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 ARHGAP4 393 broad.mit.edu 37 X 153175625 153175625 + Splice_Site SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:153175625C>T ENST00000370028.3 - 18 2333 c.2276_splice c.e18+1 p.G759_splice ARHGAP4_ENST00000370016.1_Splice_Site_p.G698_splice|ARHGAP4_ENST00000467421.1_5'UTR|ARHGAP4_ENST00000350060.5_Splice_Site_p.G719_splice|ARHGAP4_ENST00000393721.1_Splice_Site_p.G541_splice|ARHGAP4_ENST00000537206.1_Splice_Site_p.G696_splice NM_001164741.1 NP_001158213.1 P98171 RHG04_HUMAN Rho GTPase activating protein 4 719 SH3. apoptosis|cytoskeleton organization|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|Rho protein signal transduction cytosol|focal adhesion|nucleus Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1) 14 all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05) AAGGGTGTACCCCAGGCAGCT 0.677000 26 26 0 0 1 0 0 HLA-DQA1 3117 broad.mit.edu 37 6 32609250 32609250 + Silent SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:32609250G>A ENST00000343139.5 + 2 348 c.246G>A c.(244-246)ccG>ccA p.P82P HLA-DQA1_ENST00000395363.1_Silent_p.P82P|HLA-DQA1_ENST00000374949.2_Silent_p.P82P NM_002122.3 NP_002113.2 P01909 DQA1_HUMAN major histocompatibility complex, class II, DQ alpha 1 81 Alpha-1. antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex MHC class II receptor activity NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1) 6 GTTTTGACCCGCAGGGTGCAC 0.502000 20 13 0 0 1 0 0 PHOX2A 401 broad.mit.edu 37 11 71954958 71954958 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr11:71954958C>T ENST00000298231.5 - 1 262 c.91G>A c.(91-93)Ggc>Agc p.G31S PHOX2A_ENST00000544057.1_Intron NM_005169.3 NP_005160.2 O14813 PHX2A_HUMAN paired-like homeobox 2a 31 noradrenergic neuron differentiation|positive regulation of transcription from RNA polymerase II promoter nuclear chromatin RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2) 5 TGGAAGCCGCCGGGCTGGCTG 0.716000 4 11 0 0 1 0 0 DENND2C 163259 broad.mit.edu 37 1 115143531 115143531 + Silent SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr1:115143531G>A ENST00000393274.1 - 14 2491 c.1866C>T c.(1864-1866)taC>taT p.Y622Y DENND2C_ENST00000393277.1_Silent_p.Y622Y|DENND2C_ENST00000393276.3_Silent_p.Y565Y|DENND2C_ENST00000481894.1_5'UTR NM_001256404.1 NP_001243333.1 Q68D51 DEN2C_HUMAN DENN/MADD domain containing 2C 622 DENN. NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3) 37 all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211) all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|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) GCATGAATGGGTAAACAAGGG 0.418000 24 43 0 0 1 0 0 ZAN 7455 broad.mit.edu 37 7 100350456 100350456 + RNA SNP C C A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:100350456C>A ENST00000542585.1 + 0 2876 ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000348028.3_RNA NM_003386.1 NP_003377.1 Q9Y493 ZAN_HUMAN zonadhesin (gene/pseudogene) binding of sperm to zona pellucida|cell-cell adhesion integral to membrane|plasma membrane p.P910T(2) NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3) 139 Lung NSC(181;0.041)|all_lung(186;0.0581) STAD - Stomach adenocarcinoma(171;0.19) CACCATCTCCCCAGAAAAACC 0.498000 5 217 0.184627 0.184627 1 1 0 ACSL4 2182 broad.mit.edu 37 X 108911498 108911498 + Silent SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:108911498G>A ENST00000340800.2 - 12 1774 c.1270C>T c.(1270-1272)Ctg>Ttg p.L424L ACSL4_ENST00000348502.6_Silent_p.L383L|ACSL4_ENST00000469796.2_Silent_p.L424L NM_022977.2 NP_075266.1 O60488 ACSL4_HUMAN acyl-CoA synthetase long-chain family member 4 424 fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane ATP binding|long-chain fatty acid-CoA ligase activity breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(2) 22 Icosapent(DB00159)|Troglitazone(DB00197) TTTTTAAACAGTAACCTTAAT 0.438000 35 36 0 0 1 0 0 CASP4 837 broad.mit.edu 37 11 104822679 104822679 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr11:104822679G>A ENST00000444739.2 - 3 1226 c.316C>T c.(316-318)Ctc>Ttc p.L106F CASP4_ENST00000393150.3_Missense_Mutation_p.L50F|CASP4_ENST00000531333.1_Intron NM_001225.3 NP_001216.1 P49662 CASP4_HUMAN caspase 4, apoptosis-related cysteine peptidase 106 apoptosis|induction of apoptosis|proteolysis intracellular cysteine-type endopeptidase activity|protein binding central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2) 23 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357) CAAAGCTTGAGGGCATCTGTA 0.413000 18 35 0 0 1 0 0 MED12 9968 broad.mit.edu 37 X 70338671 70338671 + Missense_Mutation SNP G G T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:70338671G>T ENST00000333646.6 + 1 266 c.67G>T c.(67-69)Gat>Tat p.D23Y MED12_ENST00000374102.1_Missense_Mutation_p.D23Y|MED12_ENST00000374080.3_Missense_Mutation_p.D23Y NM_005120.2 NP_005111.2 Q93074 MED12_HUMAN mediator complex subunit 12 23 androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding p.D23Y(2) breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3) 420 Renal(35;0.156) GGGGCCTCCCGATGTTTACCC 0.677000 """M, S""" uterine leiomyoma Opitz-Kaveggia Syndrome 16 24 0.000566183 0.000585485 1 1 0 HTR5A 3361 broad.mit.edu 37 7 154863078 154863078 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:154863078G>A ENST00000287907.2 + 1 1045 c.469G>A c.(469-471)Gtc>Atc p.V157I AC093726.4_ENST00000543018.1_De_novo_Start_InFrame|AC093726.4_ENST00000493904.1_5'UTR|AC093726.4_ENST00000395731.2_De_novo_Start_InFrame NM_024012.3 NP_076917.1 P47898 5HT5A_HUMAN 5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled 157 integral to plasma membrane serotonin receptor activity NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1) 48 all_neural(206;0.119) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.0238) UCEC - Uterine corpus endometrioid carcinoma (81;0.171) CCGCAAGTGCGTCTCCAACGT 0.622000 35 67 0 0 1 0 0 ZNF470 388566 broad.mit.edu 37 19 57089191 57089191 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr19:57089191G>A ENST00000330619.8 + 6 2080 c.1394G>A c.(1393-1395)cGt>cAt p.R465H ZNF470_ENST00000391709.3_Missense_Mutation_p.R465H|ZNF470_ENST00000601902.1_Intron NM_001001668.3 NP_001001668.3 Q6ECI4 ZN470_HUMAN zinc finger protein 470 465 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 41 Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157) GBM - Glioblastoma multiforme(193;0.0294) TTCAGCCATCGTGGGTCTCTT 0.443000 34 63 0 0 1 0 0 DMP1 1758 broad.mit.edu 37 4 88584263 88584263 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr4:88584263G>A ENST00000339673.6 + 6 1432 c.1333G>A c.(1333-1335)Gag>Aag p.E445K RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Missense_Mutation_p.E429K NM_004407.3 NP_004398.1 Q13316 DMP1_HUMAN dentin matrix acidic phosphoprotein 1 445 biomineral tissue development|ossification cytoplasm|nucleus|proteinaceous extracellular matrix calcium ion binding|integrin binding breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1) 32 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227) OV - Ovarian serous cystadenocarcinoma(123;0.000516) GAGTCAGAGCGAGGAAAGCCA 0.542000 70 17 0 0 1 0 0 ALPK2 115701 broad.mit.edu 37 18 56204502 56204502 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr18:56204502C>T ENST00000361673.3 - 5 3130 c.2917G>A c.