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 NID2 22795 broad.mit.edu 37 14 52508861 52508861 + Nonsense_Mutation SNP A A T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr14:52508861A>T ENST00000216286.5 - 7 1786 c.1787T>A c.(1786-1788)tTa>tAa p.L596* NID2_ENST00000541773.1_Nonsense_Mutation_p.L543* NM_007361.3 NP_031387.3 Q14112 NID2_HUMAN nidogen 2 (osteonidogen) 596 Nidogen G2 beta-barrel. basement membrane calcium ion binding|collagen binding NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 87 Breast(41;0.0639)|all_epithelial(31;0.123) AGGTTTTTCTAAAGCAAAGAG 0.602000 37 69 0 0 1 0 0 GJB2 0 broad.mit.edu 37 13 20763342 20763342 + Missense_Mutation SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr13:20763342G>A ENST00000382844.1 - 1 577 c.379C>T c.(379-381)Cgc>Tgc p.R127C GJB2_ENST00000382848.4_Missense_Mutation_p.R127C P29033 CXB2_HUMAN gap junction protein, beta 2, 26kDa 127 R -> H (very common polymorphism in India). cell-cell signaling|cellular membrane organization|gap junction assembly|sensory perception of sound|transport connexon complex|ER-Golgi intermediate compartment|integral to membrane breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1) 7 all_cancers(29;3.95e-22)|all_epithelial(30;2.36e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822) all cancers(112;0.000435)|Epithelial(112;0.000722)|OV - Ovarian serous cystadenocarcinoma(117;0.0096)|Lung(94;0.0236)|LUSC - Lung squamous cell carcinoma(192;0.0738) CCTTCGATGCGGACCTTCTGG 0.512000 Keratitis, Ichthyosis and Deafness syndrome OREG0022282 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 27 51 0 0 1 0 0 AIFM3 150209 broad.mit.edu 37 22 21327704 21327704 + Missense_Mutation SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr22:21327704G>A ENST00000399167.2 + 3 380 c.140G>A c.(139-141)cGc>cAc p.R47H AIFM3_ENST00000399163.2_Missense_Mutation_p.R47H|AIFM3_ENST00000333607.6_Missense_Mutation_p.R47H|AIFM3_ENST00000405089.1_Missense_Mutation_p.R53H|AIFM3_ENST00000335375.5_Missense_Mutation_p.A72T|AIFM3_ENST00000440238.2_Missense_Mutation_p.R47H NM_144704.2 NP_653305.1 apoptosis-inducing factor, mitochondrion-associated, 3 breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1) 21 all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0367) LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195) GGCACGGCCCGCCACTTCCAC 0.662000 7 8 0 0 1 0 0 TTC3 7267 broad.mit.edu 37 21 38536463 38536463 + Missense_Mutation SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr21:38536463G>A ENST00000399017.2 + 32 6028 c.3281G>A c.(3280-3282)cGc>cAc p.R1094H TTC3_ENST00000354749.2_Missense_Mutation_p.R1094H|TTC3_ENST00000355666.1_Missense_Mutation_p.R1094H|TTC3_ENST00000479930.1_3'UTR NM_003316.3 NP_003307.3 P53804 TTC3_HUMAN tetratricopeptide repeat domain 3 1094 protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process nucleus protein binding|ubiquitin-protein ligase activity|zinc ion binding breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5) 75 Myeloproliferative disorder(46;0.0412) TATGTTGTCCGCAATAAGAAG 0.393000 19 40 0 0 1 0 0 POTEA 340441 broad.mit.edu 37 8 43157186 43157186 + RNA SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr8:43157186G>A ENST00000522175.2 + 0 697 Q6S8J7 POTEA_HUMAN POTE ankyrin domain family, member A breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1) 46 GCAAAATATTGATGTATTTTC 0.318000 52 180 0 0 1 0 0 OR4A47 403253 broad.mit.edu 37 11 48510647 48510647 + Silent SNP C C T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr11:48510647C>T ENST00000446524.1 + 1 379 c.303C>T c.