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 EPB41L3 23136 broad.mit.edu 37 18 5398132 5398132 + Missense_Mutation SNP G G C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr18:5398132G>C ENST00000341928.2 - 17 2700 c.2360C>G c.(2359-2361)tCt>tGt p.S787C EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000427684.2_Missense_Mutation_p.S84C|EPB41L3_ENST00000544123.1_Missense_Mutation_p.S618C|EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.S787C|EPB41L3_ENST00000542146.1_Missense_Mutation_p.S92C NM_012307.2 NP_036439.2 Q9Y2J2 E41L3_HUMAN erythrocyte membrane protein band 4.1-like 3 787 Spectrin--actin-binding (Potential). cortical actin cytoskeleton organization cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane actin binding|structural molecule activity breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 105 TTCCCCAGAAGACTGCTTAGT 0.418000 91 156 0 0 1 0 0 TUBBP5 0 broad.mit.edu 37 9 141070116 141070116 + RNA SNP G G A rs142836124 by1000genomes TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr9:141070116G>A ENST00000503395.1 + 0 1196 p.R77H(1) GACTCTGTGCGCTCGGGGCCC 0.687000 6 70 0 0 1 0 0 ADAM7 8756 broad.mit.edu 37 8 24323222 24323222 + Missense_Mutation SNP T T C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr8:24323222T>C ENST00000175238.6 + 5 406 c.323T>C c.(322-324)tTt>tCt p.F108S RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000441335.2_Missense_Mutation_p.F108S|ADAM7_ENST00000380789.1_Missense_Mutation_p.F108S NM_003817.3 NP_003808.2 Q9H2U9 ADAM7_HUMAN ADAM metallopeptidase domain 7 108 proteolysis integral to membrane metalloendopeptidase activity|zinc ion binding NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15) 64 Prostate(55;0.0181) Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182) GATCATTGTTTTTACCAAGGA 0.284000 17 24 0 0 1 0 0 HLA-DQB2 3120 broad.mit.edu 37 6 32725596 32725596 + Silent SNP C C G rs115565146 by1000genomes TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr6:32725596C>G ENST00000435145.2 - 4 772 c.711G>C c.(709-711)ctG>ctC p.L237L HLA-DQB2_ENST00000411527.1_Intron|HLA-DQB2_ENST00000437316.2_Silent_p.L237L Q5SR06 Q5SR06_HUMAN major histocompatibility complex, class II, DQ beta 2 216 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response integral to membrane|MHC class II protein complex endometrium(1)|kidney(1)|lung(1)|prostate(2) 5 CGAGGAAGATCAGCCCCAGCA 0.562000 4 14 0 0 1 0 0 HMCN1 83872 broad.mit.edu 37 1 186136027 186136027 + Missense_Mutation SNP G G A rs150494959 byFrequency TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr1:186136027G>A ENST00000271588.4 + 100 15756 c.15527G>A c.(15526-15528)cGt>cAt p.R5176H HMCN1_ENST00000367492.2_Missense_Mutation_p.R5176H NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 5176 EGF-like 2; calcium-binding (Potential). response to stimulus|visual perception basement membrane calcium ion binding p.R5176H(1) NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18) 308 TGTGTGGTCCGTTGTGGAAGT 0.463000 28 38 0 0 1 0 0 OR5D14 219436 broad.mit.edu 37 11 55563199 55563199 + Silent SNP A A G TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr11:55563199A>G ENST00000335605.1 + 1 168 c.168A>G c.(166-168)aaA>aaG p.K56K NM_001004735.1 NP_001004735.1 Q8NGL3 OR5DE_HUMAN olfactory receptor, family 5, subfamily D, member 14 56 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1) 48 all_epithelial(135;0.196) TTAACCCCAAATTTCACACTC 0.388000 4 76 0 0 1 0 0 FOLH1 2346 broad.mit.edu 37 11 49179513 49179513 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr11:49179513C>T ENST00000340334.7 - 15 1846 c.1478G>A c.