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 PIK3CD 5293 broad.mit.edu 37 1 9783218 9783218 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:9783218G>A ENST00000536656.1 + 20 2742 c.2534G>A c.(2533-2535)cGc>cAc p.R845H PIK3CD_ENST00000377346.4_Missense_Mutation_p.R821H|PIK3CD_ENST00000361110.2_Missense_Mutation_p.R845H O00329 PK3CD_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta 821 PI3K/PI4K. phosphatidylinositol-mediated signaling|protein phosphorylation phosphatidylinositol 3-kinase complex|plasma membrane 1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding p.R821H(1) central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1) 31 all_lung(157;0.222) all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419) ACCGGGGACCGCACAGGCCTC 0.602000 5 398 0 0 1 0 0 LY9 4063 broad.mit.edu 37 1 160784239 160784239 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:160784239G>A ENST00000263285.5 + 4 790 c.760G>A c.(760-762)Ggg>Agg p.G254R LY9_ENST00000368040.1_5'UTR|LY9_ENST00000341032.4_Missense_Mutation_p.G254R|LY9_ENST00000471816.1_3'UTR|LY9_ENST00000368041.2_Missense_Mutation_p.G214R NM_001261456.1|NM_002348.3 NP_001248385.1|NP_002339.2 Q9HBG7 LY9_HUMAN lymphocyte antigen 9 254 Ig-like V-type 2. cell adhesion|immunoglobulin mediated immune response integral to membrane autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 36 all_cancers(52;2.72e-17)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00737) AGGAACAACGGGGGAGACTGT 0.582000 50 92 0 0 1 0 0 POM121 9883 broad.mit.edu 37 7 72413486 72413486 + Missense_Mutation SNP C C T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr7:72413486C>T ENST00000395270.1 + 14 3200 c.2159C>T c.(2158-2160)cCg>cTg p.P720L POM121_ENST00000446813.1_Missense_Mutation_p.P720L|POM121_ENST00000257622.4_Missense_Mutation_p.P720L|POM121_ENST00000358357.3_Missense_Mutation_p.P720L|POM121_ENST00000434423.2_Missense_Mutation_p.P985L NM_001257190.1 NP_001244119.1 Q96HA1 P121A_HUMAN POM121 transmembrane nucleoporin 985 Pore side (Potential). carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction endoplasmic reticulum membrane|nuclear membrane|nuclear pore NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 Lung NSC(55;0.163) GCCGCCAAGCCGGCCCTTGCC 0.657000 8 171 0 0 1 0 0 CHEK2 11200 broad.mit.edu 37 22 29091841 29091841 + Silent SNP G G A rs146546850 byFrequency TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr22:29091841G>A ENST00000544772.1 - 12 1889 c.453C>T c.(451-453)tcC>tcT p.S151S CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382578.1_Silent_p.S281S NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 372 FHA. 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 p.S372S(8) central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 CCAAAATCTTGGAGTGCCCAA 0.413000 F breast Direct reversal of damage;Other conserved DNA damage response genes 3 68 0 0 1 0 0 TSSC2 0 broad.mit.edu 37 11 3427845 3427845 + RNA SNP C C T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr11:3427845C>T ENST00000529482.1 + 0 962 CTTCAAGTGGCAGGAGCAGAA 0.587000 4 84 0 0 1 0 0 BRICD5 283870 broad.mit.edu 37 16 2260588 2260588 + Missense_Mutation SNP G G C TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr16:2260588G>C ENST00000328540.3 - 2 1231 c.115C>G c.(115-117)Ctg>Gtg p.L39V BRICD5_ENST00000566018.1_Missense_Mutation_p.L39V|BRICD5_ENST00000562360.1_Missense_Mutation_p.L39V NM_182563.3 NP_872369.2 BRICHOS domain containing 5 GCcagcaccagcagcagcagc 0.657000 3 52 0 0 1 0 0 PHLDB2 90102 broad.mit.edu 37 3 111693318 111693318 + Missense_Mutation SNP T T A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr3:111693318T>A ENST00000431670.2 + 18 4081 c.3670T>A c.(3670-3672)Tat>Aat p.Y1224N PHLDB2_ENST00000481953.1_Missense_Mutation_p.Y1181N|PHLDB2_ENST00000495180.1_Missense_Mutation_p.Y715N|PHLDB2_ENST00000393925.3_Missense_Mutation_p.Y1224N|PHLDB2_ENST00000412622.1_Missense_Mutation_p.Y1181N|PHLDB2_ENST00000393923.3_Missense_Mutation_p.Y1208N NM_001134438.1 NP_001127910.1 Q86SQ0 PHLB2_HUMAN pleckstrin homology-like domain, family B, member 2 1224 PH. cytoplasm|intermediate filament cytoskeleton|plasma membrane breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1) 55 TGACAGAATCTATTATATGGT 0.388000 47 112 0 0 1 0 0 CGN 57530 broad.mit.edu 37 1 151491695 151491695 + Missense_Mutation SNP C C T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:151491695C>T ENST00000271636.7 + 2 833 c.700C>T c.(700-702)Cac>Tac p.H234Y NM_020770.2 NP_065821.1 Q9P2M7 CING_HUMAN cingulin 228 Head.