rs71025763 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:1651191_1651199delGGCTGTGGA ENST00000399676.2 + 1 159_167 c.121_129delGGCTGTGGA c.(121-129)del p.GCG47del NM_001001480.2 NP_001001480.2 Q701N2 KRA55_HUMAN keratin associated protein 5-5 47 keratin filament endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1) 33 all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082) ctgtggctccggctgtggaggctgtgggg 0.713 9 403 --- --- --- --- OR10A5 144124 broad.mit.edu 37 11 6867223 6867225 + In_Frame_Del DEL TTC TTC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:6867223_6867225delTTC ENST00000299454.4 + 1 341_343 c.310_312delTTC c.(310-312)del p.F108del OR10A5_ENST00000379831.2_In_Frame_Del_p.F112del Q9H207 O10A5_HUMAN olfactory receptor, family 10, subfamily A, member 5 108 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2) 21 Medulloblastoma(188;0.0523)|all_neural(188;0.236) Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129) TCAGATGTATTTCTTCTTCTTCT 0.517 7 768 --- --- --- --- SWAP70 23075 broad.mit.edu 37 11 9735070 9735070 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:9735070delA ENST00000318950.6 + 3 401 c.298delA c.(298-300)aafs p.K101fs SWAP70_ENST00000447399.2_Intron NM_015055.2 NP_055870.2 Q9UH65 SWP70_HUMAN SWAP switching B-cell complex 70kDa subunit 101 cytoplasm|lamellipodium|nucleus|plasma membrane calcium ion binding|DNA binding NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1) 11 all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649) CCTCTGTGTCAAAAAAAACCT 0.343 8 436 --- --- --- --- KCNA4 3739 broad.mit.edu 37 11 30034029 30034031 + In_Frame_Del DEL TGG TGG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:30034029_30034031delTGG ENST00000328224.6 - 2 1428_1430 c.195_197delCCA c.(193-198)cag>ca p.HQ65del NM_002233.3 NP_002224.1 P22459 KCNA4_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 4 65 Poly-His. voltage-gated potassium channel complex potassium ion binding|protein binding|voltage-gated potassium channel activity central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 78 CCCGCGTGACTGGTGGTGGTGGT 0.660 9 499 --- --- --- --- OR5A1 219982 broad.mit.edu 37 11 59210950 59210951 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:59210950_59210951insT ENST00000302030.2 + 1 334_335 c.309_310insT c.(307-312)cattttfs p.HF103fs NM_001004728.1 NP_001004728.1 Q8NGJ0 OR5A1_HUMAN olfactory receptor, family 5, subfamily A, member 1 103 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1) 28 GTGCTGCTCAGTTTTTTTTCTT 0.510 12 903 --- --- --- --- CPSF7 79869 broad.mit.edu 37 11 61183765 61183767 + In_Frame_Del DEL AGG AGG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:61183765_61183767delAGG ENST00000340437.4 - 6 984_986 c.904_906delCCT c.(904-906)del p.P302del CPSF7_ENST00000448745.1_In_Frame_Del_p.P250del|CPSF7_ENST00000394888.4_In_Frame_Del_p.P259del|CPSF7_ENST00000439958.3_In_Frame_Del_p.P250del NM_024811.3 NP_079087.3 Q8N684 CPSF7_HUMAN cleavage and polyadenylation specific factor 7, 59kDa 259 Pro-rich. mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription mRNA cleavage factor complex nucleotide binding|protein binding|RNA binding breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1) 22 AGTGGATACCAGGAGGAGGAGGA 0.611 7 325 --- --- --- --- FAU 2197 broad.mit.edu 37 11 64888248 64888250 + In_Frame_Del DEL TCT TCT - rs1065065 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:64888248_64888250delTCT ENST00000529639.1 - 5 696_698 c.305_307delAGA c.(304-309)aca>a p.KT102del FAU_ENST00000529259.1_3'UTR|FAU_ENST00000525297.1_In_Frame_Del_p.KT67del|FAU_ENST00000531743.1_In_Frame_Del_p.KT102del|FAU_ENST00000527548.1_In_Frame_Del_p.KT102del|FAU_ENST00000279259.3_In_Frame_Del_p.ED83del NM_001997.4 NP_001988.1 P35544 UBIM_HUMAN Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed 0 NS(3)|kidney(1)|large_intestine(2) 6 GCCCGACCTGTCTTCTTCTTCTT 0.542 12 607 --- --- --- --- DDX10 1662 broad.mit.edu 37 11 108788635 108788637 + In_Frame_Del DEL TGA TGA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:108788635_108788637delTGA ENST00000526794.1 + 17 2372_2374 c.2340_2342delTGA c.(2338-2343)agt>ag p.SD780del DDX10_ENST00000322536.3_In_Frame_Del_p.SD780del Q13206 DDX10_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 780 ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2) 27 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) TGGATTGGAGtgatgatgatgat 0.355 T NUP98 AML* 10 403 --- --- --- --- BCL9L 283149 broad.mit.edu 37 11 118773004 118773004 + Frame_Shift_Del DEL G G - rs147951163 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:118773004delG ENST00000334801.3 - 6 2412 c.1448delC c.(1447-1449)cgfs p.P483fs BCL9L_ENST00000526143.1_5'UTR NM_182557.2 NP_872363.1 Q86UU0 BCL9L_HUMAN B-cell CLL/lymphoma 9-like 483 Necessary for interaction with CTNNB1 (By similarity).|Pro-rich. negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent transcription coactivator activity NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2) 56 all_hematologic(175;0.0839) Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.66e-05) ATGCTCCAGCGGGGGGCCCCC 0.642 9 943 --- --- --- --- CBL 867 broad.mit.edu 37 11 119149356 119149358 + In_Frame_Del DEL ATG ATG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:119149356_119149358delATG ENST00000264033.4 + 9 1740_1742 c.1364_1366delATG c.(1363-1368)tat>t p.YD455del NM_005188.3 NP_005179.2 P22681 CBL_HUMAN Cbl proto-oncogene, E3 ubiquitin protein ligase 455 Asp/Glu-rich (acidic). 