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 MAP2 4133 broad.mit.edu 37 2 210560053 210560053 + Silent SNP T T C TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr2:210560053T>C ENST00000360351.4 + 7 3665 c.3159T>C c.(3157-3159)ttT>ttC p.F1053F MAP2_ENST00000447185.1_Silent_p.F1049F|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron NM_002374.3 NP_002365.3 P11137 MAP2_HUMAN microtubule-associated protein 2 1053 central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization cytoplasm|microtubule|microtubule associated complex beta-dystroglycan binding|calmodulin binding|structural molecule activity breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 124 Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202) UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18) Estramustine(DB01196) TTAGTGACTTTGGACAGATGG 0.468000 52 85 0 0 1 0 0 SERPINB11 89778 broad.mit.edu 37 18 61377583 61377583 + RNA SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr18:61377583G>A ENST00000544088.1 + 0 218 SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000382749.5_RNA|SERPINB11_ENST00000538847.1_RNA NM_080475.2 NP_536723.2 Q96P15 SPB11_HUMAN serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene) regulation of proteolysis cytoplasm serine-type endopeptidase inhibitor activity breast(1)|cervix(1)|kidney(1)|lung(3) 6 Esophageal squamous(42;0.129) AGACTGAAGAGCAATTGGAGA 0.438000 6 36 0 0 1 0 0 DCAF4L1 285429 broad.mit.edu 37 4 41984364 41984364 + Silent SNP C C A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr4:41984364C>A ENST00000333141.5 + 1 652 c.555C>A c.(553-555)gcC>gcA p.A185A NM_001029955.3 NP_001025126.2 Q3SXM0 DC4L1_HUMAN DDB1 and CUL4 associated factor 4-like 1 185 breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1) 37 TCCCAGAGGCCTGGTCCTGTG 0.587000 14 135 1.52009e-12 1.57639e-12 1 1 0 WDR78 79819 broad.mit.edu 37 1 67370972 67370972 + Missense_Mutation SNP T T C TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr1:67370972T>C ENST00000371026.3 - 2 312 c.257A>G c.(256-258)cAa>cGa p.Q86R WDR78_ENST00000431318.1_5'UTR|WDR78_ENST00000371022.3_Missense_Mutation_p.Q86R|WDR78_ENST00000371023.3_Missense_Mutation_p.Q86R|WDR78_ENST00000488333.1_Missense_Mutation_p.Q14R NM_024763.4 NP_079039.4 Q5VTH9 WDR78_HUMAN WD repeat domain 78 86 NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3) 32 CATTCTGCTTTGATTTGCACC 0.353000 6 111 0 0 1 0 0 TSSC2 0 broad.mit.edu 37 11 3427845 3427845 + RNA SNP C C T TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr11:3427845C>T ENST00000529482.1 + 0 962 CTTCAAGTGGCAGGAGCAGAA 0.587000 4 48 0 0 1 0 0 ATRX 546 broad.mit.edu 37 X 76939496 76939496 + Nonsense_Mutation SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chrX:76939496G>A ENST00000373344.5 - 9 1466 c.1252C>T c.(1252-1254)Cga>Tga p.R418* ATRX_ENST00000395603.3_Nonsense_Mutation_p.R380*|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 418 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) TCCATCGCTCGAAACTCGGAA 0.373000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 47 136 0 0 1 0 0 UBR2 23304 broad.mit.edu 37 6 42631096 42631096 + Missense_Mutation SNP T T C TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr6:42631096T>C ENST00000372899.1 + 32 3895 c.3637T>C c.(3637-3639)Tgt>Cgt p.C1213R UBR2_ENST00000372901.1_Missense_Mutation_p.C1213R|UBR2_ENST00000372883.3_3'UTR NM_015255.2 NP_056070.1 Q8IWV8 UBR2_HUMAN ubiquitin protein ligase E3 component n-recognin 2 1213 cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade nucleus|plasma membrane leucine binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5) 64 Colorectal(47;0.196) Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196) TTGCCCCCTTTGTGAATGCTT 0.378000 22 65 0 0 1 0 0 PCLO 27445 broad.mit.edu 37 7 82584494 82584494 + Silent SNP T T C TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr7:82584494T>C ENST00000423517.2 - 5 6112 c.5775A>G c.(5773-5775)acA>acG p.T1925T PCLO_ENST00000333891.8_Silent_p.T1925T NM_014510.2 NP_055325.2 Q9Y6V0 PCLO_HUMAN piccolo presynaptic cytomatrix protein 1856 cytoskeleton organization|synaptic vesicle exocytosis cell junction|cytoskeleton|synaptic vesicle calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2) 259 TGTATTTGTGTGTTTTATGCA 0.358000 18 23 0 0 1 0 0 IL27 246778 broad.mit.edu 37 16 28513350 28513350 + Missense_Mutation SNP G G C TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr16:28513350G>C ENST00000356897.1 - 4 431 c.409C>G c.