|Interacts with ZO-2. myosin complex|tight junction actin binding|motor activity NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 45 Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) LUSC - Lung squamous cell carcinoma(543;0.181) GTCCACCAACCACTGGACCTC 0.587000 89 176 0 0 1 0 0 GLG1 2734 broad.mit.edu 37 16 74530417 74530417 + Silent SNP C C T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr16:74530417C>T ENST00000422840.2 - 5 899 c.900G>A c.(898-900)gaG>gaA p.E300E GLG1_ENST00000205061.5_Silent_p.E300E|GLG1_ENST00000447066.2_Silent_p.E289E NM_001145667.1 NP_001139139.1 Q92896 GSLG1_HUMAN golgi glycoprotein 1 300 Golgi membrane|integral to membrane receptor binding breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1) 57 CCGATGACAGCTCAGCCACCC 0.448000 6 123 0 0 1 0 0 BTN2A3P 0 broad.mit.edu 37 6 26422353 26422353 + RNA SNP C C T rs141013110 TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr6:26422353C>T ENST00000466808.2 + 0 7 p.P3S(2) GCTCATGGAACCAGCTGCTGC 0.622000 6 213 0 0 1 0 0 CACNA1E 777 broad.mit.edu 37 1 181767534 181767534 + Missense_Mutation SNP T T C TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:181767534T>C ENST00000526775.1 + 46 6485 c.6320T>C c.(6319-6321)cTc>cCc p.L2107P CACNA1E_ENST00000358338.5_Missense_Mutation_p.L2058P|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L2150P|CACNA1E_ENST00000367573.2_Missense_Mutation_p.L2169P|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L2126P|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L1733P|CACNA1E_ENST00000357570.5_Missense_Mutation_p.L2120P NM_001205294.1 NP_001192223.1 Q15878 CAC1E_HUMAN calcium channel, voltage-dependent, R type, alpha 1E subunit 2169 energy reserve metabolic process|membrane depolarization|synaptic transmission voltage-gated calcium channel complex voltage-gated calcium channel activity NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 204 CCCCGGCCCCTCCTTTCCTAC 0.637000 4 202 0 0 1 0 0 CHEK2 11200 broad.mit.edu 37 22 29091840 29091840 + Missense_Mutation SNP T T C rs142470496 byFrequency TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr22:29091840T>C ENST00000544772.1 - 12 1890 c.454A>G c.(454-456)Aag>Gag p.K152E CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 373 FHA. 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 p.K373E(9) central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 CCCAAAATCTTGGAGTGCCCA 0.418000 F breast Direct reversal of damage;Other conserved DNA damage response genes 3 70 0 0 1 0 0 CEP170 9859 broad.mit.edu 37 1 243333027 243333027 + Silent SNP A A G rs147752333 by1000genomes TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:243333027A>G ENST00000366542.1 - 12 1797 c.1746T>C c.(1744-1746)cgT>cgC p.R582R CEP170_ENST00000366544.1_Silent_p.R484R|CEP170_ENST00000366543.1_Silent_p.R484R NM_014812.2 NP_055627.2 Q5SW79 CE170_HUMAN centrosomal protein 170kDa 582 centriole|microtubule|spindle p.R582R(3) NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1) 62 all_neural(11;0.101) all_cancers(173;0.003) all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101) GTGAAACCCAACGTTTGCTTC 0.398000 4 85 0 0 1 0 0 CCT6P1 0 broad.mit.edu 37 7 65222986 65222986 + RNA SNP G G T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr7:65222986G>T ENST00000442266.1 + 0 578 GAATTCTGGCGTTTTTTACAA 0.289000 3 23 0.150653 0.150653 1 1 0 PRDX1 5052 broad.mit.edu 37 1 45984618 45984618 + Missense_Mutation SNP T T C TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:45984618T>C ENST00000262746.1 - 2 437 c.98A>G c.(97-99)gAc>gGc p.D33G PRDX1_ENST00000319248.8_Missense_Mutation_p.D33G|PRDX1_ENST00000483583.1_5'UTR|PRDX1_ENST00000372079.1_Intron NM_002574.3|NM_181696.2 NP_002565.1|NP_859047.1 Q06830 PRDX1_HUMAN peroxiredoxin 1 33 Thioredoxin. cell proliferation|cell redox homeostasis|hydrogen peroxide catabolic process|skeletal system development melanosome|mitochondrion|nucleus protein binding|thioredoxin peroxidase activity breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|skin(1) 12 Acute lymphoblastic leukemia(166;0.155) ACCTTTGTAGTCAGACAGGCT 0.413000 6 89 0 0 1 0 0 COL1A2 1278 broad.mit.edu 37 7 94058709 94058709 + Silent SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr7:94058709G>A ENST00000297268.6 + 51 4392 c.3921G>A c.