(301-303)atC>atT p.I101I NM_001005512.2 NP_001005512.2 Q6IF82 O4A47_HUMAN olfactory receptor, family 4, subfamily A, member 47 101 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2) 29 AGCTCTTTATCGAGCACATTT 0.428000 46 65 0 0 1 0 0 PNPLA7 375775 broad.mit.edu 37 9 140392628 140392628 + Silent SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr9:140392628G>A ENST00000406427.1 - 17 2163 c.1827C>T c.(1825-1827)ttC>ttT p.F609F PNPLA7_ENST00000277531.4_Silent_p.F584F|PNPLA7_ENST00000371457.1_Silent_p.F190F NM_001098537.1 NP_001092007.1 Q6ZV29 PLPL7_HUMAN patatin-like phospholipase domain containing 7 584 lipid metabolic process endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane hydrolase activity breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 40 all_cancers(76;0.126) OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839) TTTGCCGCACGAAGGACGACA 0.632000 10 32 0 0 1 0 0 PCDHA12 0 broad.mit.edu 37 5 140257309 140257309 + Missense_Mutation SNP C C T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr5:140257309C>T ENST00000398631.2 + 1 2252 c.2252C>T c.(2251-2253)tCg>tTg p.S751L PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron NM_018903.2|NM_031864.1 NP_061726.1|NP_114070.1 NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1) 78 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGGTCTTACTCGCAGCAGAGG 0.647000 17 24 0 0 1 0 0 SAMD9 54809 broad.mit.edu 37 7 92735120 92735120 + Silent SNP T T C TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr7:92735120T>C ENST00000379958.2 - 3 560 c.291A>G c.(289-291)aaA>aaG p.K97K NM_001193307.1|NM_017654.3 NP_001180236.1|NP_060124.2 Q5K651 SAMD9_HUMAN sterile alpha motif domain containing 9 97 cytoplasm NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2) 88 all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125) STAD - Stomach adenocarcinoma(171;0.000302) CAGTTTGGTCTTTAGGAGCAT 0.378000 68 166 0 0 1 0 0 NBPF1 55672 broad.mit.edu 37 1 16918653 16918653 + Splice_Site SNP C C T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr1:16918653C>T ENST00000430580.2 - 6 853 c.e6+1 NM_017940.3 NP_060410.2 Q3BBV0 NBPF1_HUMAN neuroblastoma breakpoint family, member 1 cytoplasm UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179) TCTTAACTTACTGTTGTGAAA 0.418000 5 52 0 0 1 0 0 ANKRD52 283373 broad.mit.edu 37 12 56646642 56646642 + Missense_Mutation SNP T T C TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr12:56646642T>C ENST00000267116.7 - 12 1344 c.1223A>G c.(1222-1224)cAt>cGt p.H408R NM_173595.3 NP_775866.2 Q8NB46 ANR52_HUMAN ankyrin repeat domain 52 408 protein binding endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1) 29 TGAAAGCACATGCTCATTGCT 0.522000 13 19 0 0 1 0 0 TIGD3 220359 broad.mit.edu 37 11 65123573 65123573 + Silent SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr11:65123573G>A ENST00000309880.5 + 2 501 c.294G>A c.(292-294)acG>acA p.T98T NM_145719.2 NP_663771.1 Q6B0B8 TIGD3_HUMAN tigger transposable element derived 3 98 HTH CENPB-type. regulation of transcription, DNA-dependent chromosome, centromeric region|nucleus DNA binding endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2) 17 GGGACGTGACGGGGCCCATGC 0.642000 25 39 0 0 1 0 0 REST 5978 broad.mit.edu 37 4 57777036 57777036 + Missense_Mutation SNP C C T rs142504829 TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr4:57777036C>T ENST00000309042.7 + 2 546 c.232C>T c.