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_K477del(1) breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1) 251 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) TCCCCAAATTATGATGATGATGA 0.473 """T, Mis S, O""" MLL """AML, JMML, MDS""" Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies 7 345 --- --- --- --- CHEK1 1111 broad.mit.edu 37 11 125505377 125505378 + Frame_Shift_Ins INS - - A rs35817404 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr11:125505377_125505378insA ENST00000534070.1 + 7 922_923 c.667_668insA c.(667-669)aaafs p.K223fs CHEK1_ENST00000544373.1_Frame_Shift_Ins_p.K223fs|CHEK1_ENST00000428830.2_Frame_Shift_Ins_p.K223fs|CHEK1_ENST00000427383.2_Frame_Shift_Ins_p.K239fs|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000278916.3_Frame_Shift_Ins_p.K223fs|CHEK1_ENST00000524737.1_Frame_Shift_Ins_p.K223fs|CHEK1_ENST00000438015.1_Frame_Shift_Ins_p.K223fs NM_001274.5 NP_001265.2 O14757 CHK1_HUMAN checkpoint kinase 1 223 Protein kinase. E -> V (in dbSNP:rs35817404). 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)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1) 26 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) TGACTGGAAAGAAAAAAAAACA 0.361 Other conserved DNA damage response genes 9 530 --- --- --- --- GPR19 2842 broad.mit.edu 37 12 12814274 12814274 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:12814274delT ENST00000540510.1 - 2 1301 c.1109delA c.(1108-1110)acfs p.N370fs GPR19_ENST00000332427.2_Frame_Shift_Del_p.N370fs Q15760 GPR19_HUMAN G protein-coupled receptor 19 370 integral to plasma membrane G-protein coupled receptor activity breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 17 Prostate(47;0.0802) BRCA - Breast invasive adenocarcinoma(232;0.048) GCCAACGTAGTTTTTTTTGGC 0.398 10 750 --- --- --- --- SLCO1B3 28234 broad.mit.edu 37 12 21028267 21028267 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:21028267delT ENST00000381545.3 + 9 1045 c.826delT c.(826-828)ttfs p.F278fs SLCO1B3_ENST00000261196.2_Frame_Shift_Del_p.F278fs|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron|LST3_ENST00000540229.1_Frame_Shift_Del_p.F278fs|SLCO1B3_ENST00000553473.1_Frame_Shift_Del_p.F278fs NM_019844.3 NP_062818.1 Q9NPD5 SO1B3_HUMAN solute carrier organic anion transporter family, member 1B3 278 bile acid metabolic process|sodium-independent organic anion transport basolateral plasma membrane|cytoplasm|integral to plasma membrane bile acid transmembrane transporter activity|organic anion transmembrane transporter activity breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2) 63 Esophageal squamous(101;0.149) TTCCATACCATTTTTTTTCTT 0.363 7 556 --- --- --- --- SMARCC2 6601 broad.mit.edu 37 12 56558379 56558381 + In_Frame_Del DEL AGG AGG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:56558379_56558381delAGG ENST00000550164.1 - 28 3381_3383 c.3367_3369delCCT c.(3367-3369)del p.P1123del SMARCC2_ENST00000267064.4_In_Frame_Del_p.P1092del|SMARCC2_ENST00000347471.4_Intron|SMARCC2_ENST00000394023.3_Intron|RP11-977G19.5_ENST00000553176.1_RNA Q8TAQ2 SMRC2_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 1092 Pro-rich. HGHHHHLPFA -> MGSPPSPVR (in Ref. 1; AAC50694). chromatin remodeling|negative regulation of transcription, DNA-dependent|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 DNA binding|protein binding|transcription coactivator activity breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1) 41 OV - Ovarian serous cystadenocarcinoma(18;0.123) TGGATGGAGCAGGAGGAGGAGGA 0.591 7 225 --- --- --- --- MYO1A 4640 broad.mit.edu 37 12 57422572 57422573 + Frame_Shift_Ins INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:57422572_57422573insT ENST00000442789.2 - 29 3385_3386 c.3098_3099insA c.(3097-3099)aggfs p.R1033fs MYO1A_ENST00000300119.3_Frame_Shift_Ins_p.R1033fs|TAC3_ENST00000415231.1_5'UTR|MYO1A_ENST00000544473.1_Frame_Shift_Ins_p.R871fs NM_001256041.1 NP_001242970.1 Q9UBC5 MYO1A_HUMAN myosin IA 1033 sensory perception of sound|vesicle localization brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex actin binding|ATP binding|calmodulin binding|motor activity p.?(1) breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3) 50 AATGACTCCCCTTTTTTTTGTA 0.559 7 522 --- --- --- --- LRP1 4035 broad.mit.edu 37 12 57605740 57605742 + In_Frame_Del DEL TGC TGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:57605740_57605742delTGC ENST00000243077.3 + 87 13755_13757 c.13289_13291delTGC c.(13288-13293)ttg>t p.LL4432del NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 4432 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 NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5) 184 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CCTCTGCTGTTGCTGCTGCTGCT 0.557 8 561 --- --- --- --- R3HDM2 22864 broad.mit.edu 37 12 57674205 57674207 + In_Frame_Del DEL TGC TGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:57674205_57674207delTGC ENST00000402412.1 - 14 1668_1670 c.1278_1280delGCA c.(1276-1281)caa>ca p.QQ426del R3HDM2_ENST00000347140.3_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000441731.2_In_Frame_Del_p.QQ73del|R3HDM2_ENST00000413953.2_In_Frame_Del_p.QQ139del|RP11-123K3.4_ENST00000548184.1_RNA|R3HDM2_ENST00000393811.2_In_Frame_Del_p.QQ139del|R3HDM2_ENST00000403821.2_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000358907.2_In_Frame_Del_p.QQ412del Q9Y2K5 R3HD2_HUMAN R3H domain containing 2 412 Gln-rich. nucleus nucleic acid binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1) 22 AGCAGGAAGTtgctgctgctgct 0.576 11 516 --- --- --- --- MARS 4141 broad.mit.edu 37 12 57883053 57883053 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:57883053delT ENST00000262027.5 + 3 338 c.204delT c.