(3919-3921)agG>agA p.R1307R NM_000089.3 NP_000080.2 P08123 CO1A2_HUMAN collagen, type I, alpha 2 1307 Fibrillar collagen NC1. axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway collagen type I|extracellular space|plasma membrane extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging COL1A2/PLAG1(3) NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1) 115 all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08) STAD - Stomach adenocarcinoma(171;0.0031) Collagenase(DB00048) GCAACAGCAGGTTCACTTACA 0.453000 HNSCC(75;0.22) 28 51 0 0 1 0 0 TUBB8P7 0 broad.mit.edu 37 16 90161618 90161618 + RNA SNP C C T rs13338202 by1000genomes TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr16:90161618C>T ENST00000567960.1 + 0 354 TUBB8P7_ENST00000564451.1_RNA p.D118D(2) CAGTGATGGACGTTGTCAGAA 0.607000 3 48 0 0 1 0 0 CYSLTR2 57105 broad.mit.edu 37 13 49281729 49281729 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr13:49281729G>A ENST00000282018.3 + 1 779 c.776G>A c.(775-777)tGt>tAt p.C259Y NM_020377.2 NP_065110.1 Q9NS75 CLTR2_HUMAN cysteinyl leukotriene receptor 2 259 immune response integral to membrane|plasma membrane endometrium(2)|large_intestine(4)|lung(12)|skin(2) 20 all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787) GBM - Glioblastoma multiforme(99;1.19e-09) Nedocromil(DB00716) TTCTTCTTGTGTTTCCTGCCC 0.498000 50 63 0 0 1 0 0 SFI1 9814 broad.mit.edu 37 22 31927093 31927093 + Missense_Mutation SNP A A G TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr22:31927093A>G ENST00000432498.1 + 4 709 c.316A>G c.(316-318)Aga>Gga p.R106G SFI1_ENST00000443011.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000400288.2_Missense_Mutation_p.R106G|SFI1_ENST00000540643.1_Intron|SFI1_ENST00000414585.1_Intron NM_014775.3 NP_055590.2 A8K8P3 SFI1_HUMAN Sfi1 homolog, spindle assembly associated (yeast) 106 G2/M transition of mitotic cell cycle centriole|cytosol NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3) 38 GACTTTTGGAAGAGTATTTCC 0.318000 6 87 0 0 1 0 0 GRM2 2912 broad.mit.edu 37 3 51746586 51746586 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr3:51746586G>A ENST00000395052.3 + 3 782 c.548G>A c.(547-549)cGc>cAc p.R183H GRM2_ENST00000475478.1_Intron|GRM2_ENST00000442933.2_Missense_Mutation_p.R183H NM_000839.3 NP_000830.2 Q14416 GRM2_HUMAN glutamate receptor, metabotropic 2 183 synaptic transmission integral to plasma membrane p.R183H(1) breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 33 BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716) Acamprosate(DB00659)|Nicotine(DB00184) TACTTTGCCCGCACAGTGCCT 0.542000 4 209 0 0 1 0 0 LINC00933 0 broad.mit.edu 37 15 85121267 85121267 + RNA SNP C C T rs144259916 by1000genomes TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr15:85121267C>T ENST00000557887.1 + 0 467 NR_038273.1|NR_038274.1 GGAGGCCAGCCGAACACACAG 0.473000 4 127 0 0 1 0 0 GPR97 222487 broad.mit.edu 37 16 57718006 57718006 + Silent SNP C C T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr16:57718006C>T ENST00000333493.4 + 9 1205 c.1044C>T c.(1042-1044)ttC>ttT p.F348F GPR97_ENST00000327655.6_Silent_p.F138F|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000450388.3_Silent_p.F228F NM_170776.4 NP_740746.4 Q86Y34 GPR97_HUMAN G protein-coupled receptor 97 348 neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 30 TCCACTACTTCCTGCTCTGTG 0.587000 49 118 0 0 1 0 0 THRA 7067 broad.mit.edu 37 17 38240101 38240101 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr17:38240101G>A ENST00000450525.2 + 5 727 c.236G>A c.(235-237)cGc>cAc p.R79H THRA_ENST00000584985.1_Missense_Mutation_p.R79H|THRA_ENST00000394121.4_Missense_Mutation_p.R79H|THRA_ENST00000264637.4_Missense_Mutation_p.R79H|THRA_ENST00000546243.1_Missense_Mutation_p.R79H NM_199334.3 NP_955366.1 P10827 THA_HUMAN thyroid hormone receptor, alpha 79 negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|negative regulation of transcription initiation, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter cytosol|nucleoplasm protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|TBP-class protein binding|thyroid hormone binding|thyroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding p.R79H(2) endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1) 11 Colorectal(19;0.000442) Myeloproliferative disorder(1115;0.0255) Levothyroxine(DB00451)|Liothyronine(DB00279) TTCTTTCGCCGCACAATCCAG 0.547000 5 176 0 0 1 0 0 ALPI 248 broad.mit.edu 37 2 233321115 233321115 + Missense_Mutation SNP G G T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr2:233321115G>T ENST00000295463.3 + 2 201 c.124G>T c.(124-126)Gcc>Tcc p.A42S NM_001631.3 NP_001622.2 P09923 PPBI_HUMAN alkaline phosphatase, intestinal 42 phosphorylation anchored to membrane|integral to membrane|plasma membrane alkaline phosphatase activity|metal ion binding|protein binding NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1) 24 all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132) Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746) CCTGGATGCTGCCAAGAAGCT 0.632000 4 154 1.024e-07 1.04448e-07 1 1 0 DCAF13 25879 broad.mit.edu 37 8 104427255 104427255 + Missense_Mutation SNP G G C TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr8:104427255G>C ENST00000297579.5 + 1 314 c.37G>C c.