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 COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_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 ACHILLES_Lineage_Results_Top_Genes CGC_CancerGermlineMut CGC_CancerMolecularGenetics CGC_CancerSomaticMut CGC_CancerSyndrome CGC_Chr CGC_ChrBand CGC_GeneID CGC_Name CGC_OtherGermlineMut CGC_TissueType COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs Ensembl_so_accession Ensembl_so_term Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym annotation_transcript bcgsc broad build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP_NR dbNSFP_GERP_RS dbNSFP_GERP_RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_folddegenerate dbNSFP_genename dbNSFP_hg18_pos1coor dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon entrez_gene_id external_id_capture gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_type havana_transcript hgsc igv_bad ucsc t_alt_count t_ref_count n_alt_count n_ref_count validation_judgement_rna validation_power_rna validation_tumor_alt_count_rna validation_tumor_ref_count_rna validation_normal_alt_count_rna validation_normal_ref_count_rna min_val_count_rna validation_judgement_targeted validation_power_targeted validation_tumor_alt_count_targeted validation_tumor_ref_count_targeted validation_normal_alt_count_targeted validation_normal_ref_count_targeted min_val_count_targeted validation_judgement_localAssembly validation_power_localAssembly t_alt_count_localAssembly t_ref_count_localAssembly n_alt_count_localAssembly n_ref_count_localAssembly min_val_count_localAssembly validation_judgement_KRAS validation_power_KRAS t_alt_count_KRAS t_ref_count_KRAS n_alt_count_KRAS n_ref_count_KRAS min_val_count_KRAS pon_loglike pon_pass_loglike localAssembly_detected ExAC_AN ExAC_AC ExAC_LQ passExAC SCNA_NA SCNA_NB SCNA_q_hat SCNA_tau IS_SCNA purity ploidy dna_fraction_in_tumor CCF_hat CCF_CI95_low CCF_CI95_high CCF_mode CCF_mean CCF_median clonal CCF_CI_low CCF_CI_high TACR3 6870 broad.mit.edu 37 4 104577461 104577469 + In_Frame_Del DEL ATGGGAAAC ATGGGAAAC - TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr4:104577461_104577469delATGGGAAAC ENST00000304883.2 - 3 910_918 c.770_778delGTTTCCCAT c.(769-780)tgtttcccattg>ttg p.CFP257del NM_001059.2 NP_001050.1 P29371 NK3R_HUMAN tachykinin receptor 3 51 Hepatocellular(203;0.217) ATGATGAGCAATGGGAAACAGTACACCAG 0.392000 0 SO:0001651 inframe_deletion ENST00000304883.2 1 1 hg19 CCDS3664.1 TCGA-2J-AABR-01A-11D-A40W-08 TACR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253804.1 0 0 0 9 516 0 118 0 0 0 0 0 0 0 0 0 0 0 0 1 0.994679 16 517 0 116 2 -7.783322 1 1 0 0 1 1 2 3 2.014557 0 0.090000 1.970000 0.098921 0.430000 0.200000 1.000000 0.370000 0.513428 0.430000 0 0.290000 1.000000 CNNM2 54805 broad.mit.edu 37 10 104678687 104678687 + Silent SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr10:104678687C>T ENST00000369878.4 + 1 638 c.450C>T c.(448-450)tgC>tgT p.C150C CNNM2_ENST00000369875.3_Silent_p.C150C|CNNM2_ENST00000433628.2_Silent_p.C150C NM_017649.4 NP_060119.3 Q9H8M5 CNNM2_HUMAN cyclin and CBS domain divalent metal cation transport mediator 2 19 Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198) CCCAGCGATGCGGCATCCGCA 0.687000 0 SO:0001819 synonymous_variant ENST00000369878.4 0 1 hg19 CCDS44474.1 TCGA-2J-AABR-01A-11D-A40W-08 CNNM2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050113.3 0 0 0 8 656 0 144 0 1.185577e-03 0 4 0 144 2 0 0 0 0 0 2 1 0.989023 9 649 0 143 2 -2.095396 0 1 0 0 1 0 0 0 1.941341 0 0.090000 1.970000 0.054251 0.260000 0.120000 0.470000 0.250000 0.281374 0.260000 0 0.180000 0.370000 BCCIP 56647 broad.mit.edu 37 10 127520157 127520157 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr10:127520157C>T ENST00000278100.6 + 5 592 c.580C>T c.(580-582)Ccc>Tcc p.P194S BCCIP_ENST00000368759.5_Missense_Mutation_p.P194S|BCCIP_ENST00000429863.2_Missense_Mutation_p.P164S|BCCIP_ENST00000299130.3_Missense_Mutation_p.P194S NM_078468.2 NP_510868.1 Q9P287 BCCIP_HUMAN BRCA2 and CDKN1A interacting protein 8 all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936) GATCGCTCTGCCCATGTACCA 0.383000 0 SO:0001583 missense ENST00000278100.6 0 1 hg19 CCDS7651.1 . . . . . . . . . . C 27.2 4.808990 0.90707 . . ENSG00000107949 ENST00000278100;ENST00000299130;ENST00000368759;ENST00000429863;ENST00000392718 T;T;T;T 0.51071 0.72;0.72;0.72;0.72 5.24 5.24 0.73138 . 