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 LPPR5 163404 broad.mit.edu 37 1 99380467 99380467 + Missense_Mutation SNP C C T TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr1:99380467C>T ENST00000370188.3 - 5 1168 c.808G>A c.(808-810)Gtg>Atg p.V270M LPPR5_ENST00000263177.4_Missense_Mutation_p.V270M NM_001010861.2 NP_001010861.1 Q32ZL2 LPPR5_HUMAN 270 integral to membrane hydrolase activity TTATTCACCACGCACACAACC 0.393 4 99 --- --- --- --- USH2A 7399 broad.mit.edu 37 1 216246603 216246603 + Missense_Mutation SNP C C T rs140895792 byFrequency TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr1:216246603C>T ENST00000366943.2 - 28 5998 c.5612G>A c.(5611-5613)gGt>gAt p.G1871D USH2A_ENST00000307340.3_Missense_Mutation_p.G1871D|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 1871 Fibronectin type-III 5.|Laminin G-like 2. maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound basement membrane|cytoplasm|integral to membrane|stereocilium membrane collagen binding NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3) 527 OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875) AACGACAGCACCCCGTGTAAA 0.443 HNSCC(13;0.011) 10 6 --- --- --- --- ALMS1 7840 broad.mit.edu 37 2 73717897 73717897 + Nonsense_Mutation SNP T T G TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr2:73717897T>G ENST00000264448.6 + 10 8919 c.8808T>G c.(8806-8808)taT>taG p.Y2936* ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Y2894* NM_015120.4 NP_055935 Q8TCU4 ALMS1_HUMAN Alstrom syndrome 1 2936 G2/M transition of mitotic cell cycle centrosome|cilium|cytosol|microtubule basal body|spindle pole breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2) 147 AAGCCCCATATGTAGATCATC 0.428 5 136 --- --- --- --- IGKV1-6 28943 broad.mit.edu 37 2 89265896 89265896 + RNA SNP C C T TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr2:89265896C>T ENST00000464162.1 - 0 264 TGATGGGACCCCACTTTGTAA 0.488 37 120 --- --- --- --- POTEE 445582 broad.mit.edu 37 2 131976101 131976101 + Silent SNP C C T TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr2:131976101C>T ENST00000356920.5 + 1 220 c.126C>T c.(124-126)aaC>aaT p.N42N POTEE_ENST00000358087.5_Silent_p.N42N|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron NM_001083538.1 NP_001077007.1 Q6S8J3 POTEE_HUMAN POTE ankyrin domain family, member E 42 ATP binding GCAAGAGCAACGTGGGCACTT 0.592 4 160 --- --- --- --- ITGA2 3673 broad.mit.edu 37 5 52344214 52344214 + Missense_Mutation SNP C C A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr5:52344214C>A ENST00000296585.5 + 5 552 c.409C>A c.(409-411)Cag>Aag p.Q137K NM_002203.3 NP_002194.2 P17301 ITA2_HUMAN integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 137 axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis integrin complex collagen binding|identical protein binding|receptor activity breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 47 Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181) TCTGTGGGCACAGCAATGTGG 0.438 13 6 --- --- --- --- NRG2 9542 broad.mit.edu 37 5 139232068 139232068 + Missense_Mutation SNP G G C TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr5:139232068G>C ENST00000541337.1 - 6 1524 c.1295C>G c.