(37-39)Gtg>Ctg p.V13L SLC25A32_ENST00000297578.4_5'UTR|SLC25A32_ENST00000543107.1_5'UTR NM_015420.6 NP_056235.4 Q9NV06 DCA13_HUMAN DDB1 and CUL4 associated factor 13 0 rRNA processing CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 25 GTCGCCCCTTGTGAGCGCAAC 0.697000 16 19 0 0 1 0 0 VPS53 55275 broad.mit.edu 37 17 617889 617889 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr17:617889G>A ENST00000437048.2 - 1 207 c.61C>T c.(61-63)Ccc>Tcc p.P21S VPS53_ENST00000291074.5_Missense_Mutation_p.P21S|VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000401468.3_Missense_Mutation_p.P21S|VPS53_ENST00000571805.1_Missense_Mutation_p.P21S|VPS53_ENST00000574029.1_Missense_Mutation_p.P21S NM_001128159.2 NP_001121631.1 Q5VIR6 VPS53_HUMAN vacuolar protein sorting 53 homolog (S. cerevisiae) 21 protein transport endosome membrane|Golgi apparatus breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1) 19 UCEC - Uterine corpus endometrioid carcinoma (25;0.0265) TGCACCTCGGGCGTGAGCTGC 0.711000 16 212 0 0 1 0 0 FOXP3 50943 broad.mit.edu 37 X 49114015 49114015 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chrX:49114015G>A ENST00000376207.4 - 4 510 c.323C>T c.(322-324)aCg>aTg p.T108M FOXP3_ENST00000518685.1_Missense_Mutation_p.T73M|FOXP3_ENST00000376199.2_Missense_Mutation_p.T73M|FOXP3_ENST00000376197.1_Missense_Mutation_p.T58M|FOXP3_ENST00000455775.2_Missense_Mutation_p.T108M|FOXP3_ENST00000557224.1_Missense_Mutation_p.T73M NM_014009.3 NP_054728.2 Q9BZS1 FOXP3_HUMAN forkhead box P3 108 B cell homeostasis|cerebellum development|chromatin remodeling|embryo development|myeloid cell homeostasis|negative regulation of activated T cell proliferation|negative regulation of chronic inflammatory response|negative regulation of CREB transcription factor activity|negative regulation of cytokine secretion|negative regulation of histone acetylation|negative regulation of histone deacetylation|negative regulation of interferon-gamma biosynthetic process|negative regulation of interferon-gamma production|negative regulation of interleukin-10 production|negative regulation of interleukin-2 biosynthetic process|negative regulation of interleukin-2 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of interleukin-6 production|negative regulation of isotype switching to IgE isotypes|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell cytokine production|negative regulation of tumor necrosis factor production|pattern specification process|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation|positive regulation of histone acetylation|positive regulation of immature T cell proliferation in thymus|positive regulation of peripheral T cell tolerance induction|positive regulation of T cell anergy|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transforming growth factor-beta1 production|post-embryonic development|regulation of isotype switching to IgG isotypes|response to virus|T cell homeostasis|T cell receptor signaling pathway|tolerance induction to self antigen cytoplasm|nucleus|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|histone acetyltransferase binding|histone deacetylase binding|NF-kappaB binding|NFAT protein binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription corepressor activity|zinc ion binding endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1) 10 Ovarian(276;0.236) GGCATCCACCGTTGAGAGCTG 0.677000 3 29 0 0 1 0 0 CHMP7 91782 broad.mit.edu 37 8 23115930 23115930 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr8:23115930G>A ENST00000397677.1 + 7 1576 c.928G>A c.(928-930)Gac>Aac p.D310N CHMP7_ENST00000313219.7_Missense_Mutation_p.D310N|CHMP7_ENST00000520102.1_3'UTR NM_152272.3 NP_689485.1 Q8WUX9 CHMP7_HUMAN charged multivesicular body protein 7 310 cellular membrane organization|late endosome to vacuole transport cytosol|ESCRT III complex protein transporter activity breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1) 11 Prostate(55;0.0513) Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632) AGGCATCCTGGACCGGATCTA 0.572000 11 531 0 0 1 0 0 FLG2 388698 broad.mit.edu 37 1 152327955 152327955 + Silent SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:152327955G>A ENST00000388718.5 - 3 2379 c.2307C>T c.