0.000000 0.85682 D 0.000000 T 0.78616 0.4311 H 0.94734 3.575 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 0.998;1.0;1.0;0.999;1.0 D 0.85215 0.1023 10 0.87932 D 0 -2.8285 18.8517 0.92235 0.0:1.0:0.0:0.0 . 164;194;194;194;194 B4E318;B4DUS0;Q9P287-2;Q9P287-4;Q9P287 .;.;.;.;BCCIP_HUMAN S 194;194;194;164;194 ENSP00000278100:P194S;ENSP00000299130:P194S;ENSP00000357748:P194S;ENSP00000394758:P164S ENSP00000278100:P194S P + 1 0 BCCIP 127510147 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.470000 0.80973 2.444000 0.82710 0.650000 0.86243 CCC TCGA-2J-AABR-01A-11D-A40W-08 BCCIP-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050941.1 0 0 0 6 325 0 52 1 6.088257e-01 4 101 0 52 2 0 0 0 0 0 2 1 0.964345 6 323 0 52 2 -2.939098 1 1 121412 1 30 1 0 0 0 1.941341 0 0.090000 1.970000 0.054251 0.400000 0.160000 0.750000 0.370000 0.425568 0.400000 0 0.260000 0.570000 PDSS1 23590 broad.mit.edu 37 10 27024505 27024505 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr10:27024505G>A ENST00000376215.5 + 10 1076 c.1023G>A c.(1021-1023)caG>caA p.Q341Q PDSS1_ENST00000376203.5_Intron|PDSS1_ENST00000470978.1_3'UTR NM_014317.3 NP_055132.2 Q5T2R2 DPS1_HUMAN prenyl (decaprenyl) diphosphate synthase, subunit 1 21 TTGCCTGTCAGCAGGTAGGTT 0.498000 0 SO:0001819 synonymous_variant ENST00000376215.5 0 1 hg19 CCDS31168.1 TCGA-2J-AABR-01A-11D-A40W-08 PDSS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047276.1 0 0 0 6 154 0 36 0 1.898360e-02 0 5 0 36 2 0 0 0 0 0 2 1 0.963800 6 151 0 36 2 -8.575297 1 1 0 0 1 1 2 3 2.006452 0 0.090000 1.970000 0.097312 0.930000 0.380000 1.000000 1.000000 0.841811 0.930000 1 0.600000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2J-AABR-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 0 0 8 215 0 67 1 4.051874e-02 2 6 0 67 2 1 9.986014e-01 5 339 0 515 2 1 0.988752 8 210 0 65 2 -3.951907 1 1 0 0 1 0 1 1 1.988592 0 0.090000 1.970000 0.080483 0.790000 0.380000 1.000000 1.000000 0.785590 0.790000 0 0.560000 1.000000 EDNRB 1910 broad.mit.edu 37 13 78477390 78477390 + Silent SNP G G T rs112618428 byFrequency TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr13:78477390G>T ENST00000334286.5 - 3 938 c.702C>A c.(700-702)gtC>gtA p.V234V EDNRB_ENST00000377211.4_Silent_p.V324V|EDNRB_ENST00000446573.1_Silent_p.V234V NM_000115.3|NM_001122659.2 NP_000106.1|NP_001116131.1 P24530 EDNRB_HUMAN endothelin receptor type B 42 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268) TGGCTTCAGGGACAGCCAGAA 0.433000 0 SO:0001819 synonymous_variant ENST00000334286.5 0 1 hg19 CCDS9461.1 TCGA-2J-AABR-01A-11D-A40W-08 EDNRB-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276505.1 0 0 0 13 630 0 121 0 6.544281e-02 0 19 0 121 2 0 0 0 0 0 2 1 0.999497 13 622 0 120 2 -2.597057 1 1 0 0 1 0 0 0 1.952484 0 0.090000 1.970000 0.059529 0.430000 0.240000 0.690000 0.430000 0.455257 0.430000 0 0.330000 0.570000 KLHDC2 23588 broad.mit.edu 37 14 50249311 50249311 + Splice_Site SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr14:50249311C>T ENST00000298307.5 + 12 1957 c.1096C>T c.(1096-1098)Cgg>Tgg p.R366W NEMF_ENST00000556925.1_5'Flank|KLHDC2_ENST00000554589.1_Intron|KLHDC2_ENST00000557247.1_Intron NM_014315.2 NP_055130.1 Q9Y2U9 KLDC2_HUMAN kelch domain containing 2 16 all_epithelial(31;0.000959)|Breast(41;0.0117) ATCTCTTGTACGGTAAGTAAC 0.308000 0 SO:0001630 splice_region_variant ENST00000298307.5 1 0 hg19 CCDS9693.1 . . . . . . . . . . C 17.83 3.484982 0.63962 . . ENSG00000165516 ENST00000298307 T 0.05081 3.5 5.23 3.12 0.35913 . 0.000000 0.85682 D 0.000000 T 0.22126 0.0533 M 0.73962 2.25 0.80722 D 1 D 0.89917 1.0 D 0.75020 0.985 T 0.00440 -1.1738 10 0.87932 D 0 -15.6679 11.6456 0.51259 0.5345:0.4655:0.0:0.0 . 