(202-204)tafs p.Y68fs MARS_ENST00000447721.2_Intron|MARS_ENST00000315473.5_5'UTR NM_004990.3 NP_004981.2 P56192 SYMC_HUMAN methionyl-tRNA synthetase 68 methionyl-tRNA aminoacylation cytosol ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1) 33 GBM - Glioblastoma multiforme(3;4.27e-41) L-Methionine(DB00134) TGGGCAGATATTTTTTTTTGT 0.488 12 361 --- --- --- --- CUX2 23316 broad.mit.edu 37 12 111758235 111758237 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:111758235_111758237delTCC ENST00000261726.6 + 17 2576_2578 c.2422_2424delTCC c.(2422-2424)del p.S813del NM_015267.3 NP_056082.2 O14529 CUX2_HUMAN cut-like homeobox 2 813 Poly-Ser. nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2) 55 GCCCTCGCTGTCCTCCTCCTCCT 0.749 7 337 --- --- --- --- EP400 57634 broad.mit.edu 37 12 132547093 132547094 + In_Frame_Ins INS - - CAG rs113304321 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr12:132547093_132547094insCAG ENST00000333577.4 + 48 8398_8399 c.8289_8290insCAG c.(8287-8292)caagca>caCAGagca p.2763_2763Q>HR EP400_ENST00000389561.2_In_Frame_Ins_p.2727_2727Q>HR|EP400_ENST00000330386.6_In_Frame_Ins_p.2646_2646Q>HR|EP400_ENST00000332482.4_In_Frame_Ins_p.2690_2690Q>HR|EP400_ENST00000389562.2_In_Frame_Ins_p.2726_2726Q>HR Q96L91 EP400_HUMAN E1A binding protein p400 2763 Interaction with ZNF42 (By similarity).|Poly-Gln. histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity p.Q2726Q(9) NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3) 161 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) agcagcaacaacagcagcagca 0.564 26 324 --- --- --- --- TRAV12-3 0 broad.mit.edu 37 14 22433684 22433684 + RNA DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr14:22433684delT ENST00000390442.3 + 0 5 TTTGTTATTATTTTTTTTTCG 0.353 8 151 --- --- --- --- LRP10 26020 broad.mit.edu 37 14 23341527 23341529 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr14:23341527_23341529delCCT ENST00000359591.4 + 1 706_708 c.15_17delCCT c.(13-18)acc>ac p.TL5del LRP10_ENST00000546834.1_In_Frame_Del_p.TL5del NM_014045.3 NP_054764.2 Q7Z4F1 LRP10_HUMAN low density lipoprotein receptor-related protein 10 5 endocytosis coated pit|integral to membrane central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2) 32 all_cancers(95;4.69e-05) GBM - Glioblastoma multiforme(265;0.00549) TGTTGGCCACCCTCCTCCTCCTC 0.670 9 444 --- --- --- --- RBM25 58517 broad.mit.edu 37 14 73572607 73572608 + Frame_Shift_Del DEL AG AG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr14:73572607_73572608delAG ENST00000261973.7 + 11 1480_1481 c.1195_1196delAG c.(1195-1197)afs p.R399fs RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs NM_021239.2 NP_067062.1 P49756 RBM25_HUMAN RNA binding motif protein 25 399 Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization. apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing cytoplasm|nuclear speck mRNA binding|nucleotide binding|protein binding breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1) 31 BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688) agagcgggaaagagagagagag 0.446 10 176 --- --- --- --- ELMSAN1 91748 broad.mit.edu 37 14 74205926 74205928 + In_Frame_Del DEL CTG CTG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr14:74205926_74205928delCTG ENST00000286523.5 - 2 1566_1568 c.784_786delCAG c.(784-786)del p.Q262del ELMSAN1_ENST00000394071.2_In_Frame_Del_p.Q262del NM_194278.3 NP_919254.2 ELM2 and Myb/SANT-like domain containing 1 GTAGGgctgcctgctgctgctgc 0.650 11 180 --- --- --- --- ATXN3 4287 broad.mit.edu 37 14 92537355 92537357 + In_Frame_Del DEL CTG CTG - rs147904130 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr14:92537355_92537357delCTG ENST00000545170.1 - 10 1008_1010 c.940_942delCAG c.(940-942)del p.Q314del ATXN3_ENST00000502250.1_In_Frame_Del_p.Q126del|ATXN3_ENST00000340660.6_In_Frame_Del_p.Q250del|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000429774.2_In_Frame_Del_p.Q298del|ATXN3_ENST00000532032.1_In_Frame_Del_p.Q305del|ATXN3_ENST00000503767.1_In_Frame_Del_p.Q290del|ATXN3_ENST00000393287.5_In_Frame_Del_p.Q305del NM_001164774.1|NM_001164776.1|NM_001164777.1|NM_001164778.1|NM_004993.5 NP_001158246.1|NP_001158248.1|NP_001158249.1|NP_001158250.1|NP_004984.2 P54252 ATX3_HUMAN ataxin 3 305 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 endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1) 12 all_cancers(154;0.0768) COAD - Colon adenocarcinoma(157;0.224) ATAGGTCCCCctgctgctgctgc 0.448 8 322 --- --- --- --- ULK4P3 0 broad.mit.edu 37 15 30406088 30406089 + RNA INS - - T TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr15:30406088_30406089insT ENST00000568486.1 + 0 402 NR_026859.1 TGCCTCAAAAGTTTTTTTTTTT 0.297 7 74 --- --- --- --- SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC TGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr15:40328597_40328599delTGC ENST00000267884.6 - 5 417_419 c.346_348delGCA c.(346-348)del p.A116del SRP14_ENST00000558527.1_5'UTR|SRP14_ENST00000560773.1_In_Frame_Del_p.A36del|SRP14_ENST00000558720.1_In_Frame_Del_p.A36del NM_003134.4 NP_003125.3 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous Alu RNA binding protein) 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 endometrium(1)|skin(1)|upper_aerodigestive_tract(1) 3 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 0.478 8 313 --- --- --- --- MGA 23269 broad.mit.edu 37 15 42003383 42003385 + In_Frame_Del DEL CAG CAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr15:42003383_42003385delCAG ENST00000219905.7 + 8 3101_3103 c.2920_2922delCAG c.