(2305-2307)agC>agT p.S769S FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA NM_001014342.2 NP_001014364.1 Q5D862 FILA2_HUMAN filaggrin family member 2 769 Ser-rich. calcium ion binding|structural molecule activity p.S769S(1) NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5) 188 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GTTGGCCATAGCTAGACTGAC 0.517000 8 690 0 0 1 0 0 HK2 3099 broad.mit.edu 37 2 75081444 75081444 + Missense_Mutation SNP C C T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr2:75081444C>T ENST00000290573.2 + 2 688 c.88C>T c.(88-90)Cgc>Tgc p.R30C HK2_ENST00000409174.1_Missense_Mutation_p.R2C NM_000189.4 NP_000180.2 P52789 HXK2_HUMAN hexokinase 2 30 Regulatory. apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport cytosol|mitochondrial outer membrane ATP binding|glucokinase activity p.R30C(1) breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1) 43 CTACCACATGCGCCTCTCTGA 0.488000 5 570 0 0 1 0 0 ACACB 32 broad.mit.edu 37 12 109614053 109614053 + Silent SNP G G T TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr12:109614053G>T ENST00000338432.7 + 9 1541 c.1422G>T c.(1420-1422)ccG>ccT p.P474P ACACB_ENST00000377854.5_Silent_p.P474P|ACACB_ENST00000377848.3_Silent_p.P474P|ACACB_ENST00000543080.1_3'UTR O00763 ACACB_HUMAN acetyl-CoA carboxylase beta 474 ATP-grasp.|Biotin carboxylation. acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 95 Biotin(DB00121) AGGACTTCCCGATCCTTTTCA 0.478000 169 227 5.91303e-76 6.2826e-76 1 1 0 NCAPD3 23310 broad.mit.edu 37 11 134080347 134080347 + Splice_Site SNP G G A rs142896286 TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr11:134080347G>A ENST00000534548.2 - 4 448 c.382_splice c.e4-1 p.G128_splice NM_015261.2 NP_056076.1 P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 128 cell division|mitotic chromosome condensation nuclear centromeric heterochromatin|nuclear condensin complex methylated histone residue binding NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 71 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) TGGCTACACTGCCTATTCATG 0.358000 50 63 0 0 1 0 0 CYP24A1 0 broad.mit.edu 37 20 52775530 52775530 + Missense_Mutation SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr20:52775530G>A ENST00000216862.3 - 8 1516 c.1123C>T c.(1123-1125)Ccg>Tcg p.P375S CYP24A1_ENST00000395955.3_Missense_Mutation_p.P375S|CYP24A1_ENST00000395954.3_Missense_Mutation_p.P233S NM_000782.4 NP_000773.2 Q07973 CP24A_HUMAN cytochrome P450, family 24, subfamily A, polypeptide 1 375 hormone biosynthetic process|osteoblast differentiation|vitamin D catabolic process|vitamin D receptor signaling pathway|xenobiotic metabolic process mitochondrial inner membrane 1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity|electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 24 Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05) STAD - Stomach adenocarcinoma(23;0.206) Calcidiol(DB00146)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Paricalcitol(DB00910) TTTAAATACGGCATATTCCTC 0.388000 4 206 0 0 1 0 0 PDLIM3 27295 broad.mit.edu 37 4 186429465 186429465 + Missense_Mutation SNP G G A rs1141102 TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr4:186429465G>A ENST00000284770.5 - 5 723 c.650C>T c.(649-651)aCa>aTa p.T217I PDLIM3_ENST00000284767.5_3'UTR|PDLIM3_ENST00000284771.6_Intron NM_014476.5 NP_055291.2 Q53GG5 PDLI3_HUMAN PDZ and LIM domain 3 217 T -> I (in Ref. 1; AAC16670). sarcomere zinc ion binding breast(2)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 17 all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243) OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171) CATCAAAGGTGTTTCCCCTAG 0.393000 7 220 0 0 1 0 0 OR4C46 119749 broad.mit.edu 37 11 51515327 51515327 + Missense_Mutation SNP A A G TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr11:51515327A>G ENST00000328188.1 + 1 46 c.46A>G c.(46-48)Aca>Gca p.T16A NM_001004703.1 NP_001004703.1 A6NHA9 O4C46_HUMAN olfactory receptor, family 4, subfamily C, member 46 16 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1) 48 GCTGGGGCTTACAGAGAATCC 0.343000 5 188 0 0 1 0 0 ATP1A2 477 broad.mit.edu 37 1 160094203 160094203 + Missense_Mutation SNP T T A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:160094203T>A ENST00000361216.3 + 6 702 c.613T>A c.(613-615)Tct>Act p.S205T ATP1A2_ENST00000392233.3_Missense_Mutation_p.S205T|ATP1A2_ENST00000472488.1_3'UTR NM_000702.3 NP_000693.1 P50993 AT1A2_HUMAN ATPase, Na+/K+ transporting, alpha 2 polypeptide 205 ATP biosynthetic process ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1) 69 all_cancers(52;1.11e-16)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246) CCGGATCATCTCTTCTCATGG 0.562000 13 20 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr7:140453136A>T ENST00000288602.6 - 15 1859 c.1799T>A c.