(1477-1479)gGc>gAc p.G493D FOLH1_ENST00000356696.3_Missense_Mutation_p.G508D|FOLH1_ENST00000533034.1_Missense_Mutation_p.G493D|FOLH1_ENST00000256999.2_Missense_Mutation_p.G508D|FOLH1_ENST00000343844.4_Missense_Mutation_p.G200D NM_001193471.1|NM_001193472.1 NP_001180400.1|NP_001180401.1 Q04609 FOLH1_HUMAN folate hydrolase (prostate-specific membrane antigen) 1 508 NAALADase. proteolysis cytoplasm|integral to plasma membrane|membrane fraction|nucleus carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3) 60 Capromab(DB00089)|L-Glutamic Acid(DB00142) CCTGGGCATGCCACTGAACTC 0.348000 3 50 0 0 1 0 0 KCNA1 3736 broad.mit.edu 37 12 5021170 5021170 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr12:5021170C>T ENST00000382545.3 + 2 1733 c.626C>T c.(625-627)aCg>aTg p.T209M KCNA1_ENST00000543874.2_Intron NM_000217.2 NP_000208.2 Q09470 KCNA1_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia) 209 synaptic transmission juxtaparanode region of axon|voltage-gated potassium channel complex delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 63 Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236) GACAACACCACGGTCATCTAC 0.542000 32 28 0 0 1 0 0 GNAZ 2781 broad.mit.edu 37 22 23438508 23438508 + Missense_Mutation SNP G G A TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr22:23438508G>A ENST00000248996.4 + 2 1292 c.626G>A c.(625-627)cGc>cAc p.R209H RTDR1_ENST00000216036.4_Intron NM_002073.2 NP_002064.1 P19086 GNAZ_HUMAN guanine nucleotide binding protein (G protein), alpha z polypeptide 209 endoplasmic reticulum|heterotrimeric G-protein complex|nuclear envelope G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|metabotropic serotonin receptor binding|receptor signaling protein activity endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1) 19 all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181) READ - Rectum adenocarcinoma(21;0.166) AGGTCAGAGCGCAAAAAGTGG 0.562000 4 188 0 0 1 0 0 LIPI 149998 broad.mit.edu 37 21 15537704 15537704 + Missense_Mutation SNP T T A TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr21:15537704T>A ENST00000344577.2 - 6 829 c.804A>T c.(802-804)caA>caT p.Q268H LIPI_ENST00000536861.1_Missense_Mutation_p.Q247H NM_198996.2 NP_945347.1 Q6XZB0 LIPI_HUMAN lipase, member I 247 lipid catabolic process extracellular region|extracellular space|membrane|plasma membrane heparin binding|phospholipase activity endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1) 54 Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166) ATTTAATGAATTGAATTCCTT 0.299000 26 25 0 0 1 0 0 PTEN 5728 broad.mit.edu 37 10 89624270 89624270 + Missense_Mutation SNP G G C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr10:89624270G>C ENST00000371953.3 + 1 1401 c.44G>C c.(43-45)aGa>aCa p.R15T NM_000314.4 NP_000305.3 P60484 PTEN_HUMAN phosphatase and tensin homolog 15 Phosphatase tensin-type. R -> S (in glioma). activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.0?(37)|p.?(13)|p.R15I(3)|p.R15fs*23(1)|p.R15K(1)|p.R14fs*26(1)|p.N12fs*6(1)|p.R14_D22del(1) NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17) 2771 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) AACAAAAGGAGATATCAAGAG 0.478000 31 """D, Mis, N, F, S""" """glioma, prostate, endometrial""" """harmartoma, glioma, prostate, endometrial""" Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18) 3 68 0 0 1 0 0 FAM129B 64855 broad.mit.edu 37 9 130294013 130294013 + Missense_Mutation SNP C C G TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr9:130294013C>G ENST00000373312.3 - 2 313 c.100G>C c.