(1294-1296)tCc>tGc p.S432C NRG2_ENST00000289409.4_Missense_Mutation_p.S492C|CTB-35F21.4_ENST00000504413.1_RNA|NRG2_ENST00000340391.3_Missense_Mutation_p.S295C|NRG2_ENST00000289422.7_Missense_Mutation_p.S506C|NRG2_ENST00000545385.1_Missense_Mutation_p.S500C|NRG2_ENST00000361474.1_Missense_Mutation_p.S498C|NRG2_ENST00000358522.3_Missense_Mutation_p.S500C|NRG2_ENST00000394770.1_3'UTR NM_001184935.1 NP_001171864.1 O14511 NRG2_HUMAN neuregulin 2 498 embryo development extracellular region|integral to membrane|plasma membrane growth factor activity breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1) 25 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AGGAGAACAGGAGTGGCTCCC 0.537 11 26 --- --- --- --- PCDHGA8 9708 broad.mit.edu 37 5 140772818 140772818 + Silent SNP G G A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr5:140772818G>A ENST00000398604.2 + 1 438 c.438G>A c.(436-438)gcG>gcA p.A146A PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron NM_032088.1 NP_114477.1 endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1) 51 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ACGAAATCGCGGTTCCTGGAG 0.453 26 39 --- --- --- --- C6orf89 221477 broad.mit.edu 37 6 36891198 36891198 + Missense_Mutation SNP C C A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr6:36891198C>A ENST00000480824.2 + 9 1319 c.1025C>A c.(1024-1026)aCc>aAc p.T342N C6orf89_ENST00000510325.2_Missense_Mutation_p.T236N|C6orf89_ENST00000359359.2_Missense_Mutation_p.T236N|C6orf89_ENST00000355190.3_Missense_Mutation_p.T349N|C6orf89_ENST00000373685.1_Missense_Mutation_p.T342N Q6UWU4 CF089_HUMAN chromosome 6 open reading frame 89 342 integral to membrane breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2) 15 TGCGATGGAACCGCTTTCTCA 0.473 12 40 --- --- --- --- HGF 3082 broad.mit.edu 37 7 81359092 81359092 + Missense_Mutation SNP T T C TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr7:81359092T>C ENST00000222390.5 - 8 1095 c.869A>G c.(868-870)gAc>gGc p.D290G HGF_ENST00000457544.2_Missense_Mutation_p.D285G NM_000601.4 NP_000592.3 P14210 HGF_HUMAN hepatocyte growth factor (hepapoietin A; scatter factor) 290 epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling platelet alpha granule lumen growth factor activity|serine-type endopeptidase activity NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1) 75 CATAGTATTGTCAGCTATTGG 0.358 21 42 --- --- --- --- LAMB1 3912 broad.mit.edu 37 7 107626753 107626753 + Missense_Mutation SNP C C A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr7:107626753C>A ENST00000393561.1 - 4 735 c.551G>T c.(550-552)tGg>tTg p.W184L LAMB1_ENST00000393560.1_Missense_Mutation_p.W160L|LAMB1_ENST00000222399.6_Missense_Mutation_p.W160L P07942 LAMB1_HUMAN laminin, beta 1 160 Laminin N-terminal. axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm extracellular matrix structural constituent NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3) 82 Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) ATACACACCCCAGGTTTTCCC 0.438 15 40 --- --- --- --- GOT1L1 137362 broad.mit.edu 37 8 37794525 37794525 + Missense_Mutation SNP C C A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr8:37794525C>A ENST00000307599.4 - 5 669 c.570G>T c.(568-570)aaG>aaT p.K190N NM_152413.2 NP_689626.2 Q8NHS2 AATC2_HUMAN glutamic-oxaloacetic transaminase 1-like 1 190 biosynthetic process|cellular amino acid metabolic process cytoplasm pyridoxal phosphate binding|transaminase activity central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1) 14 Colorectal(12;0.00627) Lung NSC(58;0.118)|all_lung(54;0.195) LUSC - Lung squamous cell carcinoma(8;1.37e-11) TTGGTGTCAACTTGCAGTCGA 0.537 14 29 --- --- --- --- LRP12 29967 broad.mit.edu 37 8 105509398 105509398 + Missense_Mutation SNP T T C TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr8:105509398T>C ENST00000276654.5 - 5 1490 c.1382A>G c.