(1798-1800)gTg>gAg p.V600E NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN v-raf murine sarcoma viral oncogene homolog B 600 Protein kinase. V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis). activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3) 27380 Melanoma(164;0.00956) Sorafenib(DB00398) TCGAGATTTCACTGTAGCTAG 0.368000 V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN) 61 """Mis, T, O""" """AKAP9, KIAA1549""" """melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma""" Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome 63 76 0 0 1 0 0 RP1 6101 broad.mit.edu 37 8 55541490 55541490 + Missense_Mutation SNP C C A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr8:55541490C>A ENST00000220676.1 + 4 5196 c.5048C>A c.(5047-5049)tCt>tAt p.S1683Y NM_006269.1 NP_006260.1 P56715 RP1_HUMAN retinitis pigmentosa 1 (autosomal dominant) 1683 axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment microtubule binding NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2) 169 all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123) OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285) TTTGGCTCTTCTGAACAGGTA 0.413000 20 219 7.41877e-09 7.72158e-09 1 1 0 HACL1 26061 broad.mit.edu 37 3 15616558 15616558 + Missense_Mutation SNP A A G TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr3:15616558A>G ENST00000321169.5 - 10 1202 c.835T>C c.(835-837)Ttt>Ctt p.F279L HACL1_ENST00000457447.2_Missense_Mutation_p.F253L|HACL1_ENST00000451445.2_Missense_Mutation_p.F197L|HACL1_ENST00000456194.2_Missense_Mutation_p.F252L|HACL1_ENST00000435217.2_Intron NM_012260.2 NP_036392.2 Q9UJ83 HACL1_HUMAN 2-hydroxyacyl-CoA lyase 1 279 fatty acid alpha-oxidation peroxisomal matrix carbon-carbon lyase activity|identical protein binding|magnesium ion binding|thiamine pyrophosphate binding NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1) 16 CTGGCACCAAATAACACAATT 0.318000 12 78 0 0 1 0 0 GON4L 54856 broad.mit.edu 37 1 155734928 155734928 + Missense_Mutation SNP C C G TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:155734928C>G ENST00000437809.1 - 21 4458 c.4336G>C c.(4336-4338)Gtt>Ctt p.V1446L GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000271883.5_Missense_Mutation_p.V1446L|GON4L_ENST00000368331.1_Missense_Mutation_p.V1446L|GON4L_ENST00000361040.5_Missense_Mutation_p.V1446L Q3T8J9 GON4L_HUMAN gon-4-like (C. elegans) 1446 regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1) 45 Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195) TCTGGCCCAACTGGAGTCCCC 0.502000 22 232 0 0 1 0 0 FOXP2 93986 broad.mit.edu 37 7 114270000 114270000 + Silent SNP G G A TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr7:114270000G>A ENST00000393500.3 + 11 1132 c.312G>A c.(310-312)caG>caA p.Q104Q FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393494.2_Silent_p.Q179Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q O15409 FOXP2_HUMAN forkhead box P2 179 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding p.Q204Q(1) breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 52 agcaacaacagcagcagcagc 0.498000 4 78 0 0 1 0 0 SLC6A9 6536 broad.mit.edu 37 1 44489938 44489938 + Frame_Shift_Del DEL T T - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:44489938delT ENST00000372310.3 - 2 177 c.12delA c.(10-12)aafs p.K4fs SLC6A9_ENST00000475075.2_5'UTR|SLC6A9_ENST00000537678.1_5'UTR|SLC6A9_ENST00000492434.2_5'UTR|SLC6A9_ENST00000372306.3_Frame_Shift_Del_p.K4fs NM_001024845.2 NP_001020016.1 P48067 SC6A9_HUMAN solute carrier family 6 (neurotransmitter transporter, glycine), member 9 335 integral to plasma membrane|membrane fraction glycine:sodium symporter activity|neurotransmitter:sodium symporter activity endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2) 22 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0511) Glycine(DB00145) CTTTGGCACCTTTTCCTACCA 0.627 8 657 --- --- --- --- OR2T2 401992 broad.mit.edu 37 1 248616705 248616711 + Frame_Shift_Del DEL TGCTGCG TGCTGCG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr1:248616705_248616711delTGCTGCG ENST00000342927.3 + 1 629_635 c.607_613delTGCTGCG c.(607-615)tgfs p.CCV203fs NM_001004136.1 NP_001004136.1 Q6IF00 OR2T2_HUMAN olfactory receptor, family 2, subfamily T, member 2 203 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1) 37 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) GATGTATGCCTGCTGCGTGCTGATGCT 0.527 4 2 --- --- --- --- ERC2 26059 broad.mit.edu 37 3 55733470 55733472 + In_Frame_Del DEL TGG TGG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr3:55733470_55733472delTGG ENST00000288221.6 - 16 3036_3038 c.2781_2783delCCA c.