(100-102)Gac>Cac p.D34H FAM129B_ENST00000373314.3_Missense_Mutation_p.D21H|FAM129B_ENST00000468379.1_5'UTR NM_022833.2 NP_073744.2 Q96TA1 NIBL1_HUMAN family with sequence similarity 129, member B 34 protein binding breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2) 25 CCATACTGGTCTTCATAGAAC 0.577000 5 63 0 0 1 0 0 ZNF716 441234 broad.mit.edu 37 7 57522851 57522851 + Missense_Mutation SNP A A G TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr7:57522851A>G ENST00000420713.1 + 3 351 c.239A>G c.(238-240)aAt>aGt p.N80S NM_001159279.1 NP_001152751.1 zinc finger protein 716 breast(1)|kidney(1)|lung(20)|ovary(2) 24 ATAAAGAGAAATGAGATGGTA 0.408000 5 91 0 0 1 0 0 MYO3B 140469 broad.mit.edu 37 2 171262117 171262117 + Missense_Mutation SNP T T C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr2:171262117T>C ENST00000334231.6 + 21 2521 c.2521T>C c.(2521-2523)Ttt>Ctt p.F841L MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000408978.4_Missense_Mutation_p.F832L|MYO3B_ENST00000409044.3_Missense_Mutation_p.F832L Q8WXR4 MYO3B_HUMAN myosin IIIB 832 Myosin head-like. response to stimulus|visual perception cytoplasm|myosin complex actin binding|ATP binding|motor activity|protein serine/threonine kinase activity breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2) 59 GGAACTGTGCTTTGGCATTCA 0.418000 4 50 0 0 1 0 0 KLHL1 57626 broad.mit.edu 37 13 70293517 70293517 + Missense_Mutation SNP G G T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr13:70293517G>T ENST00000377844.4 - 9 2758 c.1999C>A c.(1999-2001)Ctg>Atg p.L667M KLHL1_ENST00000545028.1_Missense_Mutation_p.L474M NM_020866.2 NP_065917.1 Q9NR64 KLHL1_HUMAN kelch-like family member 1 667 actin cytoskeleton organization cytoplasm|cytoskeleton actin binding breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1) 84 Breast(118;0.000162) COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211) ACATAATCCAGTAGCCGGGAA 0.463000 28 40 1.55811e-20 1.60139e-20 1 1 0 SNHG14 0 broad.mit.edu 37 15 25440084 25440084 + RNA SNP A A C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr15:25440084A>C ENST00000424208.1 + 0 1460 SNORD115-14_ENST00000363090.1_RNA|SNHG14_ENST00000456576.1_RNA NR_003305.1 ATGATGAGAAACTTATATTGT 0.522000 6 265 0 0 1 0 0 TRIML1 339976 broad.mit.edu 37 4 189060901 189060901 + Silent SNP G G A rs147444946 byFrequency TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr4:189060901G>A ENST00000332517.3 + 1 329 c.189G>A c.(187-189)ccG>ccA p.P63P NM_178556.3 NP_848651.2 Q8N9V2 TRIML_HUMAN tripartite motif family-like 1 63 multicellular organismal development ligase activity|zinc ion binding NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1) 60 all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062) OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156) TGGAGGGCCCGCATTTCCAGT 0.602000 6 113 0 0 1 0 0 NEDD4 4734 broad.mit.edu 37 15 56142778 56142778 + Missense_Mutation SNP G G A TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr15:56142778G>A ENST00000508342.1 - 10 2865 c.2566C>T c.(2566-2568)Cct>Tct p.P856S NEDD4_ENST00000506154.1_Missense_Mutation_p.P840S|NEDD4_ENST00000338963.2_Missense_Mutation_p.P784S|NEDD4_ENST00000435532.3_Missense_Mutation_p.P437S P46934 NEDD4_HUMAN neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase 856 Mediates interaction with TNIK (By similarity).