(409-411)Ctg>Gtg p.L137V NM_145659.3 NP_663634.2 Q8NEV9 IL27A_HUMAN interleukin 27 137 inflammatory response|innate immune response|positive regulation of interferon-gamma biosynthetic process|regulation of defense response to virus|regulation of T cell proliferation|regulation of T-helper 1 cell differentiation extracellular space cytokine activity|interleukin-27 receptor binding endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1) 10 ATGGCCCACAGCTGCATCCTC 0.662000 6 64 0 0 1 0 0 CLIP4 79745 broad.mit.edu 37 2 29355042 29355042 + Missense_Mutation SNP A A G TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr2:29355042A>G ENST00000320081.5 + 4 553 c.298A>G c.(298-300)Aat>Gat p.N100D CLIP4_ENST00000401605.1_Missense_Mutation_p.N100D|CLIP4_ENST00000401617.2_5'UTR|CLIP4_ENST00000404424.1_Missense_Mutation_p.N100D NM_024692.4 NP_078968.3 Q8N3C7 CLIP4_HUMAN CAP-GLY domain containing linker protein family, member 4 100 endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1) 26 Acute lymphoblastic leukemia(172;0.155) TTGCAATGTGAATGATAGAGA 0.378000 8 105 0 0 1 0 0 CSPG4 1464 broad.mit.edu 37 15 75975277 75975277 + Missense_Mutation SNP C C T TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr15:75975277C>T ENST00000308508.5 - 6 4647 c.4555G>A c.(4555-4557)Ggg>Agg p.G1519R NM_001897.4 NP_001888.2 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 1519 Gly/Ser-rich (glycosaminoglycan attachment domain). angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4) 48 ACTACCCGCCCGTTGCTGGGC 0.697000 7 25 0 0 1 0 0 CPSF1 29894 broad.mit.edu 37 8 145619157 145619157 + Missense_Mutation SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr8:145619157G>A ENST00000349769.3 - 35 4050 c.3956C>T c.(3955-3957)gCc>gTc p.A1319V CPSF1_ENST00000531727.1_5'UTR NM_013291.2 NP_037423.2 Q10570 CPSF1_HUMAN cleavage and polyadenylation specific factor 1, 160kDa 1319 mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription mRNA cleavage and polyadenylation specificity factor complex mRNA 3'-UTR binding|protein binding NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 38 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055) CCCTTCAGTGGCCCCCCGGCA 0.632000 3 28 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 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 18 54 0 0 1 0 0 CLTCL1 8218 broad.mit.edu 37 22 19197859 19197859 + Missense_Mutation SNP C C A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr22:19197859C>A ENST00000263200.10 - 20 3298 c.3226G>T c.(3226-3228)Gat>Tat p.D1076Y CLTCL1_ENST00000353891.5_Missense_Mutation_p.D1076Y|CLTCL1_ENST00000427926.1_Missense_Mutation_p.D1076Y NM_007098.3 NP_009029.3 P53675 CLH2_HUMAN clathrin, heavy chain-like 1 1076 Heavy chain arm.|Proximal segment. anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 49 Colorectal(54;0.0993) GCATTCATATCAAACTTGTGG 0.552000 T ? ALCL 7 72 5.18039e-06 5.18039e-06 1 1 0 TP53 7157 broad.mit.edu 37 17 7577094 7577094 + Missense_Mutation SNP G G A rs28934574 TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr17:7577094G>A ENST00000420246.2 - 8 976 c.844C>T c.(844-846)Cgg>Tgg p.R282W TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000269305.4_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 282 Interaction with AXIN1 (By similarity).|Interaction with E4F1.|Interaction with HIPK1 (By similarity). DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934574). 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.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(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) TCTGTGCGCCGGTCTCTCCCA 0.557000 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) 34 19 0 0 1 0 0 EMR1 2015 broad.mit.edu 37 19 6926465 6926465 + Missense_Mutation SNP T T C TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr19:6926465T>C ENST00000312053.4 + 16 2112 c.2075T>C c.