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 PRG4 10216 broad.mit.edu 37 1 186276307 186276307 + Missense_Mutation SNP G G A TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr1:186276307G>A ENST00000445192.2 + 7 1501 c.1456G>A c.(1456-1458)Gcc>Acc p.A486T PRG4_ENST00000367483.4_Missense_Mutation_p.A445T|PRG4_ENST00000367486.3_Missense_Mutation_p.A443T|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.A393T NM_005807.3 NP_005798.2 Q92954 PRG4_HUMAN proteoglycan 4 486 59 X 8 AA repeats of K-X-P-X-P-T-T-X. cell proliferation|immune response extracellular region polysaccharide binding|protein binding|scavenger receptor activity p.A486T(2) NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1) 102 TGCACCCACTGCCCCCAAGAA 0.652000 8 179 0 0 1 0 0 PCDHB2 0 broad.mit.edu 37 5 140476767 140476767 + Missense_Mutation SNP C C G rs461653 TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr5:140476767C>G ENST00000194155.4 + 1 2541 c.2393C>G c.(2392-2394)aCt>aGt p.T798S NM_018936.2 NP_061759.1 Q9Y5E7 PCDB2_HUMAN 798 calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission integral to plasma membrane calcium ion binding NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2) 71 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) TTTGAATTCACTTAAGTGTTA 0.423000 4 155 0 0 1 0 0 ATRX 546 broad.mit.edu 37 X 76938788 76938788 + Silent SNP G G T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chrX:76938788G>T ENST00000373344.5 - 9 2174 c.1960C>A c.(1960-1962)Cga>Aga p.R654R ATRX_ENST00000395603.3_Silent_p.R616R|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 654 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) GGGGATCTTCGAAGATCAGAT 0.393000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 19 114 7.07596e-05 7.62026e-05 1 1 0 KAT2A 2648 broad.mit.edu 37 17 40269492 40269492 + Silent SNP C C T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr17:40269492C>T ENST00000225916.5 - 10 1604 c.1551G>A c.(1549-1551)ttG>ttA p.L517L NM_021078.2 NP_066564.2 Q92830 KAT2A_HUMAN K(lysine) acetyltransferase 2A 517 N-acetyltransferase. chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 18 CGAGCCACAGCAACACCCGCC 0.647000 4 44 0 0 1 0 0 KRTAP5-2 440021 broad.mit.edu 37 11 1619378 1619378 + Missense_Mutation SNP G G A rs138454470 byFrequency TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr11:1619378G>A ENST00000412090.1 - 1 146 c.103C>T c.(103-105)Cgt>Tgt p.R35C KRTAP5-AS1_ENST00000424148.1_RNA NM_001004325.1 NP_001004325.1 Q701N4 KRA52_HUMAN keratin associated protein 5-2 35 keratin filament large_intestine(1)|lung(2)|skin(1) 4 all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082) CAGCCCCCACGGCCGGAGCCA 0.687000 6 153 0 0 1 0 0 ALX1 8092 broad.mit.edu 37 12 85677519 85677519 + Missense_Mutation SNP A A T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr12:85677519A>T ENST00000316824.3 + 2 551 c.396A>T c.(394-396)aaA>aaT p.K132N NM_006982.2 NP_008913.2 Q15699 ALX1_HUMAN ALX homeobox 1 132 brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter sequence-specific DNA binding transcription factor activity|transcription corepressor activity breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1) 26 GBM - Glioblastoma multiforme(134;0.134) GCAGTAAGAAACGGAGGCACC 0.478000 4 154 0 0 1 0 0 TRIM33 51592 broad.mit.edu 37 1 114968295 114968295 + Missense_Mutation SNP C C T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr1:114968295C>T ENST00000358465.2 - 9 1554 c.1471G>A c.(1471-1473)Gta>Ata p.V491I TRIM33_ENST00000369543.2_Missense_Mutation_p.V491I|TRIM33_ENST00000450349.2_Missense_Mutation_p.V99I NM_015906.3 NP_056990.3 Q9UPN9 TRI33_HUMAN tripartite motif containing 33 491 negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent nucleus co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1) 48 all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184) all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) TGCCCAACTACAACATTAGGA 0.368000 T RET papillary thyroid 4 100 0 0 1 0 0 TP53 7157 broad.mit.edu 37 17 7577545 7577545 + Missense_Mutation SNP T T C TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr17:7577545T>C ENST00000420246.2 - 7 868 c.736A>G c.