366 Q9Y2U9 KLDC2_HUMAN W 366 ENSP00000298307:R366W ENSP00000298307:R366W R + 1 2 KLHDC2 49319061 1.000000 0.71417 1.000000 0.80357 0.902000 0.53008 0.984000 0.29565 0.629000 0.30376 0.655000 0.94253 CGG TCGA-2J-AABR-01A-11D-A40W-08 KLHDC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276869.1 1 0 0 8 143 0 44 1 9.617955e-01 5 101 0 44 2 0 0 0 0 0 2 1 0.988815 8 140 0 43 2 -4.409441 1 1 121386 7 33 1 1 2 3 2.014109 0 0.090000 1.970000 0.098921 0.990000 0.590000 1.000000 1.000000 0.952268 0.990000 1 0.880000 1.000000 SLC27A2 11001 broad.mit.edu 37 15 50519366 50519366 + Missense_Mutation SNP A A G TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr15:50519366A>G ENST00000267842.5 + 7 1680 c.1448A>G c.(1447-1449)gAt>gGt p.D483G SLC27A2_ENST00000544960.1_Missense_Mutation_p.D248G|SLC27A2_ENST00000380902.4_Missense_Mutation_p.D430G NM_003645.3 NP_003636.2 O14975 S27A2_HUMAN solute carrier family 27 (fatty acid transporter), member 2 25 all_lung(180;0.00177) AGAGTTGGAGATACATTCCGG 0.408000 0 SO:0001583 missense ENST00000267842.5 0 1 hg19 CCDS10133.1 . . . . . . . . . . A 26.0 4.694762 0.88830 . . ENSG00000140284 ENST00000380902;ENST00000267842;ENST00000544960 T;T;T 0.59502 0.26;0.26;0.26 5.78 5.78 0.91487 AMP-dependent synthetase/ligase (1); 0.000000 0.85682 D 0.000000 D 0.84620 0.5512 H 0.98111 4.15 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.90026 0.4131 10 0.87932 D 0 . 14.0725 0.64868 1.0:0.0:0.0:0.0 . 430;483 Q6PF09;O14975 .;S27A2_HUMAN G 430;483;248 ENSP00000370289:D430G;ENSP00000267842:D483G;ENSP00000444549:D248G ENSP00000267842:D483G D + 2 0 SLC27A2 48306658 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.027000 0.93706 2.205000 0.71048 0.533000 0.62120 GAT TCGA-2J-AABR-01A-11D-A40W-08 SLC27A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254539.2 0 0 0 9 320 0 72 0 3.047758e-02 0 9 0 72 2 0 0 0 0 0 2 1 0.994384 9 320 0 72 2 -3.081625 1 1 121412 13 41 1 1 2 3 2.007232 0 0.090000 1.970000 0.097312 0.670000 0.320000 1.000000 1.000000 0.699133 0.670000 0 0.460000 1.000000 SRRM2 23524 broad.mit.edu 37 16 2814969 2814969 + Missense_Mutation SNP T T G TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr16:2814969T>G ENST00000301740.8 + 11 4989 c.4440T>G c.(4438-4440)tgT>tgG p.C1480W NM_016333.3 NP_057417.3 Q9UQ35 SRRM2_HUMAN serine/arginine repetitive matrix 2 105 GAAGCGAATGTGATTCTTCCC 0.532000 0 SO:0001583 missense ENST00000301740.8 1 1 hg19 CCDS32373.1 . . . . . . . . . . T 8.461 0.855301 0.17106 . . ENSG00000167978 ENST00000301740;ENST00000382301;ENST00000544933 T 0.26660 1.72 6.06 2.44 0.29823 . 0.089407 0.49916 D 0.000133 T 0.23688 0.0573 L 0.29908 0.895 0.46774 D 0.999198 D 0.63880 0.993 P 0.53006 0.715 T 0.02991 -1.1085 10 0.62326 D 0.03 -5.977 4.8712 0.13633 0.1664:0.167:0.0:0.6666 . 1480 Q9UQ35 SRRM2_HUMAN W 1480;1480;732 ENSP00000301740:C1480W ENSP00000301740:C1480W C + 3 2 SRRM2 2754970 0.997000 0.39634 1.000000 0.80357 0.925000 0.55904 0.114000 0.15520 0.530000 0.28619 0.533000 0.62120 TGT TCGA-2J-AABR-01A-11D-A40W-08 SRRM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000436411.1 0 0 0 17 643 0 127 1 9.150515e-01 11 152 0 127 2 0 0 0 0 0 2 1 0.999963 17 640 0 121 2 -13.990710 1 1 0 0 1 1 2 3 2.035123 0 0.090000 1.970000 0.103316 0.630000 0.360000 1.000000 0.570000 0.689005 0.630000 0 0.480000 1.000000 FAM86A 196483 broad.mit.edu 37 16 5140142 5140142 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr16:5140142C>T ENST00000427587.4 - 6 753 c.685G>A c.(685-687)Gac>Aac p.D229N FAM86A_ENST00000458008.4_Missense_Mutation_p.D195N|FAM86A_ENST00000587133.1_Missense_Mutation_p.D168N NM_201400.2 NP_958802.1 Q96G04 FA86A_HUMAN family with sequence similarity 86, member A 12 GTCGCGACGTCCCAGTCCAGC 0.602000 0 SO:0001583 missense ENST00000427587.4 0 1 hg19 CCDS10529.1 . . . . . . . . . . c 15.70 2.911632 0.52439 . . ENSG00000118894 ENST00000458008;ENST00000427587 T;T 0.06687 3.27;3.27 5.02 5.02 0.67125 . 0.452097 0.23549 N 0.046998 T 0.12220 0.0297 L 0.50333 1.59 0.49389 D 0.999781 P;B 0.36392 0.551;0.34 B;B 0.40982 0.345;0.14 T 0.15435 -1.0437 10 0.17832 T 0.49 . 17.1053 0.86660 0.0:1.0:0.0:0.0 . 