(2779-2784)cat>ca p.HH931del NM_015576.1 NP_056391.1 O15083 ERC2_HUMAN ELKS/RAB6-interacting/CAST family member 2 931 Poly-His. cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome protein binding breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1) 31 KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219) gtggtggtgatggtggtggtggt 0.502 8 479 --- --- --- --- MUC20 200958 broad.mit.edu 37 3 195452664 195452664 + Frame_Shift_Del DEL C C - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr3:195452664delC ENST00000320736.6 + 3 803 c.677delC c.(676-678)acfs p.T226fs MUC20_ENST00000445522.2_Frame_Shift_Del_p.T362fs|MUC20_ENST00000447234.2_Frame_Shift_Del_p.T397fs|MUC20_ENST00000436408.1_Frame_Shift_Del_p.T397fs NM_001098516.1|NM_152673.2 NP_001091986.1|NP_689886.2 Q8N307 MUC20_HUMAN mucin 20, cell surface associated 397 12 X 20 AA approximate tandem repeats of S-S-E-S-S-A-S-S-D-S-P-H-P-V-I-T-P-S-R-A.|Ser-rich. Missing. protein homooligomerization apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1) 23 all_cancers(143;1.8e-08)|Ovarian(172;0.0634) Lung NSC(153;0.191) Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128) GBM - Glioblastoma multiforme(46;1.66e-05) CCAGTCATCACCCCCTCATGG 0.587 4 6 --- --- --- --- GLCCI1 113263 broad.mit.edu 37 7 8126097 8126099 + In_Frame_Del DEL CAG CAG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr7:8126097_8126099delCAG ENST00000223145.5 + 8 2130_2132 c.1573_1575delCAG c.(1573-1575)del p.Q528del NM_138426.3 NP_612435.1 Q86VQ1 GLCI1_HUMAN glucocorticoid induced transcript 1 528 Poly-Gln. endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2) 25 Ovarian(82;0.0608) UCEC - Uterine corpus endometrioid carcinoma (126;0.206) GCAGCCATCCCAGCAGCAGCAGC 0.562 7 648 --- --- --- --- TMEM66 51669 broad.mit.edu 37 8 29924352 29924353 + Frame_Shift_Ins INS - - G TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr8:29924352_29924353insG ENST00000256255.6 - 4 1039_1040 c.782_783insC c.(781-783)cggfs p.R261fs TMEM66_ENST00000536273.1_Frame_Shift_Ins_p.R89fs|TMEM66_ENST00000545648.1_Frame_Shift_Ins_p.R89fs NM_016127.4 NP_057211.4 Q96BY9 TMM66_HUMAN transmembrane protein 66 261 integral to membrane endometrium(2)|large_intestine(1)|lung(11) 14 KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119) TCCAGAACCCTGGTCCTGAATT 0.401 8 216 --- --- --- --- LZTS2 84445 broad.mit.edu 37 10 102763415 102763417 + In_Frame_Del DEL CCT CCT - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr10:102763415_102763417delCCT ENST00000370220.1 + 2 3623_3625 c.560_562delCCT c.(559-564)gcc>g p.AS187del LZTS2_ENST00000370223.3_In_Frame_Del_p.AS187del Q9BRK4 LZTS2_HUMAN leucine zipper, putative tumor suppressor 2 187 Required for centrosomal localization (By similarity). cell division|mitosis|Wnt receptor signaling pathway membrane|microtubule|microtubule organizing center breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 22 Epithelial(162;7.3e-09)|all cancers(201;3.72e-07) GGGGGCCCTGcctcctcctcctc 0.650 7 437 --- --- --- --- NUP98 4928 broad.mit.edu 37 11 3720389 3720389 + Frame_Shift_Del DEL T T - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr11:3720389delT ENST00000324932.7 - 25 4352 c.3932delA c.(3931-3933)acfs p.N1311fs NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs NM_016320.4|NM_139132.3 NP_057404.2|NP_624358.2 P52948 NUP98_HUMAN nucleoporin 98kDa 1328 carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 66 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) CACAGGGCTGTTTTTTTGGGT 0.512 T """HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11""" AML 7 505 --- --- --- --- FOLH1B 219595 broad.mit.edu 37 11 89405323 89405326 + RNA DEL TTTA TTTA - rs34562444 TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr11:89405323_89405326delTTTA ENST00000532352.1 + 0 1114 Q9HBA9 FOH1B_HUMAN folate hydrolase 1B proteolysis cytoplasm dipeptidase activity|metal ion binding|metallopeptidase activity breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2) 48 aattatattgtttatttatttttg 0.230 5 3 --- --- --- --- CADM1 23705 broad.mit.edu 37 11 115080312 115080314 + In_Frame_Del DEL TGG TGG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr11:115080312_115080314delTGG ENST00000537058.1 - 8 1078_1080 c.1058_1060delCCA c.