(2074-2076)tTg>tCg p.L692S EMR1_ENST00000250572.8_Missense_Mutation_p.L627S|EMR1_ENST00000381407.5_Missense_Mutation_p.L551S|EMR1_ENST00000450315.3_Missense_Mutation_p.L515S|EMR1_ENST00000381404.4_Missense_Mutation_p.L640S NM_001974.4 NP_001965.3 Q14246 EMR1_HUMAN egf-like module containing, mucin-like, hormone receptor-like 1 692 cell adhesion|neuropeptide signaling pathway integral to plasma membrane calcium ion binding|G-protein coupled receptor activity NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8) 62 all_hematologic(4;0.166) ATACTGTTCTTGATGGTCAGA 0.537000 10 80 0 0 1 0 0 CLCN4 0 broad.mit.edu 37 X 10180553 10180553 + Missense_Mutation SNP C C T TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chrX:10180553C>T ENST00000380833.4 + 10 1827 c.1436C>T c.(1435-1437)gCg>gTg p.A479V CLCN4_ENST00000380829.1_Missense_Mutation_p.A448V|CLCN4_ENST00000421085.2_Missense_Mutation_p.A385V NM_001256944.1|NM_001830.3 NP_001243873.1|NP_001821.2 P51793 CLCN4_HUMAN chloride channel, voltage-sensitive 4 479 early endosome membrane|integral to membrane|late endosome membrane antiporter activity|ATP binding|voltage-gated chloride channel activity breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 36 GGCGCGATAGCGGGCAGGATG 0.577000 5 43 0 0 1 0 0 ATRX 546 broad.mit.edu 37 X 76849194 76849194 + Nonsense_Mutation SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chrX:76849194G>A ENST00000373344.5 - 26 6296 c.6082C>T c.(6082-6084)Cga>Tga p.R2028* ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1990*|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 2028 Helicase C-terminal. 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) TCTGCCATTCGAAGAATTTCA 0.338000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 14 43 0 0 1 0 0 OR5P2 120065 broad.mit.edu 37 11 7817817 7817817 + Missense_Mutation SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr11:7817817G>A ENST00000329434.2 - 1 703 c.673C>T c.(673-675)Cgc>Tgc p.R225C RP11-35J10.5_ENST00000527565.1_lincRNA NM_153444.1 NP_703145.1 Q8WZ92 OR5P2_HUMAN olfactory receptor, family 5, subfamily P, member 2 225 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.R225C(1) central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4) 22 Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189) TCAGTGGAGCGCATCTTCAGG 0.493000 17 57 0 0 1 0 0 LAMP1 3916 broad.mit.edu 37 13 113960856 113960856 + Missense_Mutation SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr13:113960856G>A ENST00000332556.4 + 2 312 c.118G>A c.(118-120)Gcg>Acg p.A40T LAMP1_ENST00000397181.3_Missense_Mutation_p.A40T NM_005561.3 NP_005552.3 P11279 LAMP1_HUMAN lysosomal-associated membrane protein 1 40 First lumenal domain. VKNGNGTA -> MARGGRVR (in Ref. 6; AAA59524). endosome membrane|integral to plasma membrane|lysosomal membrane|membrane fraction NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2) 16 Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188) all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246) CAACGGGACCGCGTGCATAAT 0.507000 38 81 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414340 20414340 + Silent SNP G G A TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr9:20414340G>A ENST00000380338.4 - 5 790 c.504C>T c.(502-504)agC>agT p.S168S MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000355930.6_5'UTR|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 6 53 0 0 1 0 0 PCSK9 255738 broad.mit.edu 37 1 55505552 55505553 + In_Frame_Ins INS - - CTG rs35574083 TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr1:55505552_55505553insCTG ENST00000302118.5 + 1 332_333 c.42_43insCTG c.(40-45)cctgct>ccCTGtgct p.14_15PA>PCA PCSK9_ENST00000452118.2_In_Frame_Ins_p.14_15PA>PCA NM_174936.3 NP_777596.2 Q8NBP7 PCSK9_HUMAN proprotein convertase subtilisin/kexin type 9 14 cellular response to insulin stimulus|cellular response to starvation|cholesterol homeostasis|cholesterol metabolic process|kidney development|liver development|low-density lipoprotein particle receptor catabolic process|lysosomal transport|negative regulation of catalytic activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor recycling|neuron differentiation|positive regulation of neuron apoptosis|positive regulation of receptor internalization|protein autoprocessing|regulation of receptor activity extracellular space|late endosome|lysosome|perinuclear region of cytoplasm apolipoprotein receptor binding|identical protein binding|low-density lipoprotein particle receptor binding|serine-type endopeptidase activity|very-low-density lipoprotein particle receptor binding p.P14_L15insL(2) NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1) 32 Ggccgctgccactgctgctgct 0.703 3 4 --- --- --- --- OR2T35 403244 broad.mit.edu 37 1 248801602 248801603 + Frame_Shift_Ins INS - - CA TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr1:248801602_248801603insCA ENST00000317450.3 - 1 956_957 c.957_958insTG c.