|WW 3. development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 43 all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113) ATAAAGAAAGGCCTCCCATTT 0.428000 16 242 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_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 23 32 0 0 1 0 0 MYO7A 4647 broad.mit.edu 37 11 76903174 76903174 + Missense_Mutation SNP G G A TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr11:76903174G>A ENST00000409709.3 + 31 4275 c.4003G>A c.(4003-4005)Gcc>Acc p.A1335T MYO7A_ENST00000409619.2_Missense_Mutation_p.A1324T|MYO7A_ENST00000458637.2_Missense_Mutation_p.A1335T NM_000260.3 NP_000251.3 Q13402 MYO7A_HUMAN myosin VIIA 1335 FERM 1. actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse actin binding|ATP binding|calmodulin binding|microfilament motor activity NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 64 GGAGCAGGGCGCCCAGGAGCG 0.662000 OREG0021258 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 14 16 0 0 1 0 0 MAP3K5 4217 broad.mit.edu 37 6 136904865 136904865 + Missense_Mutation SNP G G A TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr6:136904865G>A ENST00000359015.4 - 24 3599 c.3239C>T c.(3238-3240)cCg>cTg p.P1080L MAP3K5_ENST00000463140.1_5'UTR|MAP3K5_ENST00000355845.4_Missense_Mutation_p.P327L NM_005923.3 NP_005914.1 Q99683 M3K5_HUMAN mitogen-activated protein kinase kinase kinase 5 1080 activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4) 58 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569) TTTTAGTTTCGGTTCTTCAGC 0.453000 6 94 0 0 1 0 0 KMT2C 58508 broad.mit.edu 37 7 151878079 151878079 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr7:151878079C>T ENST00000355193.2 - 36 7084 c.6866G>A c.(6865-6867)cGt>cAt p.R2289H KMT2C_ENST00000262189.6_Missense_Mutation_p.R2289H lysine (K)-specific methyltransferase 2C TGGGGAAACACGGCTAAATGT 0.517000 21 71 0 0 1 0 0 BTD 686 broad.mit.edu 37 3 15686469 15686469 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr3:15686469C>T ENST00000383778.4 + 4 1404 c.1046C>T c.(1045-1047)cCg>cTg p.P349L BTD_ENST00000303498.5_Missense_Mutation_p.P369L|BTD_ENST00000449107.1_Missense_Mutation_p.P371L|BTD_ENST00000437172.1_Missense_Mutation_p.P371L P43251 BTD_HUMAN biotinidase 369 CN hydrolase. central nervous system development|epidermis development|nitrogen compound metabolic process extracellular space biotin carboxylase activity|biotinidase activity breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1) 18 TCAGGCGATCCGTACTGTGAG 0.468000 4 109 0 0 1 0 0 POTEG 404785 broad.mit.edu 37 14 19553596 19553596 + Missense_Mutation SNP G G C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr14:19553596G>C ENST00000409832.3 + 1 232 c.180G>C c.(178-180)aaG>aaC p.K60N NM_001005356.2 NP_001005356.1 Q6S5H5 POTEG_HUMAN POTE ankyrin domain family, member G 60 cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 47 TCAGGAGCAAGATGGGCAAGT 0.612000 10 841 0 0 1 0 0 CCDC110 256309 broad.mit.edu 37 4 186380647 186380647 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr4:186380647C>T ENST00000307588.3 - 6 1169 c.1094G>A c.(1093-1095)gGc>gAc p.G365D CCDC110_ENST00000510617.1_Missense_Mutation_p.G365D|CCDC110_ENST00000393540.3_Missense_Mutation_p.G328D NM_152775.3 NP_689988.1 Q8TBZ0 CC110_HUMAN coiled-coil domain containing 110 365 nucleus NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9) 30 all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749) OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164) AATATTTTTGCCAGTGATGGG 0.323000 4 124 0 0 1 0 0 HNRNPL 3191 broad.mit.edu 37 19 39330862 39330862 + Silent SNP A A G TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr19:39330862A>G ENST00000221419.5 - 8 1473 c.1107T>C c.