(1381-1383)aAt>aGt p.N461S LRP12_ENST00000424843.2_Missense_Mutation_p.N442S NM_013437.4 NP_038465.1 Q9Y561 LRP12_HUMAN low density lipoprotein receptor-related protein 12 461 LDL-receptor class A 5. endocytosis|regulation of growth coated pit|integral to plasma membrane low-density lipoprotein receptor activity|protein binding NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 48 OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229) CACACAACGATTGTTTTTACA 0.423 13 44 --- --- --- --- A1CF 29974 broad.mit.edu 37 10 52573721 52573721 + Missense_Mutation SNP C C G TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr10:52573721C>G ENST00000374001.2 - 9 1358 c.1219G>C c.(1219-1221)Gga>Cga p.G407R A1CF_ENST00000373995.3_Missense_Mutation_p.G415R|A1CF_ENST00000493415.1_5'UTR|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000395495.1_Missense_Mutation_p.G360R|A1CF_ENST00000373997.3_Missense_Mutation_p.G407R|A1CF_ENST00000395489.2_Missense_Mutation_p.G408R|A1CF_ENST00000282641.2_Missense_Mutation_p.G415R|A1CF_ENST00000373993.1_Missense_Mutation_p.G415R Q9NQ94 A1CF_HUMAN APOBEC1 complementation factor Required for nuclear localization. cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm nucleotide binding|protein binding|single-stranded RNA binding NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3) 29 CTTTTGTCTCCTTTGACCTGG 0.493 17 39 --- --- --- --- LRRTM3 347731 broad.mit.edu 37 10 68687766 68687766 + Missense_Mutation SNP T T G TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr10:68687766T>G ENST00000361320.4 + 2 1670 c.1092T>G c.(1090-1092)agT>agG p.S364R CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron NM_178011.3 NP_821079.3 Q86VH5 LRRT3_HUMAN leucine rich repeat transmembrane neuronal 3 364 integral to membrane breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3) 41 GTGGCAAAAGTACTACAGAGA 0.512 4 36 --- --- --- --- PNLIPRP1 5407 broad.mit.edu 37 10 118352048 118352048 + Missense_Mutation SNP T T A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr10:118352048T>A ENST00000528052.1 + 4 396 c.325T>A c.(325-327)Tgc>Agc p.C109S PNLIPRP1_ENST00000480870.2_3'UTR|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.C109S P54315 LIPR1_HUMAN pancreatic lipase-related protein 1 109 lipid metabolic process calcium ion binding|triglyceride lipase activity breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 38 all cancers(201;0.0161) GACAGACATGTGCAAGGTAGG 0.448 12 28 --- --- --- --- LRP4 4038 broad.mit.edu 37 11 46924428 46924428 + Silent SNP T T G TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr11:46924428T>G ENST00000378623.1 - 2 347 c.105A>C c.(103-105)gcA>gcC p.A35A NM_002334.3 NP_002325.2 O75096 LRP4_HUMAN low density lipoprotein receptor-related protein 4 35 LDL-receptor class A 1. endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway integral to membrane calcium ion binding|receptor activity breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1) 70 Lung(87;0.159) GAGCACTCACTGCACATGTGA 0.587 11 22 --- --- --- --- OR5L2 26338 broad.mit.edu 37 11 55594965 55594965 + Missense_Mutation SNP G G A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr11:55594965G>A ENST00000378397.1 + 1 271 c.271G>A c.(271-273)Gcc>Acc p.A91T NM_001004739.1 NP_001004739.1 Q8NGL0 OR5L2_HUMAN olfactory receptor, family 5, subfamily L, member 2 91 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.A91T(1) breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1) 59 all_epithelial(135;0.208) CAAGGACAAAGCCATCTCCTT 0.463 HNSCC(27;0.073) 5 132 --- --- --- --- TBX3 6926 broad.mit.edu 37 12 115118775 115118775 + Missense_Mutation SNP T T A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr12:115118775T>A ENST00000349155.2 - 2 1529 c.566A>T c.