(2920-2922)del p.Q981del MGA_ENST00000566586.1_In_Frame_Del_p.Q981del|MGA_ENST00000389936.4_In_Frame_Del_p.Q981del|MGA_ENST00000545763.1_In_Frame_Del_p.Q981del|MGA_ENST00000570161.1_In_Frame_Del_p.Q981del NM_001164273.1 NP_001157745.1 Q8IWI9 MGAP_HUMAN MGA, MAX dimerization protein 981 Gln-rich. MLL1 complex DNA binding|sequence-specific DNA binding transcription factor activity NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 95 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) GCGGCAGGCACAGCAGCAGCAGC 0.458 7 339 --- --- --- --- ZNF106 64397 broad.mit.edu 37 15 42742957 42742957 + Frame_Shift_Del DEL A A - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr15:42742957delA ENST00000263805.4 - 2 1770 c.1444delT c.(1444-1446)ccfs p.S482fs ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron NM_022473.1 NP_071918.1 zinc finger protein 106 TCTCCAGGGGAAAAAAAATTT 0.393 7 1014 --- --- --- --- BLM 641 broad.mit.edu 37 15 91304138 91304139 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr15:91304138_91304139insA ENST00000355112.3 + 7 1653_1654 c.1535_1536insA c.(1534-1536)gaafs p.E512fs BLM_ENST00000560509.1_Frame_Shift_Ins_p.E512fs NM_000057.2 NP_000048.1 P54132 BLM_HUMAN Bloom syndrome, RecQ helicase-like 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 p.N515fs*16(1) breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 51 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) CCAAGACTAGGAAAAAAAAATG 0.371 """Mis, N, F""" """leukemia, lymphoma, skin squamous cell , other cancers""" Genes defective in diseases associated with sensitivity to DNA damaging agents Bloom syndrome 12 326 --- --- --- --- C16orf62 57020 broad.mit.edu 37 16 19580800 19580802 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:19580800_19580802delTCC ENST00000438132.3 + 3 487_489 c.439_441delTCC c.(439-441)del p.S153del C16orf62_ENST00000542263.1_In_Frame_Del_p.S153del|C16orf62_ENST00000417362.2_In_Frame_Del_p.S64del|C16orf62_ENST00000251143.5_In_Frame_Del_p.S64del|C16orf62_ENST00000538853.1_In_Frame_Del_p.S153del NM_020314.5 NP_064710.4 Q7Z3J2 CP062_HUMAN chromosome 16 open reading frame 62 64 integral to membrane breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2) 36 TTCTTCCACGTCCTCCTCCTCCT 0.562 11 287 --- --- --- --- KNOP1 400506 broad.mit.edu 37 16 19722724 19722724 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:19722724delT ENST00000219837.7 - 3 1035 c.957delA c.(955-957)aafs p.K319fs AC002550.5_ENST00000565916.1_RNA|KNOP1_ENST00000568230.1_5'UTR NM_001012991.2 NP_001013009.2 lysine-rich nucleolar protein 1 p.G320fs*5(1)|p.K319N(1) CCATGTTGCCTTTTTTTTCCA 0.562 8 539 --- --- --- --- TNRC6A 27327 broad.mit.edu 37 16 24788441 24788443 + In_Frame_Del DEL GCA GCA - rs10593509 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:24788441_24788443delGCA ENST00000395799.3 + 5 480_482 c.351_353delGCA c.(349-354)ccg>cc p.PQ117del TNRC6A_ENST00000315183.7_In_Frame_Del_p.PQ117del NM_014494.2 NP_055309.2 Q8NDV7 TNR6A_HUMAN trinucleotide repeat containing 6A 117 Gln-rich. negative regulation of translation involved in gene silencing by miRNA cytoplasmic mRNA processing body|micro-ribonucleoprotein complex nucleotide binding|RNA binding p.P117P(1) breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 64 GBM - Glioblastoma multiforme(48;0.0394) agccgcagccgcagcagcagcag 0.606 8 504 --- --- --- --- EIF3C 8663 broad.mit.edu 37 16 28734579 28734581 + In_Frame_Del DEL GAG GAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:28734579_28734581delGAG ENST00000331666.6 + 9 1057_1059 c.871_873delGAG c.(871-873)del p.E294del EIF3C_ENST00000564243.1_In_Frame_Del_p.E284del|EIF3C_ENST00000566501.1_In_Frame_Del_p.E294del|EIF3C_ENST00000566866.1_In_Frame_Del_p.E294del|EIF3C_ENST00000395587.1_In_Frame_Del_p.E294del Q99613 EIF3C_HUMAN eukaryotic translation initiation factor 3, subunit C 294 Poly-Glu. cytosol|eukaryotic translation initiation factor 3 complex protein binding|translation initiation factor activity lung(5)|skin(1) 6 GCGCCTGGATGAGGAGGAGGAGG 0.562 15 3642 --- --- --- --- RRN3P2 0 broad.mit.edu 37 16 29110406 29110406 + RNA DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:29110406delT ENST00000564580.1 + 0 1098 TTAAAAAATCTTTTTTTTTTT 0.299 14 118 --- --- --- --- TAOK2 9344 broad.mit.edu 37 16 29994531 29994533 + In_Frame_Del DEL GAG GAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:29994531_29994533delGAG ENST00000308893.4 + 12 2181_2183 c.1138_1140delGAG c.(1138-1140)del p.E392del TAOK2_ENST00000543033.1_In_Frame_Del_p.E392del|TAOK2_ENST00000416441.2_In_Frame_Del_p.E219del|TAOK2_ENST00000279394.3_In_Frame_Del_p.E392del NM_001252043.1|NM_016151.3 NP_001238972.1|NP_057235.2 Q9UL54 TAOK2_HUMAN TAO kinase 2 392 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 breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1) 22 CAACgaggaagaggaggaggagg 0.611 11 390 --- --- --- --- SRCAP 10847 broad.mit.edu 37 16 30736370 30736371 + Frame_Shift_Ins INS - - C TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:30736370_30736371insC ENST00000262518.4 + 25 6010_6011 c.5625_5626insC c.(5623-5628)caccccfs p.HP1875fs SRCAP_ENST00000344771.4_Frame_Shift_Ins_p.HP1717fs|SRCAP_ENST00000395059.2_Frame_Shift_Ins_p.HP1813fs NM_006662.2 NP_006653.2 Q6ZRS2 SRCAP_HUMAN Snf2-related CREBBP activator protein 1875 Pro-rich. interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|nucleus|protein complex ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5) 136 Colorectal(24;0.198) CTCGACGCCAGCCCCCCCCACC 0.569 20 859 --- --- --- --- SETD1A 9739 broad.mit.edu 37 16 30982809 30982811 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:30982809_30982811delTCC ENST00000262519.8 + 13 3813_3815 c.3127_3129delTCC c.