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 KCNU1 157855 broad.mit.edu 37 8 36721928 36721928 + Nonsense_Mutation SNP C C A TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr8:36721928C>A ENST00000399881.3 + 19 1935 c.1898C>A c.(1897-1899)tCg>tAg p.S633* NM_001031836.2 NP_001027006.2 A8MYU2 KCNU1_HUMAN potassium channel, subfamily U, member 1 633 voltage-gated potassium channel complex binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1) 57 KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634) GCAGTGCCATCGGTAAAGAGA 0.448000 4 68 0.00909568 0.00947467 1 1 0 IGLV5-45 0 broad.mit.edu 37 22 22730646 22730646 + RNA SNP C C G TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr22:22730646C>G ENST00000390296.2 + 0 169 GCAGTGGCATCAATGTTGGTA 0.552000 4 102 0 0 1 0 0 PAPOLA 10914 broad.mit.edu 37 14 97031339 97031339 + Missense_Mutation SNP T T G TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr14:97031339T>G ENST00000216277.8 + 22 2410 c.2190T>G c.(2188-2190)aaT>aaG p.N730K PAPOLA_ENST00000392990.2_Missense_Mutation_p.N709K NM_032632.4 NP_116021.2 P51003 PAPOA_HUMAN poly(A) polymerase alpha 730 Required for interaction with NUDT21. mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription cytoplasm|nucleoplasm ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1) 21 all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155) COAD - Colon adenocarcinoma(157;0.213) TCCCTGCAAATCCTATTCCTG 0.373000 28 60 0 0 1 0 0 HBZ 3050 broad.mit.edu 37 16 202926 202926 + Silent SNP T T C TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr16:202926T>C ENST00000252951.2 + 1 241 c.18T>C c.(16-18)acT>acC p.T6T NM_005332.2 NP_005323.1 P02008 HBAZ_HUMAN hemoglobin, zeta 6 hemoglobin complex heme binding|oxygen binding|oxygen transporter activity all_cancers(16;4.28e-07)|all_epithelial(16;2.09e-06)|Hepatocellular(16;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239) TGACCAAGACTGAGAGGACCA 0.612000 OREG0003684 type=REGULATORY REGION|Gene=HBZ|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay 20 39 0 0 1 0 0 SENP3 26168 broad.mit.edu 37 17 7474041 7474041 + Nonsense_Mutation SNP C C T TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr17:7474041C>T ENST00000321337.7 + 10 1839 c.1519C>T c.(1519-1521)Cga>Tga p.R507* SENP3_ENST00000429205.2_Nonsense_Mutation_p.R508*|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR NM_015670.5 NP_056485.2 Q9H4L4 SENP3_HUMAN SUMO1/sentrin/SMT3 specific peptidase 3 508 Protease. proteolysis MLL1 complex|nucleolus cysteine-type peptidase activity central_nervous_system(1)|ovary(1) 2 Prostate(122;0.157) AAAGAAAGACCGACTGGATTT 0.473000 6 17 0 0 1 0 0 ASTE1 28990 broad.mit.edu 37 3 130732931 130732931 + Silent SNP C C T TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr3:130732931C>T ENST00000264992.3 - 6 2451 c.2010G>A c.(2008-2010)gaG>gaA p.E670E ATP2C1_ENST00000422190.2_Intron|ATP2C1_ENST00000504381.1_Intron|ATP2C1_ENST00000533801.2_Intron|ATP2C1_ENST00000513801.1_Intron|ATP2C1_ENST00000393221.4_Intron|ATP2C1_ENST00000359644.3_Intron|ATP2C1_ENST00000328560.8_Intron|ATP2C1_ENST00000507488.2_Intron|ASTE1_ENST00000514044.1_Silent_p.E695E NM_014065.2 NP_054784.2 Q2TB18 ASTE1_HUMAN asteroid homolog 1 (Drosophila) 670 DNA repair nuclease activity endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1) 22 CACTATGTTCCTCTAAGTTTT 0.393000 12 57 0 0 1 0 0 GPR124 25960 broad.mit.edu 37 8 37698691 37698691 + Silent SNP C C T TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr8:37698691C>T ENST00000315215.7 + 16 2547 c.2184C>T c.(2182-2184)tgC>tgT p.C728C GPR124_ENST00000412232.2_Silent_p.C945C Q96PE1 GP124_HUMAN G protein-coupled receptor 124 945 GPS. central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis integral to membrane|plasma membrane G-protein coupled receptor activity central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 37 BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) ATTTCCTGTGCGCCGGGCTAC 0.627000 10 84 0 0 1 0 0 BCOR 54880 broad.mit.edu 37 X 39931690 39931690 + Missense_Mutation SNP G G A TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chrX:39931690G>A ENST00000342274.4 - 4 3271 c.2909C>T c.