(2917-2919)Gcc>Acc p.A973T RP11-1151B14.4_ENST00000591360.1_RNA NM_052947.3 NP_443179.3 Q86TB3 ALPK2_HUMAN alpha-kinase 2 973 ATP binding|protein serine/threonine kinase activity NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2) 84 GCTGGTGTGGCTGTGGTGTCT 0.458000 4 54 0 0 1 0 0 ZNF814 730051 broad.mit.edu 37 19 58385546 58385546 + Missense_Mutation SNP G G T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr19:58385546G>T ENST00000435989.2 - 3 1446 c.1212C>A c.(1210-1212)gaC>gaA p.D404E ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron NM_001144989.1 NP_001138461.1 B7Z6K7 ZN814_HUMAN zinc finger protein 814 404 regulation of transcription, DNA-dependent intracellular nucleic acid binding|zinc ion binding p.D404E(10) NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3) 25 AATGTTTTTTGTCAGTGTGAA 0.393000 4 21 0.014758 0.0150896 1 1 0 ATP10A 57194 broad.mit.edu 37 15 25928532 25928532 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr15:25928532C>T ENST00000356865.6 - 17 3504 c.3393G>A c.(3391-3393)tcG>tcA p.S1131S NM_024490.3 NP_077816.1 O60312 AT10A_HUMAN ATPase, class V, type 10A 1131 ATP biosynthetic process|regulation of cell shape integral to membrane|plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2) 103 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244) GGGGAAGTGACGAGAAGAGCA 0.527000 4 63 0 0 1 0 0 DGKH 160851 broad.mit.edu 37 13 42763366 42763366 + Silent SNP C C G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr13:42763366C>G ENST00000379274.2 + 15 1854 c.1425C>G c.(1423-1425)gcC>gcG p.A475A DGKH_ENST00000261491.4_Silent_p.A611A|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000536612.1_Silent_p.A475A|DGKH_ENST00000540693.1_Silent_p.A611A|DGKH_ENST00000538674.1_Silent_p.A366A|DGKH_ENST00000337343.4_Silent_p.A611A Q86XP1 DGKH_HUMAN diacylglycerol kinase, eta 611 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization endosome|plasma membrane ATP binding|diacylglycerol kinase activity|metal ion binding breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 43 Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114) OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109) CCCAGAAAGCCGTCAAACCAA 0.458000 22 59 0 0 1 0 0 NOS1 4842 broad.mit.edu 37 12 117723945 117723945 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr12:117723945C>T ENST00000317775.6 - 6 1939 c.1254G>A c.(1252-1254)tcG>tcA p.S418S NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000338101.4_Silent_p.S418S NM_000620.4|NM_001204218.1 NP_000611.1|NP_001191147.1 P29475 NOS1_HUMAN nitric oxide synthase 1 (neuronal) 418 multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 117 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) BRCA - Breast invasive adenocarcinoma(302;0.0561) L-Citrulline(DB00155) CCACACAGCGCGAGGCATTCC 0.562000 31 55 0 0 1 0 0 MAP1A 4130 broad.mit.edu 37 15 43820144 43820144 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr15:43820144G>A ENST00000382031.1 + 5 7218 c.7187G>A c.(7186-7188)cGa>cAa p.R2396Q MAP1A_ENST00000300231.5_Missense_Mutation_p.R2158Q|MAP1A_ENST00000399453.1_Missense_Mutation_p.R2158Q P78559 MAP1A_HUMAN microtubule-associated protein 1A 2158 cytoplasm|microtubule|microtubule associated complex protein binding|structural molecule activity breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 66 all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) GBM - Glioblastoma multiforme(94;3.05e-06) Estramustine(DB01196) GGGCCTGCCCGACCCAGTCTG 0.617000 89 87 0 0 1 0 0 FAM161A 84140 broad.mit.edu 37 2 62067002 62067002 + Silent SNP A A G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:62067002A>G ENST00000404929.1 - 3 1148 c.1137T>C c.(1135-1137)taT>taC p.Y379Y FAM161A_ENST00000405894.3_Silent_p.Y379Y NM_001201543.1 NP_001188472.1 Q3B820 F161A_HUMAN family with sequence similarity 161, member A 379 response to stimulus|visual perception centrosome breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 25 TAAGGTTTCGATAGAGCTCTT 0.433000 51 42 0 0 1 0 0 C2 717 broad.mit.edu 37 6 31913052 31913052 + Missense_Mutation SNP G G C rs147553278 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:31913052G>C ENST00000299367.5 + 18 2453 c.2177G>C c.(2176-2178)cGa>cCa p.R726P CFB_ENST00000556679.1_Intron|C2_ENST00000442278.2_Missense_Mutation_p.R594P|CFB_ENST00000456570.1_Intron|C2_ENST00000468407.1_Intron|C2_ENST00000452323.2_Missense_Mutation_p.R512P|CFB_ENST00000477310.1_Intron|C2_ENST00000469372.1_Missense_Mutation_p.R480P NM_000063.4 NP_000054.2 complement component 2 haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2) 27 Ovarian(999;0.00965) LUAD - Lung adenocarcinoma(999;0.247) CCGCCGCCACGAGACTTTCAC 0.587000 26 61 0 0 1 0 0 RBM26 64062 broad.mit.edu 37 13 79911276 79911276 + Missense_Mutation SNP A A C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr13:79911276A>C ENST00000438737.2 - 19 3134 c.2694T>G c.(2692-2694)ttT>ttG p.F898L RBM26_ENST00000438724.1_Missense_Mutation_p.F874L|RBM26_ENST00000267229.7_Missense_Mutation_p.F871L Q5T8P6 RBM26_HUMAN RNA binding motif protein 26 898 RRM 2. mRNA processing nucleotide binding|protein binding|RNA binding|zinc ion binding NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1) 33 Acute lymphoblastic leukemia(28;0.0279) GBM - Glioblastoma multiforme(99;0.0188) CGCTCTCCGTAAATGCAGAAA 0.507000 14 35 0 0 1 0 0 GRM3 0 broad.mit.edu 37 7 86468552 86468552 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:86468552C>T ENST00000361669.2 + 4 2821 c.1722C>T c.(1720-1722)gaC>gaT p.D574D GRM3_ENST00000394720.2_Intron|GRM3_ENST00000546348.1_Silent_p.D166D|GRM3_ENST00000536043.1_Silent_p.D446D|GRM3_ENST00000439827.1_Intron NM_000840.2 NP_000831.2 Q14832 GRM3_HUMAN glutamate receptor, metabotropic 3 574 synaptic transmission integral to plasma membrane NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5) 109 Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142) Acamprosate(DB00659)|Nicotine(DB00184) GGTGGGAAGACGCCTGGGCCA 0.498000 36 57 0 0 1 0 0 ZFP57 346171 broad.mit.edu 37 6 29641083 29641083 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:29641083G>A ENST00000376883.1 - 6 1156 c.745C>T c.(745-747)Cgg>Tgg p.R249W ZFP57_ENST00000376881.3_Missense_Mutation_p.R249W|ZFP57_ENST00000488757.1_Missense_Mutation_p.R269W Q9NU63 ZFP57_HUMAN ZFP57 zinc finger protein 185 DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent DNA binding|zinc ion binding NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(16)|ovary(4)|skin(4)|urinary_tract(5) 44 GACTGGTCCCGGAAGCTCTTC 0.557000 40 83 0 0 1 0 0 FIGN 55137 broad.mit.edu 37 2 164467497 164467497 + Missense_Mutation SNP G G T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:164467497G>T ENST00000333129.3 - 3 1159 c.845C>A c.