(3127-3129)del p.S1058del NM_014712.1 NP_055527.1 O15047 SET1A_HUMAN SET domain containing 1A 1058 Ser-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nuclear speck|Set1C/COMPASS complex histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 59 CAGctcctcatcctcctcctcct 0.547 11 478 --- --- --- --- CCDC135 84229 broad.mit.edu 37 16 57731885 57731887 + In_Frame_Del DEL GGA GGA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:57731885_57731887delGGA ENST00000360716.3 + 3 245_247 c.24_26delGGA c.(22-27)gtg>gt p.VE8del RP11-405F3.4_ENST00000563062.1_RNA|CCDC135_ENST00000394337.4_In_Frame_Del_p.VE8del|CCDC135_ENST00000336825.8_In_Frame_Del_p.VE8del Q8IY82 CC135_HUMAN coiled-coil domain containing 135 8 cytoplasm breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 30 Gggagaaggtggaggaggaggag 0.591 8 455 --- --- --- --- CNGB1 1258 broad.mit.edu 37 16 57983275 57983277 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:57983275_57983277delTCC ENST00000564448.1 - 14 1143_1145 c.1083_1085delGGA c.(1081-1086)gaa>ga p.EE363del CNGB1_ENST00000251102.8_In_Frame_Del_p.EE369del Q14028 CNGB1_HUMAN cyclic nucleotide gated channel beta 1 369 Poly-Glu. sensory perception of smell intracellular cyclic nucleotide activated cation channel complex cAMP binding|intracellular cAMP activated cation channel activity breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 54 ctcctcctcttcctcctcctcct 0.586 8 356 --- --- --- --- EDC4 23644 broad.mit.edu 37 16 67913786 67913788 + In_Frame_Del DEL AGC AGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:67913786_67913788delAGC ENST00000358933.5 + 16 2094_2096 c.1855_1857delAGC c.(1855-1857)del p.S629del NM_014329.4 NP_055144.3 Q6P2E9 EDC4_HUMAN enhancer of mRNA decapping 4 629 Ser-rich. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay cytoplasmic mRNA processing body|cytosol|nucleus protein binding breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2) 41 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121) cagcagcggtagcagcagcagca 0.616 13 380 --- --- --- --- ZFHX3 463 broad.mit.edu 37 16 72827324 72827324 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:72827324delT ENST00000268489.5 - 9 9929 c.9257delA c.(9256-9258)agfs p.K3086fs ZFHX3_ENST00000397992.5_Frame_Shift_Del_p.K2172fs NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 3086 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 NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) CTCGTTGGCCTTTTTAATCCG 0.517 8 801 --- --- --- --- ZFHX3 463 broad.mit.edu 37 16 72845830 72845830 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:72845830delT ENST00000268489.5 - 6 4309 c.3637delA c.(3637-3639)cafs p.T1213fs ZFHX3_ENST00000397992.5_Frame_Shift_Del_p.T299fs NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 1213 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 NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) TCCTCAGCTGTTTTTGGTCGC 0.537 8 1462 --- --- --- --- ZFHX3 463 broad.mit.edu 37 16 72991713 72991715 + In_Frame_Del DEL CCA CCA - rs4788682 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:72991713_72991715delCCA ENST00000268489.5 - 2 3002_3004 c.2330_2332delTGG c.(2329-2334)gct>g p.VA777del ZFHX3_ENST00000397992.5_Intron NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 777 Poly-Ala. V -> A (in dbSNP:rs4788682). 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 p.V777V(1) NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) gccgccgcagccaccgccgccgc 0.635 9 469 --- --- --- --- RP11-150D5.2 0 broad.mit.edu 37 16 76268905 76268905 + RNA DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr16:76268905delT ENST00000568714.1 - 0 135 ttttcttttctttttttttGC 0.418 7 304 --- --- --- --- MED9 55090 broad.mit.edu 37 17 17394705 17394707 + In_Frame_Del DEL CAG CAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:17394705_17394707delCAG ENST00000268711.3 + 2 393_395 c.337_339delCAG c.(337-339)del p.Q117del NM_018019.2 NP_060489.1 Q9NWA0 MED9_HUMAN mediator complex subunit 9 117 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent protein binding cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 7 GAGCCCCGAACAGCAGCAGCAGC 0.581 7 464 --- --- --- --- PLCD3 113026 broad.mit.edu 37 17 43192760 43192762 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:43192760_43192762delTCC ENST00000322765.5 - 9 1622_1624 c.1509_1511delGGA c.(1507-1512)gat>ga p.ED503del PLCD3_ENST00000540511.1_5'UTR NM_133373.3 NP_588614.1 Q8N3E9 PLCD3_HUMAN phospholipase C, delta 3 503 intracellular signal transduction|lipid catabolic process cleavage furrow|cytoplasm|membrane calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity p.E503D(2) breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2) 17 Phosphatidylserine(DB00144) ctcctcgtcatcctcctcctcct 0.670 8 89 --- --- --- --- RP11-798G7.5 0 broad.mit.edu 37 17 43596433 43596433 + RNA DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:43596433delT ENST00000253803.2 + 0 267 TTTTTGCCGGTTTTGGCCTAC 0.478 10 3949 --- --- --- --- RP11-156P1.3 0 broad.mit.edu 37 17 45137247 45137248 + RNA INS - - CTTTAC TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr17:45137247_45137248insCTTTAC ENST00000575173.1 - 0 124 ctttcaggctacacagctgatt 0.554 18 384 --- --- --- --- FHOD3 80206 broad.mit.edu 37 18 34261459 34261460 + Frame_Shift_Del DEL AG AG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr18:34261459_34261460delAG ENST00000257209.4 + 12 1493_1494 c.1371_1372delAG c.