(232-234)Ccg>Tcg p.P78S NM_001193508.1|NM_005612.4 NP_001180437.1|NP_005603.3 Q13127 REST_HUMAN RE1-silencing transcription factor 78 Interaction with SIN3A. cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent cytoplasm|transcriptional repressor complex calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2) 50 Glioma(25;0.08)|all_neural(26;0.181) AGAACTGATGCCGGTTGGGGA 0.448000 3 48 0 0 1 0 0 CCSER1 401145 broad.mit.edu 37 4 91229784 91229784 + Missense_Mutation SNP G G T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr4:91229784G>T ENST00000509176.1 + 2 637 c.349G>T c.(349-351)Gtt>Ttt p.V117F CCSER1_ENST00000333691.8_Missense_Mutation_p.V117F|CCSER1_ENST00000432775.2_Missense_Mutation_p.V117F NM_001145065.1 NP_001138537.1 coiled-coil serine-rich protein 1 AAGACATTCTGTTGGTTTTAG 0.363000 3 46 1 1 1 1 0 POLR1A 25885 broad.mit.edu 37 2 86258685 86258685 + Missense_Mutation SNP C C T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr2:86258685C>T ENST00000263857.6 - 30 4724 c.4346G>A c.(4345-4347)cGa>cAa p.R1449Q POLR1A_ENST00000409681.1_Missense_Mutation_p.R1449Q O95602 RPA1_HUMAN polymerase (RNA) I polypeptide A, 194kDa 1449 termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter DNA-directed RNA polymerase I complex|nucleoplasm DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5) 63 GTGGGGATTTCGTtcctcctg 0.577000 22 31 0 0 1 0 0 FHDC1 85462 broad.mit.edu 37 4 153897503 153897503 + Silent SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr4:153897503G>A ENST00000511601.1 + 12 3248 c.3060G>A c.(3058-3060)ccG>ccA p.P1020P FHDC1_ENST00000260008.3_Silent_p.P1020P Q9C0D6 FHDC1_HUMAN FH2 domain containing 1 1020 actin cytoskeleton organization actin binding ARFIP1/FHDC1(2) NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 43 all_hematologic(180;0.093) CCAAGACCCCGTCAGTGCCCA 0.612000 5 54 0 0 1 0 0 MATN4 8785 broad.mit.edu 37 20 43929859 43929859 + Missense_Mutation SNP C C A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr20:43929859C>A ENST00000537548.1 - 6 1016 c.772G>T c.(772-774)Gac>Tac p.D258Y MATN4_ENST00000372754.1_Missense_Mutation_p.D299Y|MATN4_ENST00000372756.1_Missense_Mutation_p.D258Y|MATN4_ENST00000353917.5_Intron|MATN4_ENST00000342716.4_Missense_Mutation_p.D258Y|MATN4_ENST00000372753.1_Missense_Mutation_p.D109Y|MATN4_ENST00000372751.4_Missense_Mutation_p.D109Y|MATN4_ENST00000360607.5_Missense_Mutation_p.D217Y O95460 MATN4_HUMAN matrilin 4 299 EGF-like 2. extracellular region protein binding central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 27 Myeloproliferative disorder(115;0.0122) CTGCAGTAGTCAATGGCTGGC 0.592000 OREG0025977 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 4 86 0.00024832 0.000260145 1 1 0 PAX4 5078 broad.mit.edu 37 7 127255484 127255484 + Missense_Mutation SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr7:127255484G>A ENST00000341640.2 - 1 296 c.91C>T c.(91-93)Cgg>Tgg p.R31W PAX4_ENST00000338516.3_Missense_Mutation_p.R39W|PAX4_ENST00000463946.1_5'UTR|PAX4_ENST00000378740.2_Missense_Mutation_p.R31W NM_006193.2 NP_006184.2 O43316 PAX4_HUMAN paired box 4 39 Paired. cell differentiation|endocrine pancreas development|organ morphogenesis nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity p.R31W(1) cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 35 TCACAGGGCCGCATTCCACTG 0.582000 3 73 0 0 1 0 0 LEF1 51176 broad.mit.edu 37 4 109000748 109000748 + Missense_Mutation SNP C C T rs146861754 TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr4:109000748C>T ENST00000379951.2 - 6 1849 c.661G>A c.