(844-846)cCc>cAc p.P282H FIGN_ENST00000409634.1_Intron NM_018086.2 NP_060556.2 Q5HY92 FIGN_HUMAN fidgetin 282 Pro-rich. nuclear matrix ATP binding|nucleoside-triphosphatase activity breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1) 47 TAGGGGGGTGGGAGCAGGAAT 0.602000 32 38 2.80507e-11 3.07544e-11 1 1 0 TBC1D4 9882 broad.mit.edu 37 13 75884163 75884163 + Silent SNP T T C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr13:75884163T>C ENST00000377636.3 - 14 2854 c.2508A>G c.(2506-2508)tcA>tcG p.S836S TBC1D4_ENST00000431480.2_Silent_p.S828S|TBC1D4_ENST00000425511.1_Silent_p.S53S|TBC1D4_ENST00000377625.2_Silent_p.S773S NM_014832.2 NP_055647.2 O60343 TBCD4_HUMAN TBC1 domain family, member 4 836 cytoplasm Rab GTPase activator activity breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 50 Prostate(6;0.014)|Breast(118;0.0982) GBM - Glioblastoma multiforme(99;0.0116) TCAGTTCTTTTGATTTCTTTC 0.433000 23 25 0 0 1 0 0 NTRK1 4914 broad.mit.edu 37 1 156841545 156841545 + Missense_Mutation SNP C C A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr1:156841545C>A ENST00000368196.3 + 7 968 c.848C>A c.(847-849)tCc>tAc p.S283Y NTRK1_ENST00000392302.2_Missense_Mutation_p.S253Y|NTRK1_ENST00000524377.1_Missense_Mutation_p.S283Y|NTRK1_ENST00000358660.3_Missense_Mutation_p.S283Y NM_001012331.1 NP_001012331.1 P04629 NTRK1_HUMAN neurotrophic tyrosine kinase, receptor, type 1 283 Ig-like C2-type 1. activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|integral to plasma membrane ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 74 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) Imatinib(DB00619) GTCAACGTCTCCTGTGAGTCT 0.582000 T """TPM3, TPR, TFG""" papillary thyroid TSP Lung(10;0.080) 9 72 3.07112e-06 3.24967e-06 1 1 0 FAM124A 220108 broad.mit.edu 37 13 51825708 51825708 + Missense_Mutation SNP C C A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr13:51825708C>A ENST00000322475.8 + 3 340 c.205C>A c.(205-207)Ctg>Atg p.L69M FAM124A_ENST00000280057.6_Missense_Mutation_p.L105M NM_001242312.1 NP_001229241.1 Q86V42 F124A_HUMAN family with sequence similarity 124A 69 breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1) 26 Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236) GBM - Glioblastoma multiforme(99;4.25e-07) CGACAACGTCCTGGCGTGGAT 0.692000 10 33 7.48243e-07 8.0106e-07 1 1 0 LRP2 4036 broad.mit.edu 37 2 169995843 169995843 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:169995843C>T ENST00000263816.3 - 74 13591 c.13306G>A c.(13306-13308)Gta>Ata p.V4436I NM_004525.2 NP_004516.2 P98164 LRP2_HUMAN low density lipoprotein receptor-related protein 2 4436 hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process coated pit|integral to membrane|lysosome calcium ion binding|receptor activity|SH3 domain binding biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13) 315 STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101) Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013) GCTCCAATTACGACGATCAAG 0.507000 6 73 0 0 1 0 0 TPTE2P6 0 broad.mit.edu 37 13 25168501 25168501 + RNA SNP G G A rs4770716 by1000genomes TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr13:25168501G>A ENST00000453498.1 + 0 1173 TTTTCTCTTCGGTGAGTAATC 0.388000 6 21 0 0 1 0 0 TDRD1 56165 broad.mit.edu 37 10 115981160 115981160 + Missense_Mutation SNP G G T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr10:115981160G>T ENST00000251864.2 + 20 2968 c.2815G>T c.(2815-2817)Gat>Tat p.D939Y TDRD1_ENST00000369281.2_Missense_Mutation_p.D825Y|TDRD1_ENST00000422662.1_Missense_Mutation_p.D543Y|TDRD1_ENST00000369280.1_Missense_Mutation_p.D939Y|TDRD1_ENST00000369282.1_Missense_Mutation_p.D939Y NM_198795.1 NP_942090.1 Q9BXT4 TDRD1_HUMAN tudor domain containing 1 939 DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis pi-body nucleic acid binding|protein binding|zinc ion binding breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5) 48 Colorectal(252;0.172)|Breast(234;0.188) Epithelial(162;0.0343)|all cancers(201;0.0754) ATTGCCAGTGGATAAAACTAT 0.363000 23 24 7.41877e-09 8.037e-09 1 1 0 OR2B11 127623 broad.mit.edu 37 1 247614475 247614475 + Silent SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr1:247614475G>A ENST00000318749.6 - 1 833 c.810C>T c.(808-810)taC>taT p.Y270Y NM_001004492.1 NP_001004492.1 Q5JQS5 OR2BB_HUMAN olfactory receptor, family 2, subfamily B, member 11 270 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1) 60 all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.241) OV - Ovarian serous cystadenocarcinoma(106;0.0188) GCTCTTGGGAGTAGCTGGAAG 0.493000 15 176 0 0 1 0 0 C21orf2 755 broad.mit.edu 37 21 45753071 45753071 + Missense_Mutation SNP C C T rs140451304 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr21:45753071C>T ENST00000339818.4 - 4 425 c.218G>A c.(217-219)cGc>cAc p.R73H C21orf2_ENST00000397956.3_Missense_Mutation_p.R73H|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Missense_Mutation_p.R73H|AP001062.7_ENST00000448927.1_RNA NM_004928.2 NP_004919.1 O43822 CU002_HUMAN chromosome 21 open reading frame 2 73 endometrium(2) 2 Colorectal(79;0.0806) GCTGGGGATGCGGTTCCTCCG 0.677000 10 19 0 0 1 0 0 ABCA12 26154 broad.mit.edu 37 2 215815735 215815735 + Missense_Mutation SNP C C G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:215815735C>G ENST00000272895.7 - 45 6939 c.6720G>C c.(6718-6720)gaG>gaC p.E2240D AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.E1922D NM_173076.2 NP_775099.2 Q86UK0 ABCAC_HUMAN ATP-binding cassette, sub-family A (ABC1), member 12 2240 cellular homeostasis|lipid transport integral to membrane ATP binding|ATPase activity NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 139 Renal(323;0.127) Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011) CTCTTAATCTCTCAGCCCGCA 0.383000 81 93 0 0 1 0 0 MRPL44 65080 broad.mit.edu 37 2 224831613 224831613 + Silent SNP A A G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:224831613A>G ENST00000258383.3 + 4 930 c.861A>G c.(859-861)gaA>gaG p.E287E AC073641.2_ENST00000425192.1_RNA NM_022915.3 NP_075066.1 Q9H9J2 RM44_HUMAN mitochondrial ribosomal protein L44 287 DRBM. RNA processing mitochondrion|ribosome double-stranded RNA binding|protein binding|ribonuclease III activity breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1) 13 all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189) Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008) GACCTGGGGAAACAGTATTGG 0.403000 40 105 0 0 1 0 0 CD300C 10871 broad.mit.edu 37 17 72541016 72541016 + Silent SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr17:72541016G>A ENST00000330793.1 - 2 492 c.132C>T c.(130-132)cgC>cgT p.R44R NM_006678.3 NP_006669.1 Q08708 CLM6_HUMAN CD300c molecule 44 Ig-like V-type. cellular defense response integral to plasma membrane transmembrane receptor activity endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1) 21 CCTTCTCATAGCGACACTGCA 0.532000 29 34 0 0 1 0 0 SCNN1A 0 broad.mit.edu 37 12 6472683 6472683 + Missense_Mutation SNP G G C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr12:6472683G>C ENST00000358945.3 - 2 1050 c.610C>G c.