(1369-1374)gcagfs p.AE457fs FHOD3_ENST00000359247.4_Frame_Shift_Del_p.AE457fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.AE632fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.AE419fs|FHOD3_ENST00000591635.1_Intron NM_025135.2 NP_079411.2 Q2V2M9 FHOD3_HUMAN formin homology 2 domain containing 3 457 actin cytoskeleton organization cytoplasm|cytoskeleton actin binding NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1) 90 all_epithelial(2;0.0181)|Colorectal(2;0.0195) CACTGGCAGCAGAGAGAGAGAG 0.460 10 212 --- --- --- --- MUC16 94025 broad.mit.edu 37 19 9057565 9057565 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:9057565delT ENST00000397910.4 - 3 30084 c.29881delA c.(29881-29883)gtfs p.S9962fs NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 9964 Ser-rich.|Thr-rich. cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7) 590 CCAGGAGAACTTTTTTGGGTG 0.488 9 1439 --- --- --- --- WDR88 126248 broad.mit.edu 37 19 33666419 33666421 + In_Frame_Del DEL TCA TCA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:33666419_33666421delTCA ENST00000355868.3 + 11 1436_1438 c.1360_1362delTCA c.(1360-1362)del p.S458del WDR88_ENST00000361680.2_3'UTR NM_173479.3 NP_775750.3 Q6ZMY6 WDR88_HUMAN WD repeat domain 88 458 Poly-Ser. breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1) 25 Esophageal squamous(110;0.137) TACTTCATCGTCATCATCATCAT 0.527 7 640 --- --- --- --- ATP4A 495 broad.mit.edu 37 19 36054349 36054351 + In_Frame_Del DEL CTT CTT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:36054349_36054351delCTT ENST00000262623.3 - 2 119_121 c.91_93delAAG c.(91-93)del p.K31del NM_000704.2 NP_000695.2 P20648 ATP4A_HUMAN ATPase, H+/K+ exchanging, alpha polypeptide 31 ATP biosynthetic process|ATP hydrolysis coupled proton transport integral to plasma membrane ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 53 all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831) CGCCACCCGCCTTCTTCTTCTTG 0.601 8 1524 --- --- --- --- SPRED3 399473 broad.mit.edu 37 19 38882864 38882866 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:38882864_38882866delCCT ENST00000587013.1 + 3 569_571 c.491_493delCCT c.(490-495)ccc>c p.PS164del SPRED3_ENST00000586301.1_In_Frame_Del_p.PS120del|SPRED3_ENST00000587564.2_3'UTR|SPRED3_ENST00000338502.4_In_Frame_Del_p.PS120del Q2MJR0 SPRE3_HUMAN sprouty-related, EVH1 domain containing 3 120 multicellular organismal development central_nervous_system(2)|large_intestine(1)|lung(5)|skin(1) 9 all_cancers(60;3.4e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) TCACTCAccccctcctcctcctc 0.645 9 108 --- --- --- --- FUZ 80199 broad.mit.edu 37 19 50310483 50310485 + In_Frame_Del DEL CAG CAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:50310483_50310485delCAG ENST00000313777.4 - 11 1343_1345 c.1180_1182delCTG c.(1180-1182)del p.L394del FUZ_ENST00000533418.1_In_Frame_Del_p.L344del|FUZ_ENST00000445575.2_Intron|FUZ_ENST00000528094.1_In_Frame_Del_p.L358del NM_025129.4 NP_079405.2 Q9BT04 FUZZY_HUMAN fuzzy planar cell polarity protein 394 Leu-rich. cilium assembly|embryonic body morphogenesis|embryonic skeletal system morphogenesis|establishment of planar polarity|hair follicle development|neural tube closure|protein transport|regulation of smoothened signaling pathway cytoplasm|cytoskeleton endometrium(1)|lung(3) 4 all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116) TCTGGGGAGACAGCAGCAGCAGC 0.635 11 298 --- --- --- --- SIGLEC16 400709 broad.mit.edu 37 19 50474857 50474861 + RNA DEL GACGC GACGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:50474857_50474861delGACGC ENST00000602139.1 + 0 998 sialic acid binding Ig-like lectin 16 (gene/pseudogene) endometrium(2)|kidney(2)|lung(6) 10 CAGTCTCCAGGACGCTTCCCTTTGC 0.566 11 270 --- --- --- --- SIGLEC7 27036 broad.mit.edu 37 19 51645628 51645630 + Translation_Start_Site DEL TGC TGC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:51645628_51645630delTGC ENST00000317643.6 + 0 71_73 SIGLEC7_ENST00000600577.1_Start_Codon_Del|SIGLEC7_ENST00000305628.7_Start_Codon_Del NM_014385.2 NP_055200.1 Q9Y286 SIGL7_HUMAN sialic acid binding Ig-like lectin 7 cell adhesion integral to plasma membrane receptor activity|sugar binding autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1) 29 all_neural(266;0.0199) GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297) ACCCCAGATAtgctgctgctgct 0.596 8 142 --- --- --- --- TMC4 147798 broad.mit.edu 37 19 54675747 54675749 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:54675747_54675749delTCC ENST00000376591.4 - 2 332_334 c.201_203delGGA c.(199-204)gat>ga p.ED67del TMC4_ENST00000301187.4_In_Frame_Del_p.ED61del NM_001145303.1|NM_144686.2 NP_001138775.1|NP_653287.1 Q7Z404 TMC4_HUMAN transmembrane channel-like 4 67 Poly-Glu. integral to membrane breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1) 22 all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19) CCTTCCTCCATCCTCCTCCTCCT 0.645 11 448 --- --- --- --- KIR3DL1 3811 broad.mit.edu 37 19 55341677 55341678 + Frame_Shift_Ins INS - - A TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr19:55341677_55341678insA ENST00000391728.4 + 9 1315_1316 c.1282_1283insA c.