(955-960)gttcagfs p.Q320fs NM_001001827.1 NP_001001827.1 Q8NGX2 O2T35_HUMAN olfactory receptor, family 2, subfamily T, member 35 320 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.I320fs*1(1) endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1) 6 all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) all_cancers(173;0.237) OV - Ovarian serous cystadenocarcinoma(106;0.0265) CCCTTCCTGATCACAGTCGCCA 0.545 2 4 --- --- --- --- AC016995.3 0 broad.mit.edu 37 2 38710017 38710019 + RNA DEL AAT AAT - rs2005502 by1000genomes TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr2:38710017_38710019delAAT ENST00000417039.1 - 0 696 TTCTTtaaaaaataaataaataa 0.246 3 6 --- --- --- --- PRSS3P2 0 broad.mit.edu 37 7 142481743 142481745 + RNA DEL CTA CTA - TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr7:142481743_142481745delCTA ENST00000603901.1 + 0 454 NR_001296.3 ACCCACATTTCTACTTTCTTTAT 0.517 8 165 --- --- --- --- PRSS3P2 0 broad.mit.edu 37 7 142482280 142482280 + RNA DEL T T - TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr7:142482280delT ENST00000603901.1 + 0 660 NR_001296.3 GCTATGGCTGTGCCCAGAAGA 0.517 8 82 --- --- --- --- RP11-349A22.5 0 broad.mit.edu 37 14 58752042 58752053 + RNA DEL GAAGAGGATGAG GAAGAGGATGAG - rs112158888 TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr14:58752042_58752053delGAAGAGGATGAG ENST00000554360.1 - 0 414 RP11-349A22.5_ENST00000556002.1_RNA|RP11-349A22.5_ENST00000555707.1_RNA|RP11-349A22.5_ENST00000553657.1_RNA|RP11-349A22.5_ENST00000557660.1_RNA|RP11-349A22.5_ENST00000556400.1_RNA|RP11-349A22.5_ENST00000555275.1_RNA|RP11-349A22.5_ENST00000554378.1_RNA NR_029434.1 Tgagaaagatgaagaggatgaggaagaggatg 0.392 7 5 --- --- --- --- TPTE 7179 broad.mit.edu 37 21 10944697 10944697 + Frame_Shift_Del DEL A A - TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr21:10944697delA ENST00000298232.7 - 10 850 c.483delT c.(481-483)ttfs p.F161fs TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000361285.4_Frame_Shift_Del_p.F179fs|TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs NM_199259.2 NP_954868.1 P56180 TPTE_HUMAN transmembrane phosphatase with tensin homology 179 signal transduction integral to membrane ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1) 130 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ACTTAATGTCAAAAAAAATGT 0.299 7 229 --- --- --- --- CRYBB2P1 0 broad.mit.edu 37 22 25855682 25855683 + RNA INS - - GT rs72063487 by1000genomes TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr22:25855682_25855683insGT ENST00000354451.2 + 0 366 CCTGGCAGCTGgtgtgtgtgtg 0.530 2 4 --- --- --- --- TRIOBP 11078 broad.mit.edu 37 22 38119882 38119884 + In_Frame_Del DEL CCT CCT - TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chr22:38119882_38119884delCCT ENST00000406386.3 + 7 1574_1576 c.1319_1321delCCT c.(1318-1323)gcc>g p.AS440del RP1-37E16.12_ENST00000455236.1_RNA NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 440 actin modification|barbed-end actin filament capping actin cytoskeleton|cytoplasm|nucleus actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 12 Melanoma(58;0.0574) AATCCCAGAGCCTCCTCTCCCAG 0.601 7 126 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76855019 76855019 + Frame_Shift_Del DEL T T - TCGA-DU-7011-01A-11D-2024-08 TCGA-DU-7011-10A-01D-2024-08 Untested Somatic Phase_I WXS none Illumina GAIIx a998b8e9-3711-460c-8e4b-6597b6760a15 faf5593b-8173-4404-adef-379c03202b68 g.chrX:76855019delT ENST00000373344.5 - 25 6031 c.5817delA c.(5815-5817)aafs p.K1939fs ATRX_ENST00000395603.3_Frame_Shift_Del_p.K1901fs|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 1939 Poly-Lys. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding 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) AGCTACTATCTTTTTTCCCCT 0.353 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 61 242 --- --- --- ---