(2908-2910)gCg>gTg p.A970V BCOR_ENST00000378444.4_Missense_Mutation_p.A970V|BCOR_ENST00000397354.3_Missense_Mutation_p.A970V|BCOR_ENST00000378455.4_Missense_Mutation_p.A970V NM_001123383.1 NP_001116855.1 Q6W2J9 BCOR_HUMAN BCL6 corepressor 970 heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent nucleus heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 126 CACGTAACCCGCTGAGTTGGC 0.527000 """F, N, S, T""" RARA """retinoblastoma, AML, APL(translocation)""" oculo-facio-cardio-dental genetic 4 24 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 132 R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1) NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1) 4887 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ATAAGCATGACGACCTATGAT 0.393000 Mis gliobastoma 25 60 0 0 1 0 0 STAG2 10735 broad.mit.edu 37 X 123196967 123196967 + Splice_Site SNP A A T TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chrX:123196967A>T ENST00000371160.1 + 19 2023 c.1731_splice c.e19-1 p.Y578_splice STAG2_ENST00000371145.3_Splice_Site_p.Y578_splice|STAG2_ENST00000371144.3_Splice_Site_p.Y578_splice|STAG2_ENST00000218089.9_Splice_Site_p.Y578_splice|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371157.3_Splice_Site_p.Y578_splice|STAG2_ENST00000354548.5_Splice_Site_p.Y509_splice Q8N3U4 STAG2_HUMAN stromal antigen 2 578 cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion chromatin|chromosome, centromeric region|nucleoplasm protein binding breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4) 78 ATTTCACAGTACTCTGTAGAT 0.313000 8 19 0 0 1 0 0 FAM47C 442444 broad.mit.edu 37 X 37028425 37028425 + Missense_Mutation SNP A A G rs145580328 byFrequency TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chrX:37028425A>G ENST00000358047.3 + 1 1994 c.1942A>G c.(1942-1944)Aat>Gat p.N648D NM_001013736.2 NP_001013758.1 Q5HY64 FA47C_HUMAN family with sequence similarity 47, member C 648 p.N648D(7) breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1) 120 GGAGCCTCCCAATACTGGAGT 0.642000 6 98 0 0 1 0 0 LAMC1 3915 broad.mit.edu 37 1 183087214 183087214 + Silent SNP T T C TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr1:183087214T>C ENST00000258341.4 + 11 2180 c.1923T>C c.(1921-1923)ccT>ccC p.P641P NM_002293.3 NP_002284.3 P11047 LAMC1_HUMAN laminin, gamma 1 (formerly LAMB2) 641 Laminin IV type A. axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex extracellular matrix structural constituent p.P641P(1) NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3) 76 Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) CTCTTACCCCTTTTGAATTTC 0.418000 3 53 0 0 1 0 0 TP53 7157 broad.mit.edu 37 17 7578507 7578507 + Missense_Mutation SNP G G C TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr17:7578507G>C ENST00000420246.2 - 5 555 c.423C>G c.(421-423)tgC>tgG p.C141W TP53_ENST00000359597.4_Missense_Mutation_p.C141W|TP53_ENST00000413465.2_Missense_Mutation_p.C141W|TP53_ENST00000445888.2_Missense_Mutation_p.C141W|TP53_ENST00000269305.4_Missense_Mutation_p.C141W|TP53_ENST00000455263.2_Missense_Mutation_p.C141W NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 141 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. C -> A (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|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.C141W(13)|p.C141*(11)|p.0?(8)|p.A138_P142delAKTCP(4)|p.C141C(4)|p.N131fs*27(2)|p.P142fs*7(1)|p.L137_W146del10(1)|p.C141A(1)|p.C9W(1)|p.A6_P10delAKTCP(1)|p.K139fs*4(1)|p.A45_P49delAKTCP(1)|p.T140fs*28(1)|p.A138_V143delAKTCPV(1)|p.C141fs*5(1)|p.P142del(1)|p.C48W(1)|p.C141_P142insXX(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) GCTGCACAGGGCAGGTCTTGG 0.577000 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) 24 26 0 0 1 0 0 LPHN3 23284 broad.mit.edu 37 4 62813869 62813869 + Missense_Mutation SNP C C T TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr4:62813869C>T ENST00000512091.1 + 16 3223 c.2476C>T c.