(565-567)gAc>gTc p.D189V TBX3_ENST00000257566.3_Missense_Mutation_p.D189V NM_005996.3 NP_005987.3 O15119 TBX3_HUMAN T-box 3 189 anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development nucleus sequence-specific DNA binding breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 Medulloblastoma(191;0.163)|all_neural(191;0.178) BRCA - Breast invasive adenocarcinoma(302;0.0574) AGCGGGGCTGTCCGGGTGAAT 0.468 5 58 --- --- --- --- THTPA 79178 broad.mit.edu 37 14 24026130 24026130 + Missense_Mutation SNP G G A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr14:24026130G>A ENST00000288014.6 + 1 900 c.164G>A c.(163-165)cGa>cAa p.R55Q RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000554789.1_Missense_Mutation_p.R55Q|THTPA_ENST00000556015.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000553985.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.R55Q|THTPA_ENST00000554970.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000556354.1_RNA Q9BU02 THTPA_HUMAN thiamine triphosphatase 55 dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process cytosol|nucleolus|soluble fraction thiamin-triphosphatase activity large_intestine(1)|prostate(2) 3 all_cancers(95;0.000251) GBM - Glioblastoma multiforme(265;0.00643) Thiamine(DB00152) CACTGGCTGCGACGACGAGAG 0.577 4 10 --- --- --- --- DDX24 57062 broad.mit.edu 37 14 94526642 94526642 + Missense_Mutation SNP G G C TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr14:94526642G>C ENST00000330836.5 - 5 1846 c.1715C>G c.(1714-1716)aCt>aGt p.T572S DDX24_ENST00000555054.1_Missense_Mutation_p.T529S|DDX24_ENST00000544005.1_Missense_Mutation_p.T322S NM_020414.3 NP_065147.1 Q9GZR7 DDX24_HUMAN DEAD (Asp-Glu-Ala-Asp) box helicase 24 572 RNA metabolic process cytoplasm|nucleolus ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1) 23 all_cancers(154;0.12) Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207) TTTCTCATCAGTCTCACAATG 0.498 28 46 --- --- --- --- AHNAK2 113146 broad.mit.edu 37 14 105414154 105414154 + Missense_Mutation SNP C C T TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr14:105414154C>T ENST00000333244.5 - 7 7753 c.7634G>A c.(7633-7635)gGc>gAc p.G2545D AHNAK2_ENST00000557457.1_Intron NM_138420.2 NP_612429.2 Q8IVF2 AHNK2_HUMAN AHNAK nucleoprotein 2 2545 nucleus cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3) 33 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116) GTCCACTTGGCCAGCCTGGAC 0.642 4 157 --- --- --- --- TCF12 6938 broad.mit.edu 37 15 57484403 57484403 + Silent SNP A A G TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr15:57484403A>G ENST00000267811.5 + 7 742 c.438A>G c.(436-438)ctA>ctG p.L146L TCF12_ENST00000452095.2_Silent_p.L142L|TCF12_ENST00000557843.1_Silent_p.L146L|TCF12_ENST00000333725.5_Silent_p.L146L|TCF12_ENST00000438423.2_Silent_p.L146L NM_003205.3|NM_207038.1 NP_003196.1|NP_996921.1 Q99081 HTF4_HUMAN transcription factor 12 146 immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity TCF12/NR4A3(2) breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1) 36 Colorectal(260;0.0907) all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239) CAGCACAGCTATCTTCTTCAG 0.468 T TEC extraskeletal myxoid chondrosarcoma 16 42 --- --- --- --- SPOP 8405 broad.mit.edu 37 17 47696644 47696644 + Missense_Mutation SNP A A C TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr17:47696644A>C ENST00000393331.3 - 6 774 c.304T>G c.