195;229 Q96G04-2;Q96G04 .;FA86A_HUMAN N 195;229 ENSP00000389710:D195N;ENSP00000398502:D229N ENSP00000398502:D229N D - 1 0 FAM86A 5080143 1.000000 0.71417 0.997000 0.53966 0.066000 0.16364 3.106000 0.50322 2.620000 0.88729 0.450000 0.29827 GAC TCGA-2J-AABR-01A-11D-A40W-08 FAM86A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251713.1 0 0 0 6 268 1 71 0 3.081356e-02 0 25 1 71 3 0 0 0 0 0 2 0 0.048814 0 246 1 71 13 -7.145509 1 0 0 0 1 1 2 3 2.035123 0 0.090000 1.970000 0.103316 0.590000 0.230000 1.000000 1.000000 0.646253 0.590000 0 0.370000 1.000000 MMP2 4313 broad.mit.edu 37 16 55519538 55519538 + Silent SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr16:55519538C>T ENST00000219070.4 + 5 1190 c.681C>T c.(679-681)aaC>aaT p.N227N MMP2_ENST00000543485.1_Silent_p.N151N|MMP2_ENST00000437642.2_Silent_p.N177N|MMP2_ENST00000570308.1_Silent_p.N151N NM_004530.4 NP_004521.1 P08253 MMP2_HUMAN matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) 58 Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189) Captopril(DB01197)|Marimastat(DB00786) AGTATGGGAACGCCGATGGGG 0.542000 0 SO:0001819 synonymous_variant ENST00000219070.4 1 1 hg19 CCDS10752.1 TCGA-2J-AABR-01A-11D-A40W-08 MMP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256913.3 0 0 0 20 572 1 131 0 7.571674e-01 0 497 1 131 14 0 0 0 0 0 2 1 0.786320 20 563 1 127 16 -3.744623 1 1 121412 5 40 1 1 2 3 2.015526 0 0.090000 1.970000 0.099322 0.800000 0.490000 1.000000 1.000000 0.810259 0.800000 0 0.620000 1.000000 MMP15 4324 broad.mit.edu 37 16 58074496 58074496 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr16:58074496G>A ENST00000219271.3 + 5 1589 c.804G>A c.(802-804)gaG>gaA p.E268E NM_002428.2 NP_002419.1 P51511 MMP15_HUMAN matrix metallopeptidase 15 (membrane-inserted) 18 Marimastat(DB00786) TGGGGCTGGAGCACTCCAGCA 0.607000 0 SO:0001819 synonymous_variant ENST00000219271.3 1 1 hg19 CCDS10792.1 TCGA-2J-AABR-01A-11D-A40W-08 MMP15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257342.1 0 0 1 8 282 0 57 1 7.320762e-01 13 78 0 57 2 0 0 0 0 0 2 1 0.989183 9 278 0 55 2 -8.815554 1 1 0 0 1 1 2 3 2.009490 0 0.090000 1.970000 0.097715 0.680000 0.310000 1.000000 1.000000 0.708195 0.680000 0 0.460000 1.000000 TUBG2 27175 broad.mit.edu 37 17 40817827 40817827 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr17:40817827G>A ENST00000251412.7 + 8 1024 c.825G>A c.(823-825)ccG>ccA p.P275P PLEKHH3_ENST00000456950.2_5'Flank NM_016437.2 NP_057521.1 Q9NRH3 TBG2_HUMAN tubulin, gamma 2 15 Breast(137;0.00116) GCTACACCCCGCTCACTACAG 0.637000 0 SO:0001819 synonymous_variant ENST00000251412.7 1 1 hg19 CCDS32658.1 TCGA-2J-AABR-01A-11D-A40W-08 TUBG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452326.1 1 0 0 29 594 0 96 1 4.543521e-01 2 30 0 96 2 0 0 0 0 0 2 1 1.000000 29 578 0 88 2 -3.049135 1 1 121412 1 40 1 1 2 3 2.005968 0 0.090000 1.970000 0.096909 0.990000 0.720000 1.000000 1.000000 0.958496 0.990000 1 0.880000 1.000000 TP53 7157 broad.mit.edu 37 17 7578508 7578508 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr17:7578508C>T ENST00000269305.4 - 5 611 c.422G>A c.(421-423)tGc>tAc p.C141Y TP53_ENST00000445888.2_Missense_Mutation_p.C141Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C141Y|TP53_ENST00000420246.2_Missense_Mutation_p.C141Y|TP53_ENST00000359597.4_Missense_Mutation_p.C141Y|TP53_ENST00000413465.2_Missense_Mutation_p.C141Y NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.C141Y(79)|p.0?(8)|p.C9Y(5)|p.C48Y(5)|p.A138_P142delAKTCP(4)|p.C141F(4)|p.C141S(3)|p.N131fs*27(2)|p.C9S(1)|p.K139_C141>N(1)|p.L137_W146del10(1)|p.C141A(1)|p.A6_P10delAKTCP(1)|p.K139fs*4(1)|p.A45_P49delAKTCP(1)|p.T140fs*28(1)|p.A138_V143delAKTCPV(1)|p.C48S(1)|p.C141fs*5(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CTGCACAGGGCAGGTCTTGGC 0.572000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 121 Substitution - Missense(99)|Whole gene deletion(8)|Deletion - In frame(8)|Deletion - Frameshift(5)|Complex - deletion inframe(1) GRCh37 CM993216 TP53 M SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 15.06 2.720132 0.48728 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793 D;D;D;D;D;D;D;D;D 0.99822 -6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94 5.48 4.5 0.54988 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.046412 0.85682 D 0.000000 D 0.99832 0.9924 M 0.90309 3.105 0.58432 D 0.999998 D;D;D;D;D;D;D 0.89917 1.0;1.0;0.998;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 1.0;0.998;0.987;1.0;0.999;1.0;1.0 D 0.96735 0.9542 10 0.87932 D 0 -26.1094 13.743 0.62860 0.1552:0.8448:0.0:0.0 . 