(2476-2478)Cgt>Tgt p.R826C LPHN3_ENST00000514591.1_Missense_Mutation_p.R826C|LPHN3_ENST00000514157.1_Missense_Mutation_p.R826C|LPHN3_ENST00000507625.1_Missense_Mutation_p.R894C|LPHN3_ENST00000507164.1_Missense_Mutation_p.R894C|LPHN3_ENST00000504896.1_Missense_Mutation_p.R826C|LPHN3_ENST00000508693.1_Missense_Mutation_p.R894C|LPHN3_ENST00000514996.1_Missense_Mutation_p.R826C|LPHN3_ENST00000508946.1_Missense_Mutation_p.R826C|LPHN3_ENST00000506746.1_Missense_Mutation_p.R894C|LPHN3_ENST00000511324.1_Missense_Mutation_p.R894C|LPHN3_ENST00000506700.1_Missense_Mutation_p.R826C|LPHN3_ENST00000545650.1_Missense_Mutation_p.R826C|LPHN3_ENST00000509896.1_Missense_Mutation_p.R894C|LPHN3_ENST00000506720.1_Missense_Mutation_p.R894C Q9HAR2 LPHN3_HUMAN latrophilin 3 813 GPS. neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity|sugar binding breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1) 125 CTACTCCAAGCGTACAATGAC 0.388000 5 20 0 0 1 0 0 ABCG5 64240 broad.mit.edu 37 2 44047075 44047075 + Missense_Mutation SNP A A G TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr2:44047075A>G ENST00000543989.1 - 7 2148 c.443T>C c.(442-444)cTt>cCt p.L148P ABCG5_ENST00000405322.1_Missense_Mutation_p.L372P|ABCG5_ENST00000260645.1_Missense_Mutation_p.L543P Q9H222 ABCG5_HUMAN ATP-binding cassette, sub-family G (WHITE), member 5 543 ABC transporter. cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption apical plasma membrane|integral to membrane ATP binding|ATPase activity|protein heterodimerization activity breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 33 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) AGATCCAACAAGCACCCCCGC 0.368000 18 89 0 0 1 0 0 TRIP12 9320 broad.mit.edu 37 2 230668911 230668911 + Nonsense_Mutation SNP G G A TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr2:230668911G>A ENST00000283943.5 - 18 2636 c.2458C>T c.(2458-2460)Cga>Tga p.R820* TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389044.4_Nonsense_Mutation_p.R868*|TRIP12_ENST00000389045.3_Nonsense_Mutation_p.R550* NM_004238.1 NP_004229.1 Q14669 TRIPC_HUMAN thyroid hormone receptor interactor 12 820 WWE. protein ubiquitination involved in ubiquitin-dependent protein catabolic process proteasome complex thyroid hormone receptor binding|ubiquitin-protein ligase activity breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 87 Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164) Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116) AGCTGTGCTCGAGCATCATCC 0.363000 28 51 0 0 1 0 0 ATRX 546 broad.mit.edu 37 X 76890083 76890083 + Splice_Site SNP A A C TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chrX:76890083A>C ENST00000373344.5 - 17 5024 c.e17+1 ATRX_ENST00000480283.1_Splice_Site|ATRX_ENST00000395603.3_Splice_Site NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 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) TTCAGCTCTTACCTGTAAAGT 0.398000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 31 65 0 0 1 0 0 F5 2153 broad.mit.edu 37 1 169519050 169519050 + Nonsense_Mutation SNP G G A TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr1:169519050G>A ENST00000367796.3 - 10 1801 c.1600C>T c.(1600-1602)Caa>Taa p.Q534* F5_ENST00000367797.3_Nonsense_Mutation_p.Q534*|F5_ENST00000546081.1_3'UTR P12259 FA5_HUMAN coagulation factor V (proaccelerin, labile factor) 534 F5/8 type A 2. Cleavage; by activated protein C. R -> Q (in Leiden; associated with THR- APCR; associated with susceptibility to Budd-Chiari syndrome; associated with susceptibility to ischemic stroke; dbSNP:rs6025). cell adhesion|platelet activation|platelet degranulation plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1) 128 all_hematologic(923;0.208) Drotrecogin alfa(DB00055) TGTATTCCTTGCCTGTCCAGG 0.428000 4 35 0 0 1 0 0 TP53 7157 broad.mit.edu 37 17 7577593 7577593 + Missense_Mutation SNP T T G TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr17:7577593T>G ENST00000420246.2 - 7 820 c.688A>C c.