(304-306)Ttc>Gtc p.F102V SPOP_ENST00000503676.1_Missense_Mutation_p.F102V|SPOP_ENST00000347630.2_Missense_Mutation_p.F102V|SPOP_ENST00000393328.2_Missense_Mutation_p.F102V|SPOP_ENST00000504102.1_Missense_Mutation_p.F102V NM_001007226.1|NM_001007227.1 NP_001007227.1|NP_001007228.1 O43791 SPOP_HUMAN speckle-type POZ protein 102 MATH.|Required for nuclear localization. mRNA processing nucleus protein binding endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33) 63 GAGAATTTGAATTTTGCCCGA 0.408 Prostate(2;0.17) 23 62 --- --- --- --- GYS1 2997 broad.mit.edu 37 19 49490530 49490530 + Missense_Mutation SNP T T C TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr19:49490530T>C ENST00000323798.3 - 3 609 c.413A>G c.(412-414)aAc>aGc p.N138S GYS1_ENST00000263276.6_Intron|GYS1_ENST00000541188.1_Missense_Mutation_p.N58S|GYS1_ENST00000544287.1_Intron|GYS1_ENST00000540532.1_Missense_Mutation_p.N58S|GYS1_ENST00000457974.1_5'UTR NM_002103.4 NP_002094.2 P13807 GYS1_HUMAN glycogen synthase 1 (muscle) 138 glucose metabolic process|glycogen biosynthetic process cytosol glycogen (starch) synthase activity|protein binding breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 22 all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286) CACTCCGATGTTGCAGGTATC 0.637 3 5 --- --- --- --- NCOA3 8202 broad.mit.edu 37 20 46267838 46267838 + Missense_Mutation SNP A A G TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr20:46267838A>G ENST00000372004.3 + 14 2815 c.2599A>G c.(2599-2601)Agt>Ggt p.S867G NCOA3_ENST00000371998.3_Missense_Mutation_p.S867G|NCOA3_ENST00000371997.3_Missense_Mutation_p.S877G|NCOA3_ENST00000341724.6_Intron NM_001174087.1|NM_001174088.1|NM_006534.3|NM_181659.2 NP_001167558.1|NP_001167559.1|NP_006525.2|NP_858045.1 Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 867 androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nucleoplasm androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 52 TGTTGGCTCAAGTCCTCCAGT 0.438 25 56 --- --- --- --- THOC5 8563 broad.mit.edu 37 22 29904508 29904508 + Splice_Site SNP C C A TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr22:29904508C>A ENST00000490103.1 - 20 2112 c.1990G>T c.(1990-1992)Ggt>Tgt p.G664C THOC5_ENST00000397873.2_Splice_Site_p.G664C|THOC5_ENST00000397871.1_Splice_Site_p.G664C|THOC5_ENST00000397872.1_Splice_Site_p.G664C NM_003678.4 NP_003669.4 Q13769 THOC5_HUMAN THO complex 5 664 intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex protein binding|RNA binding NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 21 CTGCTAGGACCCCTAGAGAAA 0.458 3 14 --- --- --- --- ATM 472 broad.mit.edu 37 11 108180935 108180935 + Frame_Shift_Del DEL T T - TCGA-YL-A8SH-01B-11D-A377-08 TCGA-YL-A8SH-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 340cfd1e-1582-4ee4-99b3-49e6249c4fa2 521257bd-e4e2-4c76-8154-e87abb022203 g.chr11:108180935delT ENST00000278616.4 + 39 6196 c.5811delT c.(5809-5811)aatfs p.N1937fs ATM_ENST00000452508.2_Frame_Shift_Del_p.N1937fs|C11orf65_ENST00000525729.1_Intron NM_000051.3 NP_000042 Q13315 ATM_HUMAN ataxia telangiectasia mutated 1937 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3) 448 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) TGGATTTAAATTATCTAGAAG 0.328 """D, Mis, N, F, S""" T-PLL """leukemia, lymphoma, medulloblastoma, glioma""" Genes defective in diseases associated with sensitivity to DNA damaging agents Ataxia Telangiectasia TSP Lung(14;0.12) 12 34 --- --- --- ---