(1105-1107)ccT>ccC p.P369P HNRNPL_ENST00000600873.1_Silent_p.P236P NM_001533.2 NP_001524.2 P14866 HNRPL_HUMAN heterogeneous nuclear ribonucleoprotein L 369 Pro-rich. nuclear mRNA splicing, via spliceosome cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding p.P369P(2)|p.P236P(2) NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1) 30 all_cancers(60;6.83e-06)|Ovarian(47;0.0454) Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575) GTGGTGGGGGAGGGGGTGGGG 0.622000 3 9 0 0 1 0 0 DLGAP1 9229 broad.mit.edu 37 18 3879314 3879314 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr18:3879314C>T ENST00000315677.3 - 4 1350 c.755G>A c.(754-756)cGg>cAg p.R252Q DLGAP1-AS3_ENST00000577649.1_RNA|DLGAP1_ENST00000584874.1_Missense_Mutation_p.R252Q|DLGAP1_ENST00000581527.1_Missense_Mutation_p.R252Q|DLGAP1_ENST00000515196.2_Missense_Mutation_p.R252Q NM_004746.3 NP_004737.2 O14490 DLGP1_HUMAN discs, large (Drosophila) homolog-associated protein 1 252 synaptic transmission cell junction|postsynaptic density|postsynaptic membrane breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1) 56 Colorectal(8;0.0257) GTTGTTGCTCCGGGAGGCCTT 0.657000 19 35 0 0 1 0 0 EPB41L3 23136 broad.mit.edu 37 18 5398141 5398141 + Splice_Site SNP G G C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr18:5398141G>C ENST00000341928.2 - 17 2691 c.2349_splice c.e17-1 p.T784_splice EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000427684.2_Splice_Site_p.T81_splice|EPB41L3_ENST00000544123.1_Splice_Site_p.T615_splice|EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000342933.3_Splice_Site_p.T784_splice|EPB41L3_ENST00000542146.1_Splice_Site_p.T89_splice NM_012307.2 NP_036439.2 Q9Y2J2 E41L3_HUMAN erythrocyte membrane protein band 4.1-like 3 784 Spectrin--actin-binding (Potential). cortical actin cytoskeleton organization cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane actin binding|structural molecule activity breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 105 AGACTGCTTAGTCTGAGTGAA 0.433000 85 147 0 0 1 0 0 PHGDH 26227 broad.mit.edu 37 1 120277978 120277978 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr1:120277978C>T ENST00000369407.3 + 6 2109 c.602C>T c.(601-603)gCc>gTc p.A201V PHGDH_ENST00000369409.4_Missense_Mutation_p.A235V O43175 SERA_HUMAN phosphoglycerate dehydrogenase 235 brain development|L-serine biosynthetic process electron carrier activity|NAD binding|phosphoglycerate dehydrogenase activity breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2) 18 all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219) all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347) Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593) NADH(DB00157) GTGAACTGTGCCCGTGGAGGG 0.617000 4 105 0 0 1 0 0 CNOT11 55571 broad.mit.edu 37 2 101874343 101874343 + Missense_Mutation SNP G G A TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr2:101874343G>A ENST00000289382.3 + 2 768 c.605G>A c.(604-606)cGc>cAc p.R202H NM_017546.4 NP_060016.3 CCR4-NOT transcription complex, subunit 11 AAGACGCCTCGCCAGATTGCA 0.493000 23 30 0 0 1 0 0 ARHGAP27 201176 broad.mit.edu 37 17 43475409 43475409 + Missense_Mutation SNP C C T TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr17:43475409C>T ENST00000532038.1 - 9 1217 c.1082G>A c.