(610-612)Cgt>Ggt p.R204G SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000538979.1_Intron|SCNN1A_ENST00000396966.2_Missense_Mutation_p.R204G|SCNN1A_ENST00000228916.2_Missense_Mutation_p.R204G|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R227G|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R263G P37088 SCNNA_HUMAN sodium channel, non-voltage-gated 1 alpha subunit 204 excretion|response to stimulus|sensory perception of taste apical plasma membrane WW domain binding central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1) 27 Amiloride(DB00594)|Triamterene(DB00384) GCCACGCTACGGGCTCGACGG 0.741000 18 10 0 0 1 0 0 JAM3 83700 broad.mit.edu 37 11 134009765 134009765 + Silent SNP A A G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr11:134009765A>G ENST00000299106.4 + 2 255 c.96A>G c.(94-96)gtA>gtG p.V32V JAM3_ENST00000441717.3_Silent_p.V32V|JAM3_ENST00000529443.2_Silent_p.V77V|JAM3_ENST00000524969.1_3'UTR Q9BX67 JAM3_HUMAN junctional adhesion molecule 3 32 angiogenesis|blood coagulation|regulation of neutrophil chemotaxis cell-cell contact zone|desmosome|extracellular space|integral to membrane integrin binding breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1) 10 all_hematologic(175;0.127) all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566) Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245) TAGGGGCTGTAAATCTCAAAT 0.438000 OREG0021547 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 44 31 0 0 1 0 0 RIMS2 9699 broad.mit.edu 37 8 104955062 104955062 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr8:104955062C>T ENST00000507740.1 + 11 2221 c.1985C>T c.(1984-1986)aCg>aTg p.T662M RIMS2_ENST00000406091.3_Missense_Mutation_p.T870M|RIMS2_ENST00000436393.2_Missense_Mutation_p.T648M|RIMS2_ENST00000262231.10_Missense_Mutation_p.T709M NM_014677.4 NP_055492.3 Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 932 intracellular protein transport cell junction|presynaptic membrane metal ion binding|Rab GTPase binding NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1) 144 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) AAACTTCAGACGCATGATGTC 0.418000 HNSCC(12;0.0054) 15 77 0 0 1 0 0 DSP 1832 broad.mit.edu 37 6 7580595 7580595 + Missense_Mutation SNP A A G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:7580595A>G ENST00000379802.3 + 23 4513 c.4172A>G c.(4171-4173)tAc>tGc p.Y1391C DSP_ENST00000418664.2_Intron NM_004415.2 NP_004406.2 P15924 DESP_HUMAN desmoplakin 1391 Central fibrous rod domain. cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking cornified envelope|cytoplasm|desmosome protein binding, bridging|structural constituent of cytoskeleton biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5) 101 Ovarian(93;0.0584) all_hematologic(90;0.236) OV - Ovarian serous cystadenocarcinoma(45;0.000508) ACCAGTGGCTACCGGGCTCAG 0.463000 46 79 0 0 1 0 0 OCEL1 79629 broad.mit.edu 37 19 17337954 17337954 + Missense_Mutation SNP G G C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr19:17337954G>C ENST00000215061.4 + 3 442 c.398G>C c.(397-399)gGa>gCa p.G133A OCEL1_ENST00000597836.1_Missense_Mutation_p.G77A|OCEL1_ENST00000601529.1_Missense_Mutation_p.G133A|OCEL1_ENST00000601576.1_3'UTR NM_024578.1 NP_078854.1 Q9H607 OCEL1_HUMAN occludin/ELL domain containing 1 133 central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2) 7 AAGCCTATTGGAGCCATCCCT 0.592000 12 142 0 0 1 0 0 EPG5 57724 broad.mit.edu 37 18 43526694 43526694 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr18:43526694G>A ENST00000282041.5 - 7 1646 c.1612C>T c.(1612-1614)Cgg>Tgg p.R538W NM_020964.2 NP_066015.2 Q9HCE0 EPG5_HUMAN ectopic P-granules autophagy protein 5 homolog (C. elegans) 538 autophagy NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 95 GATGGCTTCCGCTCGCTGGGC 0.478000 16 41 0 0 1 0 0 DMD 1756 broad.mit.edu 37 X 31525450 31525450 + Missense_Mutation SNP C C G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:31525450C>G ENST00000357033.4 - 56 8544 c.8338G>C c.(8338-8340)Gat>Cat p.D2780H DMD_ENST00000378707.3_Missense_Mutation_p.D320H|DMD_ENST00000474231.1_Missense_Mutation_p.D320H|DMD_ENST00000378677.2_Missense_Mutation_p.D2776H|DMD_ENST00000343523.2_Missense_Mutation_p.D320H|DMD_ENST00000445312.1_5'UTR|DMD_ENST00000541735.1_Missense_Mutation_p.D320H|DMD_ENST00000359836.1_Missense_Mutation_p.D320H NM_000109.3|NM_004006.2|NM_004007.2|NM_004011.3|NM_004012.3|NM_004014.2 NP_000100.2|NP_003997.1|NP_003998.1|NP_004002.2|NP_004003.1|NP_004005.1 P11532 DMD_HUMAN dystrophin 2780 muscle filament sliding|peptide biosynthetic process cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2) 77 all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203) TTCATGTTATCCAAACGTCTT 0.413000 20 27 0 0 1 0 0 LINC00264 0 broad.mit.edu 37 10 26880338 26880338 + RNA SNP G G C rs3118888 by1000genomes TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr10:26880338G>C ENST00000412114.1 + 0 573 NR_026793.1 GCTGAAACATGGAAGGTAAAA 0.483000 5 68 0 0 1 0 0 TP53 7157 broad.mit.edu 37 17 7577538 7577538 + Missense_Mutation SNP C C T rs11540652 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr17:7577538C>T ENST00000420246.2 - 7 875 c.743G>A c.(742-744)cGg>cAg p.R248Q TP53_ENST00000269305.4_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 248 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain. NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652).|R -> W (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.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(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) GATGGGCCTCCGGTTCATGCC 0.572000 R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 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) 45 8 0 0 1 0 0 SRRM2 23524 broad.mit.edu 37 16 2816009 2816009 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr16:2816009G>A ENST00000301740.8 + 11 6029 c.5480G>A c.(5479-5481)cGg>cAg p.R1827Q NM_016333.3 NP_057417.3 Q9UQ35 SRRM2_HUMAN serine/arginine repetitive matrix 2 1827 Arg-rich.|Ser-rich. Cajal body|catalytic step 2 spliceosome|nuclear speck C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7) 105 TCACCTGCCCGGCAGGAAAGT 0.652000 10 45 0 0 1 0 0 ARHGAP31 57514 broad.mit.edu 37 3 119013766 119013766 + Silent SNP T T A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr3:119013766T>A ENST00000264245.4 + 1 547 c.15T>A c.(13-15)ggT>ggA p.G5G NM_020754.2 NP_065805.2 Q2M1Z3 RHG31_HUMAN Rho GTPase activating protein 31 5 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol|focal adhesion|lamellipodium GTPase activator activity breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 67 AGAACAAGGGTGCTAAGCAGA 0.587000 9 80 0 0 1 0 0 ESX1 80712 broad.mit.edu 37 X 103497474 103497474 + Missense_Mutation SNP T T A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:103497474T>A ENST00000372588.4 - 3 625 c.542A>T c.(541-543)gAc>gTc p.D181V NM_153448.3 NP_703149.1 Q8N693 ESX1_HUMAN ESX homeobox 1 181 negative regulation of transcription, DNA-dependent|regulation of cell cycle cytoplasm|nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2) 27 CTGCACTCTGTCTTCAGTCAA 0.393000 64 136 0 0 1 0 0 TREX2 11219 broad.mit.edu 37 X 152713287 152713287 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:152713287C>T ENST00000334497.2 - 10 1155 c.14G>A c.