(688-690)Acc>Ccc p.T230P TP53_ENST00000359597.4_Missense_Mutation_p.T230P|TP53_ENST00000413465.2_Missense_Mutation_p.T230P|TP53_ENST00000445888.2_Missense_Mutation_p.T230P|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000269305.4_Missense_Mutation_p.T230P|TP53_ENST00000455263.2_Missense_Mutation_p.T230P NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 230 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation).|T -> N (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|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.0?(8)|p.?(5)|p.T230P(2)|p.T230fs*6(2)|p.T230S(2)|p.C229_H233delCTTIH(2)|p.T230fs*17(2)|p.T230fs*9(1)|p.T230_Y234delTTIHY(1)|p.C229_T230insX(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)|p.T230A(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) TGGATGGTGGTACAGTCAGAG 0.532000 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) 17 47 0 0 1 0 0 KRT27 342574 broad.mit.edu 37 17 38936093 38936093 + Silent SNP G G A TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr17:38936093G>A ENST00000301656.3 - 4 745 c.705C>T c.(703-705)tgC>tgT p.C235C NM_181537.3 NP_853515.2 Q7Z3Y8 K1C27_HUMAN keratin 27 235 Linker 12.|Rod. cytoplasm|intermediate filament structural molecule activity NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1) 21 Breast(137;0.000812) CTCCAGCCGCGCACTGAAGAG 0.483000 10 35 0 0 1 0 0 CPS1 1373 broad.mit.edu 37 2 211454894 211454894 + Frame_Shift_Del DEL T T - TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr2:211454894delT ENST00000233072.5 + 8 972 c.776delT c.(775-777)atfs p.I259fs CPS1_ENST00000430249.2_Frame_Shift_Del_p.I265fs NM_001875.4 NP_001866.2 P31327 CPSM_HUMAN carbamoyl-phosphate synthase 1, mitochondrial 259 Glutamine amidotransferase type-1. carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle mitochondrial nucleoid ATP binding|carbamoyl-phosphate synthase (ammonia) activity breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2) 142 Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843) TATGATGGGATTTTGATCGCG 0.448 15 361 --- --- --- --- MAP3K4 4216 broad.mit.edu 37 6 161413044 161413045 + In_Frame_Ins INS - - CCG TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr6:161413044_161413045insCCG ENST00000392142.4 + 1 229_230 c.81_82insCCG c.(79-84)cccgcc>ccCCGcgcc p.27_28PA>PRA MAP3K4_ENST00000366919.2_In_Frame_Ins_p.27_28PA>PRA|MAP3K4_ENST00000366920.2_In_Frame_Ins_p.27_28PA>PRA|MAP3K4_ENST00000348824.7_In_Frame_Ins_p.27_28PA>PRA NM_005922.2 NP_005913.2 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 27 Poly-Pro. activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity perinuclear region of cytoplasm ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1) 77 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) Agccgccgccaccgccgccgcc 0.738 3 3 --- --- --- --- AC007255.7 0 broad.mit.edu 37 7 29720482 29720483 + RNA INS - - G rs70980562 TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr7:29720482_29720483insG ENST00000426767.1 - 0 366 NR_024278.1 CTCTCAGATCAGTGATGCCCTG 0.485 3 6 --- --- --- --- SLC12A1 6557 broad.mit.edu 37 15 48580649 48580649 + Frame_Shift_Del DEL A A - TCGA-HT-7610-01A-21D-2086-08 TCGA-HT-7610-10A-01D-2086-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0a5d3919-f656-43ca-ab7a-e7df56b6cdbe 49080164-b5e3-47b2-a79a-784695523809 g.chr15:48580649delA ENST00000396577.3 + 23 3024 c.2809delA c.(2809-2811)aafs p.K937fs SLC12A1_ENST00000558405.1_Frame_Shift_Del_p.K937fs|SLC12A1_ENST00000380993.3_Frame_Shift_Del_p.K937fs NM_001184832.1 NP_001171761.1 Q13621 S12A1_HUMAN solute carrier family 12 (sodium/potassium/chloride transporter), member 1 937 potassium ion transport|sodium ion transport integral to membrane|membrane fraction sodium:potassium:chloride symporter activity NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1) 59 all_lung(180;0.00219) all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06) Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021) AAAAAAATGGAAAGACTGTAA 0.328 2 4 --- --- --- ---