(1282-1284)cacfs p.H428fs KIR3DL1_ENST00000358178.4_Frame_Shift_Ins_p.H333fs|KIR3DL1_ENST00000541392.1_Frame_Shift_Ins_p.H411fs|KIR3DL1_ENST00000538269.1_Frame_Shift_Ins_p.H428fs|KIR3DL1_ENST00000326542.7_Frame_Shift_Ins_p.H411fs|KIR3DL1_ENST00000402254.2_Intron NM_013289.2 NP_037421.2 killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1 breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 11 GBM - Glioblastoma multiforme(193;0.0192) TACCATCTTGTACACGGAACTT 0.520 15 1620 --- --- --- --- RP4-777D9.2 0 broad.mit.edu 37 20 21146805 21146805 + RNA DEL G G - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr20:21146805delG ENST00000591761.1 - 0 5051 PLK1S1_ENST00000457464.1_RNA TTTTTTTTTTGTCCATGAGGC 0.383 9 112 --- --- --- --- FRG1B 0 broad.mit.edu 37 20 29628226 29628226 + Splice_Site DEL G G - rs78710112 by1000genomes TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr20:29628226delG ENST00000278882.3 + 6 608 c.e6-1 FRG1B_ENST00000439954.2_Splice_Site|FRG1B_ENST00000358464.4_Splice_Site endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 GTTTCACTTAGGGGAAAATGG 0.358 28 888 --- --- --- --- CTCFL 140690 broad.mit.edu 37 20 56099187 56099187 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr20:56099187delT ENST00000426658.2 - 1 736 c.75delA c.(73-75)aafs p.K25fs CTCFL_ENST00000371196.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000243914.3_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000433949.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000432255.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000429804.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000423479.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000422869.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000422109.2_Frame_Shift_Del_p.K25fs Q8NI51 CTCFL_HUMAN CCCTC-binding factor (zinc finger protein)-like 25 cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent cytoplasm|nucleus histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07) CCTTCAGGCCTTTTTCCGGCA 0.502 16 2218 --- --- --- --- PRDM15 63977 broad.mit.edu 37 21 43221415 43221417 + In_Frame_Del DEL CTG CTG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr21:43221415_43221417delCTG ENST00000422911.1 - 25 3681_3683 c.3580_3582delCAG c.(3580-3582)del p.Q1194del PRDM15_ENST00000538201.1_In_Frame_Del_p.Q1157del|PRDM15_ENST00000398548.1_In_Frame_Del_p.Q1174del|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000269844.3_In_Frame_Del_p.Q1503del|PRDM15_ENST00000447207.2_In_Frame_Del_p.Q1137del P57071 PRD15_HUMAN PR domain containing 15 1503 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1) 43 AGCTGTACATCTGCTGCTGCTGC 0.611 9 405 --- --- --- --- PTTG1IP 754 broad.mit.edu 37 21 46276194 46276196 + In_Frame_Del DEL GCA GCA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr21:46276194_46276196delGCA ENST00000330938.3 - 4 581_583 c.361_363delTGC c.(361-363)del p.C121del PTTG1IP_ENST00000494690.1_5'UTR|PTTG1IP_ENST00000397886.3_In_Frame_Del_p.C100del|PTTG1IP_ENST00000397887.3_Intron|PTTG1IP_ENST00000445724.2_Intron NM_004339.3 NP_004330.1 P53801 PTTG_HUMAN pituitary tumor-transforming 1 interacting protein 121 Poly-Cys. protein import into nucleus cytoplasm|integral to membrane|nucleus ovary(1)|prostate(1) 2 Colorectal(79;0.0659) TCTTCCTCCTGCAGCAGCAGCAG 0.616 7 306 --- --- --- --- CCT8L2 150160 broad.mit.edu 37 22 17071787 17071787 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:17071787delT ENST00000359963.3 - 1 1913 c.1654delA c.(1654-1656)tcfs p.I552fs NM_014406.4 NP_055221.1 Q96SF2 TCPQM_HUMAN chaperonin containing TCP1, subunit 8 (theta)-like 2 552 cellular protein metabolic process cytoplasm anion channel activity|ATP binding|calcium-activated potassium channel activity breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1) 67 all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977) all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175) AATCCAAGGATTTTTTTTGTT 0.408 8 507 --- --- --- --- MYH9 4627 broad.mit.edu 37 22 36689419 36689421 + In_Frame_Del DEL CCT CCT - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:36689419_36689421delCCT ENST00000216181.5 - 30 4279_4281 c.4049_4051delAGG c.(4048-4053)gcc>g p.EA1350del NM_002473.4 NP_002464.1 P35579 MYH9_HUMAN myosin, heavy chain 9, non-muscle 1350 E -> EE (in Ref. 7). 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 NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3) 86 TTGTGCTTGGCCTCCTCCTCCTC 0.650 T ALK ALCL """Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome""" Hereditary Macrothrombocytopenia, MYH9-associated 8 415 --- --- --- --- MYH9 4627 broad.mit.edu 37 22 36696948 36696950 + In_Frame_Del DEL CTC CTC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:36696948_36696950delCTC ENST00000216181.5 - 22 3015_3017 c.2785_2787delGAG c.(2785-2787)del p.E929del NM_002473.4 NP_002464.1 P35579 MYH9_HUMAN myosin, heavy chain 9, non-muscle 929 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 NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3) 86 GCTGGCAGCGCTCCTCCTCCTCC 0.665 T ALK ALCL """Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome""" Hereditary Macrothrombocytopenia, MYH9-associated 18 661 --- --- --- --- TCF20 6942 broad.mit.edu 37 22 42610573 42610575 + In_Frame_Del DEL AGG AGG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chr22:42610573_42610575delAGG ENST00000359486.3 - 1 873_875 c.737_739delCCT c.(736-741)ttc>t p.SF246del TCF20_ENST00000335626.4_In_Frame_Del_p.SF246del NM_005650.1 NP_005641.1 Q9UGU0 TCF20_HUMAN transcription factor 20 (AR1) 246 Ser-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|transcription coactivator activity|zinc ion binding breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5) 66 GGTGAAGGGAaggaggaggagga 0.507 9 331 --- --- --- --- CNKSR2 22866 broad.mit.edu 37 X 21627678 21627680 + In_Frame_Del DEL GAG GAG - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:21627678_21627680delGAG ENST00000425654.2 + 19 3025_3027 c.2545_2547delGAG c.