(736-738)Atg>Gtg p.M246V TP53_ENST00000445888.2_Missense_Mutation_p.M246V|TP53_ENST00000359597.4_Missense_Mutation_p.M246V|TP53_ENST00000413465.2_Missense_Mutation_p.M246V|TP53_ENST00000455263.2_Missense_Mutation_p.M246V|TP53_ENST00000269305.4_Missense_Mutation_p.M246V NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 246 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain. M -> I (in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (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.M246V(34)|p.0?(8)|p.?(5)|p.M246L(3)|p.G244_M246>V(3)|p.M246fs*1(2)|p.M153V(2)|p.M246_P250delMNRRP(2)|p.G151_M153>V(1)|p.G244fs*17(1)|p.C242fs*98(1)|p.G245fs*17(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*14(1)|p.G245fs*16(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) CTCCGGTTCATGCCGCCCATG 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) 10 76 0 0 1 0 0 PKN3 29941 broad.mit.edu 37 9 131475882 131475882 + Silent SNP G G C TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr9:131475882G>C ENST00000291906.4 + 9 1590 c.1197G>C c.(1195-1197)ctG>ctC p.L399L NM_013355.3 NP_037487.2 Q6P5Z2 PKN3_HUMAN protein kinase N3 399 signal transduction Golgi apparatus|nucleus|perinuclear region of cytoplasm ATP binding|protein binding|protein kinase C activity breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1) 24 GTCACCAACTGTCCCTCAGCC 0.632000 6 85 0 0 1 0 0 ATRX 546 broad.mit.edu 37 X 76937900 76937900 + Nonsense_Mutation SNP T T A TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chrX:76937900T>A ENST00000373344.5 - 9 3062 c.2848A>T c.(2848-2850)Aaa>Taa p.K950* ATRX_ENST00000395603.3_Nonsense_Mutation_p.K912*|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 950 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) GTTTTGGTTTTGAGATGCTTG 0.358000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 17 76 0 0 1 0 0 SPOCK2 9806 broad.mit.edu 37 10 73827431 73827431 + Missense_Mutation SNP G G T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr10:73827431G>T ENST00000373109.2 - 7 1093 c.649C>A c.(649-651)Ctc>Atc p.L217I SPOCK2_ENST00000460053.1_5'UTR|SPOCK2_ENST00000317376.4_Missense_Mutation_p.L217I|SPOCK2_ENST00000536168.1_Missense_Mutation_p.L217I NM_001244950.1 NP_001231879.1 Q92563 TICN2_HUMAN sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2 217 extracellular matrix organization|regulation of cell differentiation|signal transduction|synapse assembly proteinaceous extracellular matrix calcium ion binding endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 9 TCATGAAGGAGCTGGAACCAG 0.607000 3 38 6.4e-05 7.168e-05 1 1 0 MYO1E 4643 broad.mit.edu 37 15 59445849 59445849 + Missense_Mutation SNP C C A TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr15:59445849C>A ENST00000288235.4 - 26 3419 c.3020G>T c.(3019-3021)cGa>cTa p.R1007L NM_004998.3 NP_004989.2 Q12965 MYO1E_HUMAN myosin IE 1007 actin filament-based movement myosin complex actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1) 33 all cancers(107;0.207) CTGTGACACTCGGTCTGAACT 0.592000 4 103 0.150653 0.150653 1 1 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c 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 13 50 0 0 1 0 0 PTPN14 5784 broad.mit.edu 37 1 214557534 214557534 + Missense_Mutation SNP G G A TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr1:214557534G>A ENST00000366956.5 - 13 1858 c.1664C>T c.(1663-1665)aCg>aTg p.T555M PTPN14_ENST00000543945.1_3'UTR NM_005401.4 NP_005392.2 Q15678 PTN14_HUMAN protein tyrosine phosphatase, non-receptor type 14 555 lymphangiogenesis cytoplasm|cytoskeleton protein tyrosine phosphatase activity|receptor tyrosine kinase binding NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155) CATGTGGGCCGTGCTGTAGTT 0.637000 10 118 0 0 1 0 0 POM121 9883 broad.mit.edu 37 7 72413479 72413479 + Missense_Mutation SNP G G A TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr7:72413479G>A ENST00000395270.1 + 14 3193 c.2152G>A c.