(13-15)gGa>gAa p.G5E HAUS7_ENST00000370219.3_3'UTR|TREX2_ENST00000402951.1_Missense_Mutation_p.G5E|HAUS7_ENST00000370211.4_3'UTR|HAUS7_ENST00000421080.2_3'UTR|TREX2_ENST00000370232.1_Missense_Mutation_p.G5E|TREX2_ENST00000393862.2_5'UTR|HAUS7_ENST00000484394.1_5'UTR|TREX2_ENST00000330912.2_5'UTR|TREX2_ENST00000414588.1_5'UTR|TREX2_ENST00000338525.2_5'UTR Q9BQ50 TREX2_HUMAN three prime repair exonuclease 2 5 DNA repair nucleus 3'-5'-exodeoxyribonuclease activity|exodeoxyribonuclease III activity|nucleic acid binding endometrium(4)|large_intestine(2)|lung(3)|ovary(2) 11 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) GAGAGGGCTTCCTGCCCGCCC 0.537000 Editing and processing nucleases 111 249 0 0 1 0 0 GTF2IRD2P1 0 broad.mit.edu 37 7 72657505 72657505 + RNA SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:72657505G>A ENST00000425256.1 - 0 2406 NR_002164.1 ccaccttgtcgtatttcgtct 0.512000 13 159 0 0 1 0 0 KIAA1279 26128 broad.mit.edu 37 10 70748846 70748846 + Silent SNP C C G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr10:70748846C>G ENST00000361983.4 + 1 360 c.258C>G c.(256-258)ccC>ccG p.P86P NM_015634.3 NP_056449.1 Q96EK5 KBP_HUMAN KIAA1279 86 cell differentiation|mitochondrial transport|nervous system development mitochondrion kinesin binding breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1) 14 CCGAGGGGCCCGTCGCCCAGC 0.721000 4 65 0 0 1 0 0 MAGEB2 4113 broad.mit.edu 37 X 30236752 30236752 + Nonsense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:30236752C>T ENST00000378988.4 + 2 156 c.55C>T c.(55-57)Cga>Tga p.R19* NM_002364.4 NP_002355.2 O15479 MAGB2_HUMAN melanoma antigen family B, 2 19 protein binding breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1) 23 CCGCAAGGCCCGAGATGAGAC 0.547000 18 26 0 0 1 0 0 PCDH8 5100 broad.mit.edu 37 13 53422054 53422054 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr13:53422054C>T ENST00000377942.3 - 1 721 c.518G>A c.(517-519)cGc>cAc p.R173H PCDH8_ENST00000338862.4_Missense_Mutation_p.R173H NM_002590.3 NP_002581.2 O95206 PCDH8_HUMAN protocadherin 8 173 Cadherin 2. cell-cell signaling|homophilic cell adhesion cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane calcium ion binding breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1) 36 Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;2.19e-08) CTCGGCCAGGCGCACGGTCTG 0.716000 6 11 0 0 1 0 0 RRN3P2 0 broad.mit.edu 37 16 29110458 29110458 + RNA SNP T T C rs151074589 by1000genomes TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr16:29110458T>C ENST00000564580.1 + 0 1131 p.W375R(25) GAATTTTGAGTGGATAGTGAT 0.328000 4 45 0 0 1 0 0 PHF1 5252 broad.mit.edu 37 6 33383699 33383699 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:33383699C>T ENST00000374516.3 + 15 1799 c.1528C>T c.(1528-1530)Cgc>Tgc p.R510C PHF1_ENST00000374512.3_3'UTR NM_024165.2 NP_077084.1 O43189 PHF1_HUMAN PHD finger protein 1 510 chromatin modification nucleus nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 19 Ovarian(999;0.0443) TCTTCCTAGACGCTCAGCACC 0.592000 48 92 0 0 1 0 0 VPS13B 157680 broad.mit.edu 37 8 100865978 100865978 + Missense_Mutation SNP T T G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr8:100865978T>G ENST00000358544.2 + 56 10547 c.10436T>G c.(10435-10437)aTt>aGt p.I3479S VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.I3454S NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) 3479 protein transport NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) GCAGAACCCATTCAGTGTTCC 0.418000 241 33 0 0 1 0 0 UGGT1 56886 broad.mit.edu 37 2 128938646 128938646 + Splice_Site SNP G G C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:128938646G>C ENST00000375990.3 + 36 4414 c.4011_splice c.e36+1 p.Q1337_splice UGGT1_ENST00000259253.6_Splice_Site_p.Q1361_splice Q9NYU2 UGGG1_HUMAN UDP-glucose glycoprotein glucosyltransferase 1 1361 Glucosyltransferase (By similarity). 'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine endoplasmic reticulum lumen|ER-Golgi intermediate compartment UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 63 ATGCTGATCAGGTAGGCCCTT 0.378000 29 43 0 0 1 0 0 RPLP0P2 0 broad.mit.edu 37 11 61405179 61405179 + RNA SNP A A T rs143569110 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr11:61405179A>T ENST00000496593.1 + 0 1783 NR_002775.2 ttacttctttaaaaaaaaaaa 0.299000 4 7 0 0 1 0 0 ZNF571 51276 broad.mit.edu 37 19 38056900 38056900 + Missense_Mutation SNP A A G TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr19:38056900A>G ENST00000328550.2 - 4 529 c.430T>C c.(430-432)Tgc>Cgc p.C144R ZNF571-AS1_ENST00000586013.1_RNA|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF571_ENST00000451802.2_Missense_Mutation_p.C144R|ZNF540_ENST00000592533.1_Intron|ZNF571_ENST00000590751.1_Intron|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571_ENST00000358744.3_Missense_Mutation_p.C144R|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.C144R|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000589750.1_RNA Q7Z3V5 ZN571_HUMAN zinc finger protein 571 144 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1) 25 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) CCTTGTCTGCATTCCTTACAT 0.353000 6 54 0 0 1 0 0 OBSL1 23363 broad.mit.edu 37 2 220421348 220421348 + Silent SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:220421348G>A ENST00000404537.1 - 13 4220 c.4164C>T c.(4162-4164)gcC>gcT p.A1388A OBSL1_ENST00000265317.5_Silent_p.A287A|OBSL1_ENST00000373876.1_Silent_p.A1296A|OBSL1_ENST00000265318.4_Silent_p.A1296A|OBSL1_ENST00000603926.1_Silent_p.A1388A NM_015311.2 NP_056126.1 O75147 OBSL1_HUMAN obscurin-like 1 1388 Ig-like 12. cardiac myofibril assembly intercalated disc|M band|perinuclear region of cytoplasm|Z disc cytoskeletal adaptor activity Renal(207;0.0376) Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834) AGGTGACATCGGCATCTGGTG 0.617000 24 56 0 0 1 0 0 MAGEA12 4111 broad.mit.edu 37 X 151899865 151899865 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:151899865C>T ENST00000393900.3 - 3 1289 c.936G>A c.(934-936)ggG>ggA p.G312G CSAG4_ENST00000361201.4_RNA|MAGEA12_ENST00000393869.3_Silent_p.G312G|MAGEA12_ENST00000357916.4_Silent_p.G312G NM_001166386.1 NP_001159858.1 P43365 MAGAC_HUMAN melanoma antigen family A, 12 312 breast(5)|large_intestine(5)|liver(1)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 28 Acute lymphoblastic leukemia(192;6.56e-05) CTCACTCTTCCCCCTCTCTAA 0.547000 80 102 0 0 1 0 0 NF1 4763 broad.mit.edu 37 17 29701048 29701048 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr17:29701048G>A ENST00000358273.4 + 58 8778 c.8395G>A c.(8395-8397)Gtt>Att p.V2799I NF1_ENST00000356175.3_Missense_Mutation_p.V2778I|NF1_ENST00000444181.2_Missense_Mutation_p.V592I NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 2799 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.?