(661-663)Ggt>Agt p.G221S LEF1_ENST00000438313.2_Missense_Mutation_p.G221S|LEF1_ENST00000510624.1_Missense_Mutation_p.G153S|LEF1_ENST00000265165.1_Missense_Mutation_p.G249S NM_001130713.2|NM_001130714.2 NP_001124185.1|NP_001124186.1 Q9UJU2 LEF1_HUMAN lymphoid enhancer-binding factor 1 249 Pro-rich. canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation cytoplasm|protein-DNA complex|transcription factor complex armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding p.G249S(1) endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1) 25 OV - Ovarian serous cystadenocarcinoma(123;0.000224) CCAGGAGGACCGGGAATCATA 0.468000 3 44 0 0 1 0 0 ISLR 3671 broad.mit.edu 37 15 74468241 74468241 + Missense_Mutation SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr15:74468241G>A ENST00000249842.3 + 2 1399 c.1042G>A c.(1042-1044)Ggt>Agt p.G348S ISLR_ENST00000395118.1_Missense_Mutation_p.G348S|RP11-665J16.1_ENST00000561647.1_RNA NM_005545.3 NP_005536.1 O14498 ISLR_HUMAN immunoglobulin superfamily containing leucine-rich repeat 348 cell adhesion extracellular region central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1) 20 GGCCACGCCCGGTGAGGGTGG 0.632000 8 15 0 0 1 0 0 POM121L9P 0 broad.mit.edu 37 22 24659591 24659591 + RNA SNP A A G TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr22:24659591A>G ENST00000414583.2 + 0 3116 NR_003714.1 ACTCACTGACATCGAAGGCTG 0.632000 3 13 0 0 1 0 0 CDH23 64072 broad.mit.edu 37 10 73437354 73437354 + Missense_Mutation SNP G G T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr10:73437354G>T ENST00000224721.6 + 15 1676 c.1671G>T c.(1669-1671)ttG>ttT p.L557F CDH23_ENST00000299366.7_Missense_Mutation_p.L597F NM_022124.5 NP_071407.4 Q9H251 CAD23_HUMAN cadherin-related 23 552 Cadherin 5. calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound cytosol|integral to membrane|plasma membrane|stereocilium calcium ion binding|protein binding NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3) 133 TCAATGTGTTGGATGTCAACG 0.617000 9 7 2.17888e-05 2.33831e-05 1 1 0 RP11-114H24.7 0 broad.mit.edu 37 15 78211648 78211648 + RNA SNP A A G TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr15:78211648A>G ENST00000565869.1 + 0 111 RP11-114H24.2_ENST00000567226.1_RNA CGCCAGGGATAGGGGCTCAGC 0.522000 4 60 0 0 1 0 0 AGPS 8540 broad.mit.edu 37 2 178386036 178386036 + Silent SNP C C T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr2:178386036C>T ENST00000264167.4 + 18 1883 c.1737C>T c.(1735-1737)ttC>ttT p.F579F AGPS_ENST00000409888.1_Intron NM_003659.3 NP_003650.1 O00116 ADAS_HUMAN alkylglycerone phosphate synthase 579 ether lipid biosynthetic process peroxisomal matrix|peroxisomal membrane|plasma membrane alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1) 32 OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358) GTATCTACTTCTATTTTGCCT 0.388000 33 75 0 0 1 0 0 PPFIA3 8541 broad.mit.edu 37 19 49636536 49636536 + Missense_Mutation SNP G G A TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr19:49636536G>A ENST00000334186.4 + 9 1418 c.1069G>A c.(1069-1071)Gcc>Acc p.A357T PPFIA3_ENST00000602351.1_Missense_Mutation_p.A357T NM_003660.2 NP_003651.1 O75145 LIPA3_HUMAN protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3 357 cell surface|cytoplasm protein binding NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1) 35 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677) GTTGGACGACGCCAAGCAGAA 0.687000 4 40 0 0 1 0 0 KRTAP5-5 439915 broad.mit.edu 37 11 1651241 1651241 + Silent SNP A A C TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr11:1651241A>C ENST00000399676.2 + 1 209 c.171A>C c.