102;141;141;48;141;141;141 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. Y 141;141;141;141;141;141;130;48;9;48;9;141 ENSP00000410739:C141Y;ENSP00000352610:C141Y;ENSP00000269305:C141Y;ENSP00000398846:C141Y;ENSP00000391127:C141Y;ENSP00000391478:C141Y;ENSP00000425104:C9Y;ENSP00000423862:C48Y;ENSP00000424104:C141Y ENSP00000269305:C141Y C - 2 0 TP53 7519233 1.000000 0.71417 0.996000 0.52242 0.022000 0.10575 6.016000 0.70798 1.427000 0.47276 -0.182000 0.12963 TGC TCGA-2J-AABR-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 8 197 0 56 1 7.237210e-01 7 56 0 56 2 1 9.999863e-01 55 1722 3 2018 9 1 0.989584 8 196 0 53 2 -3.302200 1 1 0 0 1 0 0 0 1.979295 0 0.090000 1.970000 0.072470 0.840000 0.400000 1.000000 1.000000 0.816712 0.840000 0 0.600000 1.000000 PSG11 5680 broad.mit.edu 37 19 43528993 43528993 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr19:43528993C>T ENST00000401740.1 - 2 383 c.280G>A c.(280-282)Gca>Aca p.A94T PSG11_ENST00000320078.7_Missense_Mutation_p.A94T|PSG11_ENST00000403486.1_Intron|PSG11_ENST00000306322.7_Intron Q00887 PSG9_HUMAN pregnancy specific beta-1-glycoprotein 11 26 Prostate(69;0.00682) CCACTGTATGCCGGTCCATAT 0.443000 0 SO:0001583 missense ENST00000401740.1 0 1 hg19 CCDS12614.2 . . . . . . . . . . c 9.498 1.102465 0.20632 . . ENSG00000243130 ENST00000320078;ENST00000401740 T;T 0.66280 -0.2;-0.2 0.929 -1.86 0.07760 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1); . . . . T 0.64023 0.2561 M 0.80746 2.51 0.09310 N 1 B 0.25563 0.129 B 0.39904 0.313 T 0.63812 -0.6552 9 0.62326 D 0.03 . 2.5413 0.04726 0.0:0.4411:0.3119:0.247 . 94 Q9UQ72 PSG11_HUMAN T 94 ENSP00000319140:A94T;ENSP00000384995:A94T ENSP00000319140:A94T A - 1 0 PSG11 48220833 0.000000 0.05858 0.001000 0.08648 0.001000 0.01503 -0.352000 0.07701 -0.979000 0.03529 -1.140000 0.01884 GCA TCGA-2J-AABR-01A-11D-A40W-08 PSG11-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323079.1 0 0 0 8 1146 0 234 0 0 0 0 234 2 0 0 0 0 0 2 1 0.988769 8 1131 0 233 2 -1.522631 0 1 0 0 1 1 2 3 2.011089 0 0.090000 1.970000 0.098117 0.170000 0.070000 1.000000 0.160000 0.298524 0.170000 0 0.110000 0.340000 NLRP9 338321 broad.mit.edu 37 19 56244158 56244158 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr19:56244158C>T ENST00000332836.2 - 2 1066 c.1039G>A c.(1039-1041)Gtg>Atg p.V347M NM_176820.2 NP_789790.2 Q7RTR0 NALP9_HUMAN NLR family, pyrin domain containing 9 74 Colorectal(82;0.000133)|Ovarian(87;0.133) CTCTGTTTCACACAAGTACAG 0.418000 0 SO:0001583 missense ENST00000332836.2 1 1 hg19 CCDS12934.1 . . . . . . . . . . C 0.863 -0.734758 0.03111 . . ENSG00000185792 ENST00000332836;ENST00000333452 D 0.84298 -1.83 2.56 -5.13 0.02884 . . . . . T 0.57504 0.2058 N 0.01493 -0.835 0.09310 N 1 B 0.06786 0.001 B 0.08055 0.003 T 0.46512 -0.9186 9 0.59425 D 0.04 . 2.9394 0.05825 0.192:0.1001:0.4605:0.2475 . 347 Q7RTR0 NALP9_HUMAN M 347 ENSP00000331857:V347M ENSP00000331857:V347M V - 1 0 NLRP9 60935970 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -2.639000 0.00865 -2.030000 0.00929 -0.313000 0.08912 GTG TCGA-2J-AABR-01A-11D-A40W-08 NLRP9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000453653.1 0 0 0 20 617 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 0.999994 20 607 0 118 2 -3.660984 1 1 0 0 1 1 2 3 2.023719 0 0.090000 1.970000 0.100924 0.760000 0.450000 1.000000 1.000000 0.776638 0.760000 0 0.580000 1.000000 NLRP5 126206 broad.mit.edu 37 19 56539375 56539375 + Silent SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr19:56539375C>T ENST00000390649.3 + 7 1776 c.1776C>T c.