(3) 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) CAAGGAGAACGTTGAACTCTC 0.493000 """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) 6 62 0 0 1 0 0 PLSCR2 57047 broad.mit.edu 37 3 146177862 146177862 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr3:146177862C>T ENST00000497985.1 - 4 488 c.49G>A c.(49-51)Gga>Aga p.G17R PLSCR2_ENST00000336685.2_5'UTR NM_001199978.1 NP_001186907.1 Q9NRY7 PLS2_HUMAN phospholipid scramblase 2 0 phospholipid scrambling integral to membrane|plasma membrane calcium ion binding|phospholipid scramblase activity endometrium(2)|large_intestine(5)|lung(7)|stomach(1) 15 ACAATATGTCCGGGAGGTCCT 0.483000 3 4 0 0 1 0 0 RP1L1 94137 broad.mit.edu 37 8 10470756 10470756 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr8:10470756C>T ENST00000382483.3 - 4 1075 c.852G>A c.(850-852)ccG>ccA p.P284P NM_178857.5 NP_849188.4 A6NKC6 A6NKC6_HUMAN retinitis pigmentosa 1-like 1 284 intracellular signal transduction breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3) 148 COAD - Colon adenocarcinoma(149;0.0811) CAGGGCCCACCGGGGGGTTGC 0.662000 7 71 0 0 1 0 0 SLC22A3 6581 broad.mit.edu 37 6 160858039 160858039 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:160858039G>A ENST00000392145.1 + 7 1111 c.1084G>A c.(1084-1086)Gca>Aca p.A362T SLC22A3_ENST00000275300.2_Missense_Mutation_p.A362T O75751 S22A3_HUMAN solute carrier family 22 (organic cation transporter), member 3 362 integral to plasma membrane|membrane fraction protein binding|quaternary ammonium group transmembrane transporter activity NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1) 27 Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218) OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06) GTTCACAAGCGCAGTGGTGTA 0.448000 10 102 0 0 1 0 0 AKAP4 8852 broad.mit.edu 37 X 49958838 49958838 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:49958838G>A ENST00000376056.2 - 5 649 c.499C>T c.(499-501)Cgt>Tgt p.R167C AKAP4_ENST00000376064.3_Missense_Mutation_p.R167C|AKAP4_ENST00000358526.2_Missense_Mutation_p.R176C|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.R167C Q5JQC9 AKAP4_HUMAN A kinase (PRKA) anchor protein 4 176 cell projection organization|single fertilization|sperm motility cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum protein kinase A binding NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4) 41 Ovarian(276;0.236) ATTTCTAGACGTAGGTTTTGA 0.448000 49 90 0 0 1 0 0 SEC31A 22872 broad.mit.edu 37 4 83793139 83793139 + Missense_Mutation SNP C C A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr4:83793139C>A ENST00000432794.1 - 7 903 c.740G>T c.(739-741)cGa>cTa p.R247L SEC31A_ENST00000311785.7_Missense_Mutation_p.R247L|SEC31A_ENST00000443462.2_Missense_Mutation_p.R242L|SEC31A_ENST00000508479.1_Missense_Mutation_p.R247L|SEC31A_ENST00000513858.1_Missense_Mutation_p.R247L|SEC31A_ENST00000509142.1_Missense_Mutation_p.R247L|SEC31A_ENST00000508502.1_Missense_Mutation_p.R247L|SEC31A_ENST00000505984.1_Missense_Mutation_p.R247L|SEC31A_ENST00000395310.2_Missense_Mutation_p.R247L|SEC31A_ENST00000505472.1_Missense_Mutation_p.R247L|SEC31A_ENST00000500777.2_Missense_Mutation_p.R247L|SEC31A_ENST00000448323.1_Missense_Mutation_p.R247L|SEC31A_ENST00000355196.2_Missense_Mutation_p.R247L|SEC31A_ENST00000348405.4_Missense_Mutation_p.R247L|SEC31A_ENST00000326950.5_Missense_Mutation_p.R247L|SEC31A_ENST00000436790.2_5'UTR O94979 SC31A_HUMAN SEC31 homolog A (S. cerevisiae) 247 Interaction with SEC13. COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm calcium-dependent protein binding SEC31A/ALK(3)|SEC31A/JAK2(4) breast(1) 1 Hepatocellular(203;0.114) GGAAGCAAATCGAAGATCCCA 0.473000 44 14 1.32136e-16 1.46638e-16 1 1 0 GPR63 0 broad.mit.edu 37 6 97246772 97246772 + Missense_Mutation SNP T T A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr6:97246772T>A ENST00000229955.3 - 2 1181 c.836A>T c.(835-837)tAc>tTc p.Y279F GPR63_ENST00000417980.1_Missense_Mutation_p.Y279F NM_001143957.2|NM_030784.3 NP_001137429.1|NP_110411.1 Q9BZJ6 GPR63_HUMAN G protein-coupled receptor 63 279 integral to membrane|plasma membrane G-protein coupled receptor activity|protein binding kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 25 all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721) BRCA - Breast invasive adenocarcinoma(108;0.0912) ACCTTCAGGGTAGCTATGGAT 0.468000 19 64 0 0 1 0 0 ENPP7 339221 broad.mit.edu 37 17 77709178 77709178 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr17:77709178G>A ENST00000328313.5 + 3 957 c.736G>A c.(736-738)Gac>Aac p.D246N NM_178543.3 NP_848638.2 Q6UWV6 ENPP7_HUMAN ectonucleotide pyrophosphatase/phosphodiesterase 7 246 negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process Golgi apparatus|integral to membrane|microvillus sphingomyelin phosphodiesterase activity breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3) 34 OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224) CATCACATCCGACCACGGCAT 0.612000 7 94 0 0 1 0 0 MIS18BP1 55320 broad.mit.edu 37 14 45711965 45711965 + Splice_Site SNP G G T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr14:45711965G>T ENST00000310806.4 - 3 1115 c.658_splice c.e3+1 p.Y219_splice NM_018353.4 NP_060823.3 Q6P0N0 M18BP_HUMAN MIS18 binding protein 1 219 cell division|CenH3-containing nucleosome assembly at centromere|mitosis chromosome, centromeric region|nucleoplasm DNA binding NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2) 39 ATAGTTTACCGTAAGTTAAAT 0.343000 4 84 0.150653 0.152327 1 1 0 AC024560.3 0 broad.mit.edu 37 3 197348739 197348739 + RNA SNP G G C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr3:197348739G>C ENST00000418868.1 - 0 520 NR_003266.2 TAATTTTCTAGCTGTGAAAGA 0.398000 4 120 0 0 1 0 0 CHEK2 11200 broad.mit.edu 37 22 29092971 29092971 + Missense_Mutation SNP A A C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr22:29092971A>C ENST00000544772.1 - 11 1786 c.350T>G c.(349-351)cTt>cGt p.L117R CHEK2_ENST00000464581.1_5'UTR|CHEK2_ENST00000348295.3_Intron|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000405598.1_Missense_Mutation_p.L338R|CHEK2_ENST00000382580.2_Missense_Mutation_p.L381R|CHEK2_ENST00000328354.6_Missense_Mutation_p.L338R|CHEK2_ENST00000403642.1_Missense_Mutation_p.L247R|CHEK2_ENST00000382578.1_Missense_Mutation_p.L247R|CHEK2_ENST00000402731.1_Intron|CHEK2_ENST00000404276.1_Missense_Mutation_p.L338R NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 338 FHA. R -> G (in dbSNP:rs28909982). cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 GTTTTCATGAAGGTACTACAC 0.398000 F breast Direct reversal of damage;Other conserved DNA damage response genes 6 12 0 0 1 0 0 NAP1L2 4674 broad.mit.edu 37 X 72433770 72433770 + Missense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:72433770C>T ENST00000373517.3 - 1 914 c.559G>A c.(559-561)Ggt>Agt p.G187S NAP1L2_ENST00000536638.1_Missense_Mutation_p.G45S NM_021963.3 NP_068798.1 Q9ULW6 NP1L2_HUMAN nucleosome assembly protein 1-like 2 187 Glu-rich (acidic). nucleosome assembly chromatin assembly complex p.G187S(1) NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(3) 29 Renal(35;0.156) TCCTCATTACCATACATCTCT 0.408000 9 81 0 0 1 0 0 PIK3CA 5290 broad.mit.edu 37 3 178916936 178916936 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr3:178916936G>A ENST00000263967.3 + 2 480 c.323G>A c.