(2152-2154)Gcc>Acc p.A718T POM121_ENST00000257622.4_Missense_Mutation_p.A718T|POM121_ENST00000446813.1_Missense_Mutation_p.A718T|POM121_ENST00000434423.2_Missense_Mutation_p.A983T|POM121_ENST00000358357.3_Missense_Mutation_p.A718T NM_001257190.1 NP_001244119.1 Q96HA1 P121A_HUMAN POM121 transmembrane nucleoporin 983 Pore side (Potential). carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction endoplasmic reticulum membrane|nuclear membrane|nuclear pore NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 Lung NSC(55;0.163) ACCGGGGGCCGCCAAGCCGGC 0.652000 5 250 0 0 1 0 0 AFF2 2334 broad.mit.edu 37 X 148037448 148037448 + Missense_Mutation SNP A A G TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chrX:148037448A>G ENST00000370460.2 + 11 2352 c.1873A>G c.(1873-1875)Aca>Gca p.T625A AFF2_ENST00000370457.5_Missense_Mutation_p.T592A|AFF2_ENST00000286437.5_Missense_Mutation_p.T266A|AFF2_ENST00000342251.3_Missense_Mutation_p.T592A NM_001169123.1|NM_002025.3 NP_001162594.1|NP_002016.2 P51816 AFF2_HUMAN AF4/FMR2 family, member 2 625 brain development|mRNA processing|regulation of RNA splicing|RNA splicing nuclear speck G-quadruplex RNA binding|protein binding breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 109 Acute lymphoblastic leukemia(192;6.56e-05) GTCTCAAAGGACAATTGGGAA 0.443000 16 104 0 0 1 0 0 TMEM198 130612 broad.mit.edu 37 2 220412578 220412578 + Missense_Mutation SNP A A C TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr2:220412578A>C ENST00000344458.2 + 4 1102 c.517A>C c.(517-519)Acc>Ccc p.T173P TMEM198_ENST00000373883.3_Missense_Mutation_p.T173P Q66K66 TM198_HUMAN transmembrane protein 198 173 Leu-rich. integral to membrane NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 16 Renal(207;0.0376) Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802) CCCACTCACCACCCTGGCCAC 0.697000 6 15 0 0 1 0 0 RAPH1 65059 broad.mit.edu 37 2 204305768 204305768 + Silent SNP A A G TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr2:204305768A>G ENST00000319170.5 - 14 2444 c.2145T>C c.(2143-2145)ccT>ccC p.P715P RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Silent_p.P767P NM_213589.1 NP_998754.1 Q70E73 RAPH1_HUMAN Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 715 cell-matrix adhesion|signal transduction cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 32 ggggtggaggagggggagggg 0.622000 5 37 0 0 1 0 0 UBBP4 0 broad.mit.edu 37 17 21730847 21730847 + Missense_Mutation SNP G G T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr17:21730847G>T ENST00000584755.1 + 2 546 c.149G>T c.(148-150)cGg>cTg p.R50L UBBP4_ENST00000583708.1_Intron|UBBP4_ENST00000584398.1_Intron|UBBP4_ENST00000578713.1_Missense_Mutation_p.R50L endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4) 24 GGCAAGCAGCGGGAAGATGGC 0.522000 3 38 0.004672 0.00484504 1 1 0 SEMA3B 7869 broad.mit.edu 37 3 50311108 50311108 + RNA SNP A A G TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr3:50311108A>G ENST00000418948.1 + 0 1156 Q13214 SEM3B_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B axon guidance|cell-cell signaling endoplasmic reticulum|extracellular region|membrane receptor activity central_nervous_system(2)|kidney(1)|lung(2)|skin(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605) GGGGTTGGGGAGGGGGGCAGC 0.701000 OREG0015583 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 8 48 0 0 1 0 0 FAH 2184 broad.mit.edu 37 15 80452128 80452128 + Nonsense_Mutation SNP C C T TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr15:80452128C>T ENST00000539156.1 + 2 2251 c.13C>T c.(13-15)Cag>Tag p.Q5* FAH_ENST00000407106.1_Nonsense_Mutation_p.Q75*|FAH_ENST00000261755.5_Nonsense_Mutation_p.Q75*|FAH_ENST00000561421.1_Nonsense_Mutation_p.Q75* P16930 FAAA_HUMAN fumarylacetoacetate hydrolase (fumarylacetoacetase) 75 L-phenylalanine catabolic process|tyrosine catabolic process cytosol fumarylacetoacetase activity|metal ion binding endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 GGGCCTGGGTCAGGCTGCCTG 0.527000 Tyrosinemia, type 1 4 93 0 0 1 0 0 PTPN18 26469 broad.mit.edu 37 2 131129929 131129934 + In_Frame_Del DEL GACGGG GACGGG - rs112040677 TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr2:131129929_131129934delGACGGG ENST00000175756.5 + 13 1214_1219 c.1113_1118delGACGGG c.