(169-171)ggA>ggC p.G57G NM_001001480.2 NP_001001480.2 Q701N2 KRA55_HUMAN keratin associated protein 5-5 57 keratin filament endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1) 33 all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082) gctgtgggggatgtggctccg 0.682000 4 77 0 0 1 0 0 TUBB8P7 0 broad.mit.edu 37 16 90162513 90162513 + RNA SNP T T C TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr16:90162513T>C ENST00000564451.1 + 0 1866 TUBB8P7_ENST00000567960.1_RNA p.N415N(2) GCAACATGAATGACCTGGTGT 0.537000 3 59 0 0 1 0 0 KRT85 3891 broad.mit.edu 37 12 52761081 52761081 + Missense_Mutation SNP C C T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr12:52761081C>T ENST00000257901.3 - 1 184 c.109G>A c.(109-111)Gcc>Acc p.A37T NM_002283.3 NP_002274.1 P78386 KRT85_HUMAN keratin 85 37 Head. epidermis development keratin filament protein binding|structural molecule activity NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 36 Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088) BRCA - Breast invasive adenocarcinoma(357;0.189) CGGTAGGGGGCGGCGCTGATG 0.672000 3 24 0 0 1 0 0 HSP90AA1 3320 broad.mit.edu 37 14 102548543 102548543 + Nonsense_Mutation SNP A A T TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr14:102548543A>T ENST00000334701.7 - 11 2641 c.2360T>A c.(2359-2361)tTg>tAg p.L787* HSP90AA1_ENST00000216281.8_Nonsense_Mutation_p.L665* NM_001017963.2 NP_001017963.2 P07900 HS90A_HUMAN heat shock protein 90kDa alpha (cytosolic), class A member 1 665 axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction cytosol|melanosome|plasma membrane ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1) 28 Rifabutin(DB00615) TTCATAAAGCAAGATGACCAG 0.458000 42 115 0 0 1 0 0 DUSP27 92235 broad.mit.edu 37 1 167095398 167095400 + In_Frame_Del DEL GAG GAG - TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr1:167095398_167095400delGAG ENST00000361200.2 + 6 1196_1198 c.1030_1032delGAG c.(1030-1032)del p.E348del DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_In_Frame_Del_p.E348del|DUSP27_ENST00000443333.1_In_Frame_Del_p.E348del Q5VZP5 DUS27_HUMAN dual specificity phosphatase 27 (putative) 348 protein dephosphorylation protein tyrosine/serine/threonine phosphatase activity NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3) 89 CCTCATAGACGAGGAGGAGGAGG 0.655 3 6 --- --- --- --- PCSK5 5125 broad.mit.edu 37 9 78790207 78790208 + Frame_Shift_Ins INS - - GAATA rs55947300 TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr9:78790207_78790208insGAATA ENST00000376767.3 + 14 2574_2575 c.2062_2063insGAATA c.(2062-2064)aatfs p.N688fs PCSK5_ENST00000376752.4_Intron|PCSK5_ENST00000545128.1_Intron Q92824 PCSK5_HUMAN proprotein convertase subtilisin/kexin type 5 0 CRM (Cys-rich motif). anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release extracellular space|Golgi lumen|stored secretory granule peptide binding|serine-type endopeptidase activity NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3) 55 cgaatcgaatcgaatagaatag 0.342 2 4 --- --- --- --- RP11-909M7.3 0 broad.mit.edu 37 14 101440134 101440137 + RNA DEL AATA AATA - TCGA-KK-A8I8-01A-11D-A364-08 TCGA-KK-A8I8-11A-11D-A362-08 Untested Somatic Phase_I WXS none Illumina GAIIx 99d7021e-f0da-44fb-8f6c-5bcd2c433a0e fe39a0c2-56d9-445c-ab4b-744d4d21f8c2 g.chr14:101440134_101440137delAATA ENST00000554693.2 + 0 384 TCAAGGGCAGaataaataaattta 0.279 4 5 --- --- --- ---