(322-324)cGt>cAt p.R108H NM_006218.2 NP_006209.2 P42336 PK3CA_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha 108 PI3K-ABD. epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity p.R108H(11)|p.R108L(2)|p.G106_R108delGNR(2)|p.G106_R108del(2)|p.R108P(1)|p.R108del(1) NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208) 5269 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) GTAGGCAACCGTGAAGAAAAG 0.338000 57 Mis """colorectal, gastric, gliobastoma, breast""" HNSCC(19;0.045)|TSP Lung(28;0.18) 58 37 0 0 1 0 0 MMP21 118856 broad.mit.edu 37 10 127464289 127464289 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr10:127464289C>T ENST00000368808.3 - 1 101 c.102G>A c.(100-102)tcG>tcA p.S34S NM_147191.1 NP_671724.1 Q8N119 MMP21_HUMAN matrix metallopeptidase 21 34 proteolysis extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1) 16 all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936) GCTCCAGGTCCGAGCGGTCCC 0.677000 19 46 0 0 1 0 0 SBK1 388228 broad.mit.edu 37 16 28331566 28331566 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr16:28331566G>A ENST00000341901.4 + 4 1388 c.599G>A c.(598-600)cGc>cAc p.R200H NM_001024401.2 NP_001019572.1 Q52WX2 SBK1_HUMAN SH3 domain binding kinase 1 200 Protein kinase. cytoplasm ATP binding|protein serine/threonine kinase activity kidney(1)|lung(3)|ovary(1) 5 ATGACGCGCCGCGTGGGCTGC 0.726000 17 14 0 0 1 0 0 EFR3A 23167 broad.mit.edu 37 8 132980594 132980594 + Missense_Mutation SNP G G A rs148528328 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr8:132980594G>A ENST00000254624.5 + 9 1133 c.908G>A c.(907-909)cGt>cAt p.R303H EFR3A_ENST00000334503.4_Missense_Mutation_p.R303H|EFR3A_ENST00000519656.1_Missense_Mutation_p.R267H NM_015137.4 NP_055952.2 Q14156 EFR3A_HUMAN EFR3 homolog A (S. cerevisiae) 303 plasma membrane binding breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2) 35 Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102) CTTGATGCTCGTAAAAAAGAT 0.428000 18 66 0 0 1 0 0 P2RY10 0 broad.mit.edu 37 X 78216443 78216443 + Missense_Mutation SNP A A T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chrX:78216443A>T ENST00000171757.2 + 4 706 c.426A>T c.(424-426)agA>agT p.R142S P2RY10_ENST00000475374.1_3'UTR|P2RY10_ENST00000544091.1_Missense_Mutation_p.R142S NM_014499.2 NP_055314.1 O00398 P2Y10_HUMAN purinergic receptor P2Y, G-protein coupled, 10 142 integral to membrane|plasma membrane purinergic nucleotide receptor activity, G-protein coupled breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2) 42 TCAGGGCCAGAGACTGGAAGC 0.498000 9 98 0 0 1 0 0 PTEN 5728 broad.mit.edu 37 10 89624296 89624296 + Missense_Mutation SNP G G C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr10:89624296G>C ENST00000371953.3 + 1 1427 c.70G>C c.(70-72)Gac>Cac p.D24H NM_000314.4 NP_000305.3 P60484 PTEN_HUMAN phosphatase and tensin homolog 24 Phosphatase tensin-type. 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.D24Y(4)|p.D24N(2)|p.D24fs*20(2)|p.D24_L25del(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) ATTCGACTTAGACTTGACCTG 0.463000 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) 30 47 0 0 1 0 0 GCK 2645 broad.mit.edu 37 7 44185169 44185169 + Missense_Mutation SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:44185169G>A ENST00000403799.3 - 9 1649 c.1180C>T c.(1180-1182)Cgc>Tgc p.R394C GCK_ENST00000395796.3_Missense_Mutation_p.R393C|GCK_ENST00000437084.1_Missense_Mutation_p.R377C|GCK_ENST00000345378.2_Missense_Mutation_p.R395C NM_000162.3 NP_000153.1 P35557 HXK4_HUMAN glucokinase (hexokinase 4) 394 cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport cytosol|nucleoplasm ATP binding|glucokinase activity|glucose binding|protein binding central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1) 37 CGGCTCTCGCGCATGCGGTTG 0.692000 9 20 0 0 1 0 0 PTPN23 25930 broad.mit.edu 37 3 47451557 47451557 + Nonsense_Mutation SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr3:47451557C>T ENST00000265562.4 + 20 2346 c.2269C>T c.(2269-2271)Cga>Tga p.R757* PTPN23_ENST00000431726.1_Nonsense_Mutation_p.R631* NM_015466.2 NP_056281.1 Q9H3S7 PTN23_HUMAN protein tyrosine phosphatase, non-receptor type 23 757 Pro-rich. cilium morphogenesis cilium|cytoplasmic membrane-bounded vesicle|microtubule basal body protein tyrosine phosphatase activity breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1) 23 BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632) GGCTGGCCCACGACTGCCTGA 0.677000 3 14 0 0 1 0 0 LRP1 4035 broad.mit.edu 37 12 57572304 57572304 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr12:57572304C>T ENST00000243077.3 + 27 4990 c.4524C>T c.(4522-4524)acC>acT p.T1508T NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 1508 aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5) 184 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) ACAAGTGGACCGGCCACAATG 0.617000 30 137 0 0 1 0 0 POMT1 10585 broad.mit.edu 37 9 134385763 134385763 + Silent SNP C C T TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr9:134385763C>T ENST00000423007.1 + 9 1258 c.816C>T c.(814-816)caC>caT p.H272H POMT1_ENST00000402686.3_Silent_p.H272H|POMT1_ENST00000404875.2_Silent_p.H155H|POMT1_ENST00000541219.1_Silent_p.H50H|POMT1_ENST00000354713.4_Silent_p.H242H|POMT1_ENST00000419118.2_Silent_p.H120H|POMT1_ENST00000372228.3_Silent_p.H294H|POMT1_ENST00000341012.7_Silent_p.H218H NM_001136113.1 NP_001129585.1 Q9Y6A1 POMT1_HUMAN protein-O-mannosyltransferase 1 294 multicellular organismal development|protein O-linked glycosylation endoplasmic reticulum membrane|integral to membrane dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 31 Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259) CTGGGCCCCACGACCAAATCA 0.542000 22 29 0 0 1 0 0 LYST 1130 broad.mit.edu 37 1 235969411 235969411 + Missense_Mutation SNP G G C TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr1:235969411G>C ENST00000389794.3 - 6 3199 c.3025C>G c.(3025-3027)Caa>Gaa p.Q1009E LYST_ENST00000536965.1_Missense_Mutation_p.Q1009E|LYST_ENST00000389793.2_Missense_Mutation_p.Q1009E Q99698 LYST_HUMAN lysosomal trafficking regulator 1009 defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport cytoplasm|microtubule cytoskeleton protein binding NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1) 162 Ovarian(103;0.0634)|Breast(184;0.23) all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228) OV - Ovarian serous cystadenocarcinoma(106;0.000674) TTTTTTCCTTGCTCCTCTTTG 0.348000 36 50 0 0 1 0 0 ASPSCR1 79058 broad.mit.edu 37 17 79974988 79974988 + Splice_Site SNP G G A TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr17:79974988G>A ENST00000306729.7 + 16 2026 c.1930_splice c.e16+1 p.P643_splice ASPSCR1_ENST00000306739.4_Splice_Site_p.P549_splice|ASPSCR1_ENST00000580534.1_Splice_Site_p.P497_splice|ASPSCR1_ENST00000582404.1_3'UTR NM_001251888.1 NP_001238817.1 Q9BZE9 ASPC1_HUMAN alveolar soft part sarcoma chromosome region, candidate 1 549 protein binding ASPSCR1/TFE3(167) breast(2)|large_intestine(2) 4 all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246) BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191) TGAAGCTGCCGGGTACTGCGG 0.721000 T TFE3 alveolar soft part sarcoma 11 20 0 0 1 0 0 ARID1A 8289 broad.mit.edu 37 1 27057848 27057848 + Frame_Shift_Del DEL C C - TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr1:27057848delC ENST00000324856.7 + 3 1927 c.1556delC c.