(1774-1776)gcC>gcT p.A592A NM_153447.4 NP_703148.4 P59047 NALP5_HUMAN NLR family, pyrin domain containing 5 25 Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157) ACTTCTGTGCCGCCTTGTACT 0.532000 0 SO:0001819 synonymous_variant ENST00000390649.3 0 1 hg19 CCDS12938.1 TCGA-2J-AABR-01A-11D-A40W-08 NLRP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313735.1 0 0 0 5 137 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.937517 5 136 0 39 2 -3.273354 1 1 120936 5 34 1 1 2 3 2.023719 0 0.090000 1.970000 0.100924 0.930000 0.340000 1.000000 1.000000 0.828862 0.930000 1 0.570000 1.000000 TPR 7175 broad.mit.edu 37 1 186328936 186328936 + Missense_Mutation SNP T T C TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr1:186328936T>C ENST00000367478.4 - 12 1680 c.1384A>G c.(1384-1386)Atg>Gtg p.M462V TPR_ENST00000474852.1_5'UTR NM_003292.2 NP_003283.2 P12270 TPR_HUMAN translocated promoter region, nuclear basket protein 123 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) CCAACCTTCATAGCTTGTTCA 0.368000 T NTRK1 papillary thyroid Dom yes 1 1q25 7175 translocated promoter region E 0 SO:0001583 missense ENST00000367478.4 1 1 hg19 CCDS41446.1 . . . . . . . . . . T 10.51 1.369874 0.24771 . . ENSG00000047410 ENST00000367478 T 0.00940 5.52 5.76 5.76 0.90799 . 0.176337 0.64402 D 0.000009 T 0.00906 0.0030 N 0.16656 0.425 0.45690 D 0.998602 B;B 0.21753 0.06;0.025 B;B 0.22386 0.039;0.008 T 0.61515 -0.7047 10 0.08381 T 0.77 . 16.0697 0.80914 0.0:0.0:0.0:1.0 . 462;462 Q15624;P12270 .;TPR_HUMAN V 462 ENSP00000356448:M462V ENSP00000356448:M462V M - 1 0 TPR 184595559 0.998000 0.40836 0.993000 0.49108 0.996000 0.88848 2.901000 0.48695 2.194000 0.70268 0.528000 0.53228 ATG TCGA-2J-AABR-01A-11D-A40W-08 TPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086353.2 0 0 0 15 267 0 67 1 4.469519e-01 2 25 0 67 2 0 0 0 0 0 2 1 0.999880 15 266 0 66 2 -18.044060 1 1 120804 6 35 1 0 1 1 1.993890 0 0.090000 1.970000 0.081736 0.990000 0.680000 1.000000 1.000000 0.961146 0.990000 1 0.890000 1.000000 NLRP3 114548 broad.mit.edu 37 1 247597507 247597507 + Silent SNP C C T rs147154764 TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr1:247597507C>T ENST00000336119.3 + 5 3176 c.2430C>T c.(2428-2430)ctC>ctT p.L810L NLRP3_ENST00000391827.2_Silent_p.L753L|NLRP3_ENST00000348069.2_Silent_p.L753L|NLRP3_ENST00000391828.3_Silent_p.L810L|NLRP3_ENST00000366496.2_Silent_p.L810L|NLRP3_ENST00000366497.2_Silent_p.L810L NM_001127462.2|NM_001243133.1|NM_004895.4 NP_001120934.1|NP_001230062.1|NP_004886.3 Q96P20 NALP3_HUMAN NLR family, pyrin domain containing 3 142 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) ACAACGCCCTCGGTGACTTCG 0.567000 0 SO:0001819 synonymous_variant ENST00000336119.3 0 1 hg19 CCDS1632.1 TCGA-2J-AABR-01A-11D-A40W-08 NLRP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097740.1 0 0 0 6 434 0 81 0 2.848522e-02 0 16 0 81 2 0 0 0 0 0 2 1 0.963701 6 428 0 79 2 -2.560650 1 1 121412 10 46 1 0 1 1 1.993890 0 0.090000 1.970000 0.081736 0.310000 0.130000 0.600000 0.290000 0.339876 0.310000 0 0.210000 0.460000 HIVEP3 59269 broad.mit.edu 37 1 42046110 42046110 + Silent SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr1:42046110C>T ENST00000372583.1 - 4 5244 c.4359G>A c.(4357-4359)gaG>gaA p.E1453E HIVEP3_ENST00000372584.1_Silent_p.E1453E|HIVEP3_ENST00000429157.2_Silent_p.E1453E|HIVEP3_ENST00000247584.5_Silent_p.E1453E|HIVEP3_ENST00000460604.1_5'Flank NM_024503.4 NP_078779.2 Q5T1R4 ZEP3_HUMAN human immunodeficiency virus type I enhancer binding protein 3 85 Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0367) TGGAAGCCTCCTCCTCCTTCA 0.512000 0 SO:0001819 synonymous_variant ENST00000372583.1 1 1 hg19 CCDS463.1 TCGA-2J-AABR-01A-11D-A40W-08 HIVEP3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000016978.1 0 0 0 19 685 0 167 0 0 0 1 0 167 2 0 0 0 0 0 2 1 0.999989 19 678 0 161 2 -2.865752 1 1 0 0 1 0 1 1 1.993890 0 0.090000 1.970000 0.081736 0.590000 0.370000 0.880000 0.590000 0.613537 0.590000 0 0.470000 0.740000 ZSWIM5 57643 broad.mit.edu 37 1 45484833 45484833 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr1:45484833G>A ENST00000359600.5 - 14 3056 c.2851C>T c.(2851-2853)Cgc>Tgc p.R951C NM_020883.1 NP_065934.1 Q9P217 ZSWM5_HUMAN zinc finger, SWIM-type containing 5 28 Acute lymphoblastic leukemia(166;0.155) GCCAGTGTGCGAGCACAGCTA 0.542000 OREG0013450 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000359600.5 0 1 hg19 CCDS41319.1 . . . . . . . . . . G 15.57 2.871440 0.51695 . . ENSG00000162415 ENST00000359600 T 0.52295 0.67 4.74 4.74 0.60224 . 