(1081-1083)cGg>cAg p.R361Q ARHGAP27_ENST00000376922.2_Missense_Mutation_p.R242Q|ARHGAP27_ENST00000528384.1_Missense_Mutation_p.R215Q|ARHGAP27_ENST00000582826.1_5'UTR|ARHGAP27_ENST00000428638.1_Missense_Mutation_p.R583Q|ARHGAP27_ENST00000455881.1_Missense_Mutation_p.R242Q|ARHGAP27_ENST00000532891.2_Missense_Mutation_p.R561Q|ARHGAP27_ENST00000442348.1_Missense_Mutation_p.R556Q Q6ZUM4 RHG27_HUMAN Rho GTPase activating protein 27 583 positive regulation of Cdc42 GTPase activity|receptor-mediated endocytosis|signal transduction cytoplasm|membrane Rac GTPase activator activity|SH3 domain binding endometrium(4)|large_intestine(9)|lung(3)|skin(1) 17 Renal(3;0.0405) ATCTCGGCTCCGTAGCTGGAG 0.592000 25 26 0 0 1 0 0 POTEC 388468 broad.mit.edu 37 18 14513675 14513675 + Missense_Mutation SNP T T C TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr18:14513675T>C ENST00000358970.5 - 10 1518 c.1519A>G c.(1519-1521)Aaa>Gaa p.K507E NM_001137671.1 NP_001131143.1 B2RU33 POTEC_HUMAN POTE ankyrin domain family, member C 507 p.K507E(2) NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3) 52 GAATTCATTTTCTTTTCAGCC 0.284000 3 65 0 0 1 0 0 LINC00877 0 broad.mit.edu 37 3 72136648 72136648 + RNA DEL G G - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr3:72136648delG ENST00000468646.2 - 0 366 CTGACTACCAGGCCCCGGAGG 0.587 2 4 --- --- --- --- AZGP1P1 0 broad.mit.edu 37 7 99578514 99578516 + RNA DEL AGG AGG - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr7:99578514_99578516delAGG ENST00000425474.1 + 0 87 NR_036679.1 GAGGACTGGAAGGAGGTGAGGAA 0.596 9 170 --- --- --- --- FOXE1 2304 broad.mit.edu 37 9 100616701 100616706 + In_Frame_Del DEL GCCGCC GCCGCC - rs11279082 TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr9:100616701_100616706delGCCGCC ENST00000375123.3 + 1 1166_1171 c.505_510delGCCGCC c.(505-510)del p.AA177del NM_004473.3 NP_004464.2 O00358 FOXE1_HUMAN forkhead box E1 (thyroid transcription factor 2) 177 Ala-rich.|Poly-Ala. cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1) 5 Acute lymphoblastic leukemia(62;0.158) Ggctgccgcagccgccgccgccgccg 0.767 4 6 --- --- --- --- NOTCH1 4851 broad.mit.edu 37 9 139413070 139413072 + In_Frame_Del DEL AGA AGA - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr9:139413070_139413072delAGA ENST00000277541.6 - 6 1145_1147 c.1070_1072delTCT c.(1069-1074)tac>t p.FY357del NM_017617.3 NP_060087.3 P46531 NOTC1_HUMAN notch 1 357 EGF-like 9; calcium-binding (Potential). aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity p.F357delF(4) breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3) 1359 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) CACTCGCAGTAGAAGGAGGCCAC 0.655 """T, Mis, O""" TRB@ T-ALL HNSCC(8;0.001) 8 17 --- --- --- --- TRIM3 10612 broad.mit.edu 37 11 6486802 6486804 + In_Frame_Del DEL AGA AGA - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr11:6486802_6486804delAGA ENST00000525074.1 - 2 516_518 c.122_124delTCT c.(121-126)tgt>t p.FC41del TRIM3_ENST00000537602.1_In_Frame_Del_p.FC41del|TRIM3_ENST00000536344.1_Intron|TRIM3_ENST00000345851.3_In_Frame_Del_p.FC41del|TRIM3_ENST00000359518.3_In_Frame_Del_p.FC41del NM_001248006.1 NP_001234935.1 O75382 TRIM3_HUMAN tripartite motif containing 3 41 nervous system development|protein transport early endosome protein C-terminus binding|zinc ion binding breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3) 27 all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212) Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135) CACCTCTCACAGAAGGTGTGCAG 0.596 9 88 --- --- --- --- RORA 6095 broad.mit.edu 37 15 61521357 61521357 + Frame_Shift_Del DEL C C - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr15:61521357delC ENST00000335670.6 - 1 161 c.61delG c.