(1111-1119)cag>ca p.QTG371del PTPN18_ENST00000347849.3_In_Frame_Del_p.QTG264del NM_014369.3 NP_055184.2 Q99952 PTN18_HUMAN protein tyrosine phosphatase, non-receptor type 18 (brain-derived) 371 cytoplasm|nucleus non-membrane spanning protein tyrosine phosphatase activity p.T378_G379delTG(1) endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1) 15 Colorectal(110;0.1) gtgggacgcagacggggacggggacg 0.777 5 9 --- --- --- --- HDAC2 3066 broad.mit.edu 37 6 114292110 114292112 + In_Frame_Del DEL CTG CTG - TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr6:114292110_114292112delCTG ENST00000398283.2 - 1 247_249 c.243_245delCAG c.(241-246)agg>ag p.SR81del HDAC2_ENST00000519065.1_5'UTR|RP3-399L15.3_ENST00000520554.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000449620.2_RNA|RP3-399L15.3_ENST00000436876.2_RNA|HDAC2_ENST00000368632.2_5'UTR NM_001527.3 NP_001518.3 Q92769 HDAC2_HUMAN histone deacetylase 2 0 Histone deacetylase. blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding p.S81R(1) biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2) 27 all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24) all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832) Vorinostat(DB02546) GCTCCTCCTCctgctgctgctgc 0.685 2 4 --- --- --- --- MICALCL 84953 broad.mit.edu 37 11 12316384 12316389 + In_Frame_Del DEL CTCCTA CTCCTA - rs3812754 byFrequency TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr11:12316384_12316389delCTCCTA ENST00000256186.2 + 3 1697_1702 c.1406_1411delCTCCTA c.(1405-1413)cca>c p.PPT469del NM_032867.2 NP_116256.2 Q6ZW33 MICLK_HUMAN MICAL C-terminal like 469 Poly-Pro. cell differentiation|multicellular organismal development|spermatogenesis cytoplasm mitogen-activated protein kinase binding p.T471delT(2) breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1) 30 Epithelial(150;0.00177) cctcctcctcctcctACAGCGGGAGG 0.573 6 11 --- --- --- --- FOXJ2 55810 broad.mit.edu 37 12 8200558 8200560 + In_Frame_Del DEL CAG CAG - TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr12:8200558_8200560delCAG ENST00000162391.3 + 7 2043_2045 c.898_900delCAG c.(898-900)del p.Q306del FOXJ2_ENST00000428177.2_In_Frame_Del_p.Q306del NM_018416.2 NP_060886.1 Q9P0K8 FOXJ2_HUMAN forkhead box J2 306 Poly-Gln. embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development nucleolus|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2) 16 Kidney(36;0.0944) gccacctcaacagcagcagcagc 0.640 7 76 --- --- --- --- EP400 57634 broad.mit.edu 37 12 132547093 132547094 + In_Frame_Ins INS - - CAG rs113304321 by1000genomes TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr12:132547093_132547094insCAG ENST00000333577.4 + 48 8398_8399 c.8289_8290insCAG c.(8287-8292)caagca>caCAGagca p.2763_2763Q>HR EP400_ENST00000389562.2_In_Frame_Ins_p.2726_2726Q>HR|EP400_ENST00000389561.2_In_Frame_Ins_p.2727_2727Q>HR|EP400_ENST00000330386.6_In_Frame_Ins_p.2646_2646Q>HR|EP400_ENST00000332482.4_In_Frame_Ins_p.2690_2690Q>HR Q96L91 EP400_HUMAN E1A binding protein p400 2763 Interaction with ZNF42 (By similarity).|Poly-Gln. histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity p.Q2726Q(9) NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3) 161 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) agcagcaacaacagcagcagca 0.564 14 63 --- --- --- --- LA16c-306E5.3 0 broad.mit.edu 37 16 3546140 3546141 + RNA INS - - A rs74546027 TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr16:3546140_3546141insA ENST00000574423.2 + 0 111 gactccgtctcaaaaaaaaaaa 0.559 2 4 --- --- --- --- NF1 4763 broad.mit.edu 37 17 29562657 29562660 + Frame_Shift_Del DEL TGTT TGTT - TCGA-HT-7880-01A-11D-2395-08 TCGA-HT-7880-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a061c9f4-52fe-4b46-8e9f-0fcc76dbc1c8 8838112e-a2bd-4211-b5f9-990637c86c8c g.chr17:29562657_29562660delTGTT ENST00000358273.4 + 28 4120_4123 c.3737_3740delTGTT c.(3736-3741)ctfs p.LF1246fs NF1_ENST00000356175.3_Frame_Shift_Del_p.LF1246fs NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 1246 Ras-GAP. actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.0?(8)|p.?(4)|p.F1247fs*16(1) NF1/ACCN1(2) autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CTGGTTACTCTGTTTGATTCTCGG 0.412 """D, Mis, N, F, S, O""" """neurofibroma, glioma""" """neurofibroma, glioma""" Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) 20 226 --- --- --- ---