0.000000 0.85682 D 0.000000 T 0.66096 0.2755 M 0.69823 2.125 0.80722 D 1 D 0.76494 0.999 P 0.61275 0.886 T 0.68693 -0.5341 10 0.52906 T 0.07 -7.752 18.6023 0.91253 0.0:0.0:1.0:0.0 . 951 Q9P217 ZSWM5_HUMAN C 951 ENSP00000352614:R951C ENSP00000352614:R951C R - 1 0 ZSWIM5 45257420 1.000000 0.71417 1.000000 0.80357 0.865000 0.49528 4.475000 0.60210 2.558000 0.86282 0.555000 0.69702 CGC TCGA-2J-AABR-01A-11D-A40W-08 ZSWIM5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000024823.2 0 0 0 4 213 0 35 0 1.828550e-03 0 3 0 35 2 0 0 0 0 0 2 1 0.885619 4 208 0 35 2 -3.250930 1 1 120956 2 33 1 0 1 1 1.993890 0 0.090000 1.970000 0.081736 0.440000 0.150000 0.920000 0.390000 0.474505 0.440000 0 0.260000 0.670000 AKR1A1 10327 broad.mit.edu 37 1 46032622 46032622 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr1:46032622C>T ENST00000372070.3 + 5 1033 c.286C>T c.(286-288)Cgg>Tgg p.R96W AKR1A1_ENST00000471651.1_Missense_Mutation_p.R96W|AKR1A1_ENST00000351829.4_Missense_Mutation_p.R96W NM_001202413.1|NM_001202414.1|NM_006066.3 NP_001189342.1|NP_001189343.1|NP_006057.1 P14550 AK1A1_HUMAN aldo-keto reductase family 1, member A1 (aldehyde reductase) 5 Acute lymphoblastic leukemia(166;0.155) Doxorubicin(DB00997) GCCTGCCCTCCGGAAGACTCT 0.607000 0 SO:0001583 missense ENST00000372070.3 1 1 hg19 CCDS523.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 C 14.21 2.468661 0.43839 . . ENSG00000117448 ENST00000372070;ENST00000434299;ENST00000351829 T;T;T 0.31510 1.49;1.49;1.49 6.01 2.85 0.33270 NADP-dependent oxidoreductase domain (3); 0.201358 0.43260 D 0.000588 T 0.44477 0.1295 L 0.56769 1.78 0.45272 D 0.998272 D 0.76494 0.999 D 0.64877 0.93 T 0.36383 -0.9750 10 0.87932 D 0 . 7.8215 0.29290 0.528:0.3896:0.0:0.0824 . 96 P14550 AK1A1_HUMAN W 96 ENSP00000361140:R96W;ENSP00000398414:R96W;ENSP00000312606:R96W ENSP00000312606:R96W R + 1 2 AKR1A1 45805209 0.997000 0.39634 0.988000 0.46212 0.032000 0.12392 3.428000 0.52792 0.863000 0.35553 -0.151000 0.13558 CGG TCGA-2J-AABR-01A-11D-A40W-08 AKR1A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000020851.1 1 0 0 12 247 0 45 1 9.995491e-01 26 260 0 45 2 0 0 0 0 0 2 1 0.999006 12 240 0 44 2 -2.713547 1 1 121412 4 36 1 0 1 1 1.993890 0 0.090000 1.970000 0.081736 0.990000 0.560000 1.000000 1.000000 0.912728 0.990000 1 0.760000 1.000000 CHD6 84181 broad.mit.edu 37 20 40052243 40052243 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr20:40052243G>A ENST00000373233.3 - 30 4621 c.4444C>T c.(4444-4446)Cgc>Tgc p.R1482C NM_032221.3 NP_115597.3 Q8TD26 CHD6_HUMAN chromodomain helicase DNA binding protein 6 129 Myeloproliferative disorder(115;0.00425) GAAATGATGCGGAACTGTGTC 0.443000 0 SO:0001583 missense ENST00000373233.3 0 1 hg19 CCDS13317.1 . . . . . . . . . . G 28.5 4.928613 0.92389 . . ENSG00000124177 ENST00000373233 D 0.94793 -3.52 6.07 6.07 0.98685 SANT domain, DNA binding (1); 0.000000 0.64402 D 0.000007 D 0.97876 0.9302 M 0.89287 3.02 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 D 0.97909 1.0307 10 0.87932 D 0 -12.954 20.6439 0.99570 0.0:0.0:1.0:0.0 . 1482 Q8TD26 CHD6_HUMAN C 1482 ENSP00000362330:R1482C ENSP00000362330:R1482C R - 1 0 CHD6 39485657 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 6.405000 0.73272 2.884000 0.98904 0.655000 0.94253 CGC TCGA-2J-AABR-01A-11D-A40W-08 CHD6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079270.1 0 0 0 6 844 1 173 0 4.731315e-03 0 12 1 173 2 0 0 0 0 0 2 0 0.015487 6 835 1 170 17 -1.734834 0 1 0 0 1 1 2 3 2.009716 0 0.090000 1.970000 0.097715 0.180000 0.060000 1.000000 0.160000 0.301090 0.180000 0 0.110000 0.360000 PREX1 57580 broad.mit.edu 37 20 47309283 47309283 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr20:47309283G>A ENST00000371941.3 - 8 985 c.963C>T c.