(61-63)acfs p.D21fs NM_134261.2 NP_599023.1 P35398 RORA_HUMAN RAR-related orphan receptor A 0 Modulating. positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor nucleoplasm protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1) 21 GCGGCCGCGTCCGCGCCGCTG 0.692 2 4 --- --- --- --- WWP2 11060 broad.mit.edu 37 16 69833165 69833166 + Frame_Shift_Del DEL CT CT - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr16:69833165_69833166delCT ENST00000359154.2 + 4 408_409 c.307_308delCT c.(307-309)cfs p.L103fs WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Frame_Shift_Del_p.L103fs|WWP2_ENST00000356003.2_Frame_Shift_Del_p.L103fs|WWP2_ENST00000569174.1_Frame_Shift_Del_p.L103fs NM_001270454.1|NM_007014.4 NP_001257383.1|NP_008945.2 O00308 WWP2_HUMAN WW domain containing E3 ubiquitin protein ligase 2 103 entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus|ubiquitin ligase complex RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1) 42 ATCTGTCAACCTCTCCAACGTC 0.490 OREG0023909 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 27 47 --- --- --- --- TP53 7157 broad.mit.edu 37 17 7579319 7579323 + Frame_Shift_Del DEL GTCAC GTCAC - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr17:7579319_7579323delGTCAC ENST00000420246.2 - 4 496_500 c.364_368delGTGAC c.(364-369)tfs p.VT122fs TP53_ENST00000269305.4_Frame_Shift_Del_p.VT122fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.VT122fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.VT122fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.VT122fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.VT122fs NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 122 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. V -> L (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(8)|p.V122fs*26(5)|p.G59fs*23(3)|p.T123I(1)|p.V73fs*9(1)|p.T123fs*24(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.V122L(1)|p.P13fs*18(1)|p.S33fs*23(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) GACCGTGCAAGTCACAGACTTGGCT 0.551 111 """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) 63 11 --- --- --- --- TRIM65 201292 broad.mit.edu 37 17 73892940 73892940 + Frame_Shift_Del DEL A A - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chr17:73892940delA ENST00000269383.3 - 1 144 c.79delT c.(79-81)gcfs p.C27fs NM_001256124.1|NM_173547.3 NP_001243053.1|NP_775818.2 Q6PJ69 TRI65_HUMAN tripartite motif containing 65 27 intracellular zinc ion binding endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 12 Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154) TTGTGGCCGCAGGGCAGCGTC 0.721 2 4 --- --- --- --- DGKK 139189 broad.mit.edu 37 X 50165596 50165597 + RNA DEL AC AC - rs72026364 TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chrX:50165596_50165597delAC ENST00000376025.2 - 0 816 Q5KSL6 DGKK_HUMAN diacylglycerol kinase, kappa activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress cytoplasm|plasma membrane ATP binding|diacylglycerol kinase activity|metal ion binding central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 Ovarian(276;0.236) TAAAAGGTAAacacacacacac 0.411 2 4 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76937611 76937615 + Frame_Shift_Del DEL CTTTT CTTTT - TCGA-QH-A6X3-01A-21D-A32B-08 TCGA-QH-A6X3-10B-01D-A329-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec60d9fe-8eeb-4461-b98a-1a1d913e86cb 808dfeb8-ac5b-44c3-8007-fd214fda4ab2 g.chrX:76937611_76937615delCTTTT ENST00000373344.5 - 9 3347_3351 c.3133_3137delAAAAG c.(3133-3138)tfs p.KS1045fs ATRX_ENST00000395603.3_Frame_Shift_Del_p.KS1007fs|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 1045 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) TATTTTTTTACTTTTCTTTTCTCCA 0.337 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 35 19 --- --- --- ---