(1057-1062)atc>a p.TI353del CADM1_ENST00000331581.6_In_Frame_Del_p.TI353del|CADM1_ENST00000542447.2_Intron|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000536727.1_Intron|CADM1_ENST00000452722.2_In_Frame_Del_p.TI353del Q9BY67 CADM1_HUMAN cell adhesion molecule 1 353 PPTTIPPPTTTTTTTTTTTTTILTIIT -> TTATTEPAVH GLTQLPNSAEELDSEDLS (in Ref. 3; BAC11657). adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity basolateral plasma membrane|cell-cell junction|integral to membrane PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1) 32 all_hematologic(175;0.0628) all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237) BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303) atggtaaggatggtggtggtggt 0.429 7 119 --- --- --- --- FAM155A 728215 broad.mit.edu 37 13 108518687 108518689 + In_Frame_Del DEL CTG CTG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr13:108518687_108518689delCTG ENST00000375915.2 - 1 394_396 c.256_258delCAG c.(256-258)del p.Q86del NM_001080396.2 NP_001073865.1 B1AL88 F155A_HUMAN family with sequence similarity 155, member A 86 Poly-Gln. integral to membrane binding breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1) 33 gccgctgcctctgctgctgctgc 0.719 8 106 --- --- --- --- RTL1 388015 broad.mit.edu 37 14 101350670 101350671 + In_Frame_Ins INS - - TCT rs55755518 by1000genomes TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr14:101350670_101350671insTCT ENST00000534062.1 - 1 513_514 c.455_456insAGA c.(454-456)gca>gAGAca p.152_152A>ET NM_001134888.2 NP_001128360.1 E9PKS8 E9PKS8_HUMAN retrotransposon-like 1 152 breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2) 21 TCTGGTTTTGCTCTTGAGGAGT 0.520 5 5 --- --- --- --- RP11-439I14.2 0 broad.mit.edu 37 16 64770704 64770705 + RNA INS - - CCAGTGATGGTCACCT rs140029302 by1000genomes TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr16:64770704_64770705insCCAGTGATGGTCACCT ENST00000564293.1 + 0 453_454 TGTCACCACTGCCACCTTGTTC 0.371 3 4 --- --- --- --- RAMP2-AS1 0 broad.mit.edu 37 17 40905932 40905933 + RNA DEL TT TT - rs74319303 TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr17:40905932_40905933delTT ENST00000592670.1 - 0 3116_3117 NR_024461.1 CTCCAACttctttttttttttt 0.540 2 4 --- --- --- --- FAM98C 147965 broad.mit.edu 37 19 38899502 38899504 + In_Frame_Del DEL AAG AAG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr19:38899502_38899504delAAG ENST00000252530.5 + 8 1049_1051 c.1030_1032delAAG c.(1030-1032)del p.K349del FAM98C_ENST00000343358.7_In_Frame_Del_p.K267del|FAM98C_ENST00000588262.1_3'UTR NM_174905.3 NP_777565.3 Q17RN3 FA98C_HUMAN family with sequence similarity 98, member C 349 endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1) 15 all_cancers(60;3.95e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) TTGGGGTCGCAAGAAGAAGAAGA 0.606 7 154 --- --- --- --- FUZ 80199 broad.mit.edu 37 19 50310483 50310485 + In_Frame_Del DEL CAG CAG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr19:50310483_50310485delCAG ENST00000313777.4 - 11 1343_1345 c.1180_1182delCTG c.(1180-1182)del p.L394del FUZ_ENST00000445575.2_Intron|FUZ_ENST00000533418.1_In_Frame_Del_p.L344del|FUZ_ENST00000528094.1_In_Frame_Del_p.L358del NM_025129.4 NP_079405.2 Q9BT04 FUZZY_HUMAN fuzzy planar cell polarity protein 394 Leu-rich. cilium assembly|embryonic body morphogenesis|embryonic skeletal system morphogenesis|establishment of planar polarity|hair follicle development|neural tube closure|protein transport|regulation of smoothened signaling pathway cytoplasm|cytoskeleton endometrium(1)|lung(3) 4 all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116) TCTGGGGAGACAGCAGCAGCAGC 0.635 7 107 --- --- --- --- KB-1592A4.15 0 broad.mit.edu 37 22 21470220 21470220 + RNA DEL G G - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chr22:21470220delG ENST00000420508.1 - 0 3508 BCRP2_ENST00000461808.1_RNA TCCCGCAGGAGAGAGAGGTCC 0.627 3 6 --- --- --- --- MED12 9968 broad.mit.edu 37 X 70360648 70360650 + In_Frame_Del DEL CAG CAG - TCGA-ET-A2N4-01A-12D-A19J-08 TCGA-ET-A2N4-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e2107cb-8c52-4f2a-8c41-1a305c14044c c9f32c4e-5746-4269-9e5b-e8816cf87b93 g.chrX:70360648_70360650delCAG ENST00000333646.6 + 42 6416_6418 c.6217_6219delCAG c.(6217-6219)del p.Q2079del MED12_ENST00000478889.1_3'UTR|MED12_ENST00000374080.3_In_Frame_Del_p.Q2076del|MED12_ENST00000374102.1_In_Frame_Del_p.Q2075del NM_005120.2 NP_005111.2 Q93074 MED12_HUMAN mediator complex subunit 12 2076 Gln-rich. 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 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) gcaacagcaacagcagcagcagc 0.621 """M, S""" uterine leiomyoma Opitz-Kaveggia Syndrome 7 99 --- --- --- ---