(2545-2547)del p.E856del CNKSR2_ENST00000279451.4_In_Frame_Del_p.E886del|CNKSR2_ENST00000379510.3_In_Frame_Del_p.E886del|CNKSR2_ENST00000543067.1_In_Frame_Del_p.E837del NM_001168647.1 NP_001162118.1 Q8WXI2 CNKR2_HUMAN connector enhancer of kinase suppressor of Ras 2 886 regulation of signal transduction cytoplasm|membrane protein binding breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3) 61 ggtggaggaagaggaggaggagg 0.517 12 258 --- --- --- --- PRRG1 5638 broad.mit.edu 37 X 37312611 37312611 + Frame_Shift_Del DEL C C - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:37312611delC ENST00000542554.1 + 5 666 c.394delC c.(394-396)ccfs p.P135fs PRRG1_ENST00000449135.2_Frame_Shift_Del_p.P135fs|PRRG1_ENST00000378628.4_Frame_Shift_Del_p.P135fs|TM4SF2_ENST00000465127.1_Intron|PRRG1_ENST00000543642.1_Frame_Shift_Del_p.P135fs|PRRG1_ENST00000491253.1_3'UTR NM_001173489.1 NP_001166960.1 O14668 TMG1_HUMAN proline rich Gla (G-carboxyglutamic acid) 1 135 Poly-Pro. extracellular region|integral to plasma membrane calcium ion binding p.P135fs*3(1)|p.P134fs*19(1) breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1) 15 TATCACCCCACCCCCCCCACC 0.488 8 733 --- --- --- --- DGKK 139189 broad.mit.edu 37 X 50165595 50165596 + RNA INS - - AC rs59226442 TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:50165595_50165596insAC ENST00000376025.2 - 0 816 Q5KSL6 DGKK_HUMAN diacylglycerol kinase, kappa activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress cytoplasm|plasma membrane ATP binding|diacylglycerol kinase activity|metal ion binding central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 Ovarian(276;0.236) TTAAAAGGTAAacacacacaca 0.411 8 70 --- --- --- --- MED12 9968 broad.mit.edu 37 X 70360680 70360682 + In_Frame_Del DEL GCA GCA - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:70360680_70360682delGCA ENST00000333646.6 + 42 6448_6450 c.6249_6251delGCA c.(6247-6252)cgg>cg p.RQ2083del MED12_ENST00000374080.3_In_Frame_Del_p.RQ2080del|MED12_ENST00000374102.1_In_Frame_Del_p.RQ2079del NM_005120.2 NP_005111.2 Q93074 MED12_HUMAN mediator complex subunit 12 2080 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 breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3) 420 Renal(35;0.156) accacatccggcagcagcagcag 0.586 """M, S""" uterine leiomyoma Opitz-Kaveggia Syndrome 12 310 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76907782 76907784 + In_Frame_Del DEL TCC TCC - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:76907782_76907784delTCC ENST00000373344.5 - 15 4591_4593 c.4377_4379delGGA c.(4375-4380)gaa>ga p.EE1463del ATRX_ENST00000395603.3_In_Frame_Del_p.EE1425del|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 1463 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 p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) ctcctcctcttcctcctcctcct 0.389 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 8 644 --- --- --- --- MAP7D3 79649 broad.mit.edu 37 X 135314194 135314194 + Frame_Shift_Del DEL G G - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:135314194delG ENST00000316077.9 - 8 1142 c.922delC c.(922-924)agfs p.Q308fs MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.Q290fs|MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.Q273fs NM_024597.3 NP_078873.2 Q8IWC1 MA7D3_HUMAN MAP7 domain containing 3 308 cytoplasm|spindle central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1) 44 Acute lymphoblastic leukemia(192;0.000127) ACATTCACCTGGGGGGGTGCA 0.532 9 1470 --- --- --- --- CXorf66 347487 broad.mit.edu 37 X 139038886 139038886 + Frame_Shift_Del DEL T T - TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:139038886delT ENST00000370540.1 - 3 278 c.255delA c.(253-255)aafs p.K85fs NM_001013403.2 NP_001013421.1 Q5JRM2 CX066_HUMAN chromosome X open reading frame 66 85 integral to membrane breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1) 26 CTGCTATGCCTTTTTTCTTGA 0.388 8 844 --- --- --- --- CD99L2 83692 broad.mit.edu 37 X 149937526 149937528 + In_Frame_Del DEL GGC GGC - rs7877654 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:149937526_149937528delGGC ENST00000370377.3 - 11 885_887 c.768_770delGCC c.(766-771)ccc>cc p.PP256del CD99L2_ENST00000466436.1_In_Frame_Del_p.PP207del|CD99L2_ENST00000355149.3_In_Frame_Del_p.PP184del|CD99L2_ENST00000437787.2_In_Frame_Del_p.PP183del|CD99L2_ENST00000346693.4_5'UTR NM_001242614.1|NM_031462.3 NP_001229543.1|NP_113650.2 Q8TCZ2 C99L2_HUMAN CD99 molecule-like 2 256 Poly-Pro. cell adhesion cell junction|integral to membrane endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1) 23 Acute lymphoblastic leukemia(192;6.56e-05) GGCTGGTTCGGGCGGCGGCGGCG 0.611 8 1125 --- --- --- --- ATP2B3 492 broad.mit.edu 37 X 152845611 152845611 + Frame_Shift_Del DEL C C - rs149428057 byFrequency TCGA-IB-7644-01A-11D-2154-08 TCGA-IB-7644-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx c574c0a2-c4ac-4f49-a776-2dc79e6de2d4 7596f60b-cd8b-4848-84ca-bab2c65c74d5 g.chrX:152845611delC ENST00000263519.4 + 20 3644 c.3518delC c.(3517-3519)gcfs p.A1173fs ATP2B3_ENST00000349466.2_Frame_Shift_Del_p.A1173fs|ATP2B3_ENST00000359149.3_3'UTR|ATP2B3_ENST00000370181.2_3'UTR|ATP2B3_ENST00000370186.1_3'UTR NM_001001344.2 NP_001001344.1 Q16720 AT2B3_HUMAN ATPase, Ca++ transporting, plasma membrane 3 1173 ATP biosynthetic process|platelet activation integral to membrane|plasma membrane ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3) 50 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CGCCTCCGGGCCCCCCCGCCC 0.587 8 1337 --- --- --- ---