(1555-1557)tcfs p.S519fs ARID1A_ENST00000374152.2_Frame_Shift_Del_p.S136fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.S519fs NM_006015.4 NP_006006.3 O14497 ARI1A_HUMAN AT rich interactive domain 1A (SWI-like) 519 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ARID1A/MAST2_ENST00000361297(2) NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24) 411 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) CCTCCATACTCCCAGCAGCCA 0.632 """Mis, N, F, S, D""" """clear cell ovarian carcinoma, RCC""" 152 284 --- --- --- --- ARID1A 8289 broad.mit.edu 37 1 27106527 27106528 + Frame_Shift_Ins INS - - GAGT TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr1:27106527_27106528insGAGT ENST00000324856.7 + 20 6509_6510 c.6138_6139insGAGT c.(6136-6141)gtagtgfs p.V2047fs ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.V1664fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.V375fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.V1830fs NM_006015.4 NP_006006.3 O14497 ARI1A_HUMAN AT rich interactive domain 1A (SWI-like) 2047 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding p.E2047*(3) ARID1A/MAST2_ENST00000361297(2) NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24) 411 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) GCAACAAAGTGGAGTGGTGGTG 0.550 """Mis, N, F, S, D""" """clear cell ovarian carcinoma, RCC""" 41 84 --- --- --- --- AC018890.6 0 broad.mit.edu 37 2 175584494 175584494 + RNA DEL T T - TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:175584494delT ENST00000442996.1 + 0 217 TTGCTTCTGATTTTTTTTTTT 0.532 OREG0015078 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 4 4 --- --- --- --- KIF1A 547 broad.mit.edu 37 2 241696841 241696843 + In_Frame_Del DEL TCC TCC - rs71779512 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr2:241696841_241696843delTCC ENST00000498729.2 - 27 2997_2999 c.2751_2753delGGA c.(2749-2754)gat>ga p.ED917del KIF1A_ENST00000320389.7_Intron NM_001244008.1 NP_001230937.1 Q12756 KIF1A_HUMAN kinesin family member 1A 697 anterograde axon cargo transport cytoplasm|microtubule|nucleus ATP binding|microtubule motor activity NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1) 66 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176) ctcctcctcatcctcctcctcct 0.675 3 6 --- --- --- --- AC004540.5 0 broad.mit.edu 37 7 26518689 26518690 + RNA DEL CT CT - TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:26518689_26518690delCT ENST00000418758.2 + 0 468 CCTCATtttcctctcccacctg 0.579 2 4 --- --- --- --- CCT6P3 0 broad.mit.edu 37 7 64532452 64532452 + RNA DEL T T - rs67432959 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr7:64532452delT ENST00000426828.1 + 0 1228 NR_033416.1 atgcccagccttttttttttt 0.408 3 4 --- --- --- --- MYC 4609 broad.mit.edu 37 8 128750605 128750607 + In_Frame_Del DEL CAG CAG - rs61752959 byFrequency TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr8:128750605_128750607delCAG ENST00000377970.2 + 2 652_654 c.142_144delCAG c.(142-144)del p.Q52del MYC_ENST00000524013.1_In_Frame_Del_p.Q51del|MYC_ENST00000259523.6_In_Frame_Del_p.Q37del NM_002467.4 NP_002458.2 P01106 MYC_HUMAN v-myc avian myelocytomatosis viral oncogene homolog 37 branching involved in ureteric bud morphogenesis|cell cycle arrest|cell proliferation|cellular iron ion homeostasis|positive regulation of metanephric cap mesenchymal cell proliferation|positive regulation of transcription, DNA-dependent|regulation of telomere maintenance|regulation of transcription from RNA polymerase II promoter|response to drug nucleolus|nucleoplasm E-box binding|protein binding|sequence-specific DNA binding transcription factor activity p.Q33H(1) central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1) 16 all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185) Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22) Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151) KIRC - Kidney renal clear cell carcinoma(542;0.248) GAACTTCTACCAGCAGCAGCAGC 0.611 3 """A, T""" """IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@""" """Burkitt lymphoma, amplified in other cancers, B-CLL""" OREG0018982 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 7 246 --- --- --- --- OR11H12 440153 broad.mit.edu 37 14 19377911 19377911 + Frame_Shift_Del DEL C C - TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr14:19377911delC ENST00000550708.1 + 1 390 c.318delC c.(316-318)aafs p.N106fs NM_001013354.1|NM_001197287.1 NP_001013372.1|NP_001184216.1 B2RN74 O11HC_HUMAN olfactory receptor, family 11, subfamily H, member 12 106 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 22 all_cancers(95;0.00108) Epithelial(56;9.96e-07)|all cancers(55;2.95e-06) GBM - Glioblastoma multiforme(265;0.00327) AGAAAAAAAACATCTCCTTTG 0.388 22 82 --- --- --- --- KTN1-AS1 0 broad.mit.edu 37 14 56014174 56014174 + RNA DEL G G - rs72015246 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr14:56014174delG ENST00000554558.1 - 0 364 aaaaaaaaaagaaTTGGCACA 0.443 7 6 --- --- --- --- RRN3P2 0 broad.mit.edu 37 16 29113498 29113498 + RNA DEL T T - rs11366120 TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr16:29113498delT ENST00000564580.1 + 0 1360 AGGAGGTGGAttttttttttc 0.542 8 42 --- --- --- --- VEZF1 7716 broad.mit.edu 37 17 56056605 56056607 + In_Frame_Del DEL TGC TGC - rs61731354 byFrequency TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr17:56056605_56056607delTGC ENST00000584396.1 - 5 1105_1107 c.1017_1019delGCA c.(1015-1020)caa>ca p.QQ343del VEZF1_ENST00000581208.1_In_Frame_Del_p.QQ352del Q14119 VEZF1_HUMAN vascular endothelial zinc finger 1 352 Poly-Gln. cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleus DNA binding|zinc ion binding breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1) 10 ttgttgttgttgctgctgctgct 0.463 8 175 --- --- --- --- CHMP2A 27243 broad.mit.edu 37 19 59063715 59063716 + Frame_Shift_Del DEL AC AC - TCGA-NF-A5CP-01A-12D-A28R-08 TCGA-NF-A5CP-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5a5cd1b0-e7bd-4f5f-afb5-e9fc3be14d5d 9abdb8aa-e659-4785-9f8a-3664d9dcca2a g.chr19:59063715_59063716delAC ENST00000600118.1 - 2 683_684 c.258_259delGT c.(256-261)gtccfs p.VS86fs CHMP2A_ENST00000601220.1_Frame_Shift_Del_p.VS86fs|CHMP2A_ENST00000312547.2_Frame_Shift_Del_p.VS86fs O43633 CHM2A_HUMAN charged multivesicular body protein 2A 86 Interaction with VPS4B. cellular membrane organization|endosome transport|protein transport cytosol|late endosome membrane protein domain specific binding endometrium(1)|kidney(1)|large_intestine(3)|lung(2) 7 all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184) UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179) ATCTTGAGGGACACAGCCTGGA 0.545 55 123 --- --- --- ---