(961-963)aaC>aaT p.N321N PREX1_ENST00000396220.1_Silent_p.N321N NM_020820.3 NP_065871 Q8TCU6 PREX1_HUMAN phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1 110 BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198) AGAGGGAGCCGTTGATGGATT 0.552000 0 SO:0001819 synonymous_variant ENST00000371941.3 0 1 hg19 CCDS13410.1 TCGA-2J-AABR-01A-11D-A40W-08 PREX1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079623.1 0 0 0 11 418 0 77 0 1.368641e-01 0 23 0 77 2 0 0 0 0 0 2 1 0.998199 11 410 0 77 2 -3.035764 1 1 121412 28 46 1 1 2 3 2.009716 0 0.090000 1.970000 0.097715 0.620000 0.320000 1.000000 1.000000 0.665409 0.620000 0 0.450000 1.000000 FAM65C 140876 broad.mit.edu 37 20 49218732 49218732 + Silent SNP C C A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr20:49218732C>A ENST00000327979.2 - 13 1935 c.1524G>T c.(1522-1524)ggG>ggT p.G508G FAM65C_ENST00000535356.1_Silent_p.G512G|FAM65C_ENST00000045083.2_Silent_p.G508G Q96MK2 FA65C_HUMAN family with sequence similarity 65, member C 29 CCACGCCAGGCCCGTCCTCTC 0.697000 0 SO:0001819 synonymous_variant ENST00000327979.2 0 1 hg19 CCDS13431.2 TCGA-2J-AABR-01A-11D-A40W-08 FAM65C-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257962.1 0 0 0 5 169 0 34 0 1.348228e-03 0 2 0 34 2 0 0 0 0 0 2 1 0.933571 5 164 0 31 2 -7.333112 1 1 0 0 1 1 2 3 2.009716 0 0.090000 1.970000 0.097715 0.740000 0.270000 1.000000 1.000000 0.735669 0.740000 0 0.460000 1.000000 CRYBB1 1414 broad.mit.edu 37 22 27008105 27008105 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr22:27008105G>A ENST00000215939.2 - 3 360 c.230C>T c.(229-231)tCg>tTg p.S77L NM_001887.3 NP_001878.1 P53674 CRBB1_HUMAN crystallin, beta B1 p.S77L(1) 31 GCACTCCCCCGAGAATTCTGC 0.612000 1 Substitution - Missense(1) SO:0001583 missense ENST00000215939.2 1 1 hg19 CCDS13840.1 . . . . . . . . . . G 10.30 1.312232 0.23908 . . ENSG00000100122 ENST00000215939 T 0.77489 -1.1 3.85 3.85 0.44370 Beta/gamma crystallin (4);Gamma-crystallin-related (1); 0.811995 0.11262 N 0.582484 T 0.71213 0.3313 L 0.54863 1.705 0.33899 D 0.638222 B 0.31209 0.313 B 0.27887 0.084 T 0.76088 -0.3087 10 0.51188 T 0.08 . 8.8646 0.35278 0.1045:0.0:0.8955:0.0 . 77 P53674 CRBB1_HUMAN L 77 ENSP00000215939:S77L ENSP00000215939:S77L S - 2 0 CRYBB1 25338105 0.935000 0.31712 0.999000 0.59377 0.438000 0.31896 1.500000 0.35682 1.961000 0.56991 0.491000 0.48974 TCG TCGA-2J-AABR-01A-11D-A40W-08 CRYBB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320767.1 1 0 0 19 378 0 74 0 3.405871e-02 0 6 0 74 2 0 0 0 0 0 2 1 0.999986 14 364 0 72 2 -2.774725 1 1 121412 1 36 1 0 1 1 1.990456 0 0.090000 1.970000 0.080901 0.990000 0.650000 1.000000 1.000000 0.940938 0.990000 1 0.830000 1.000000 MICALL1 85377 broad.mit.edu 37 22 38323617 38323617 + Silent SNP T T A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr22:38323617T>A ENST00000215957.6 + 9 1791 c.1665T>A c.(1663-1665)tcT>tcA p.S555S MICALL1_ENST00000402631.1_3'UTR NM_033386.3 NP_203744.1 Q8N3F8 MILK1_HUMAN MICAL-like 1 24 Melanoma(58;0.045) TCAGCCTCTCTACCAACTCCT 0.632000 0 SO:0001819 synonymous_variant ENST00000215957.6 0 1 hg19 CCDS13961.1 . . . . . . . . . . T 0.550 -0.849771 0.02651 . . ENSG00000100139 ENST00000454685 . . . 5.14 -10.3 0.00346 . . . . . T 0.46229 0.1382 . . . 0.53688 D 0.999975 . . . . . . T 0.57394 -0.7819 4 . . . . 8.7087 0.34371 0.1652:0.5937:0.0749:0.1661 . . . . N 133 . . Y + 1 0 MICALL1 36653563 0.000000 0.05858 0.020000 0.16555 0.047000 0.14425 -3.105000 0.00602 -2.558000 0.00475 0.454000 0.30748 TAC TCGA-2J-AABR-01A-11D-A40W-08 MICALL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319545.4 0 0 0 17 689 0 132 1 1.514673e-01 3 24 0 132 2 0 0 0 0 0 2 1 0.999954 17 666 0 130 2 -3.178041 1 1 0 0 1 0 1 1 1.990456 0 0.090000 1.970000 0.080901 0.530000 0.320000 0.800000 0.520000 0.550302 0.530000 0 0.410000 0.670000 L3MBTL2 83746 broad.mit.edu 37 22 41609955 41609955 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr22:41609955G>A ENST00000216237.5 + 3 479 c.321G>A c.(319-321)aaG>aaA p.K107K RP4-756G23.5_ENST00000451176.1_RNA|RP4-756G23.5_ENST00000441316.1_RNA|L3MBTL2_ENST00000489136.1_3'UTR NM_031488.4 NP_113676.2 Q969R5 LMBL2_HUMAN l(3)mbt-like 2 (Drosophila) p.K107N(1) 24 CCAAGACCAAGAGGTTCTGCA 0.512000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000216237.5 1 1 hg19 CCDS14011.1 TCGA-2J-AABR-01A-11D-A40W-08 L3MBTL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320613.1 0 0 0 15 520 0 83 0 2.151038e-01 1 28 0 83 2 0 0 0 0 0 2 1 0.999859 15 512 0 83 2 -3.584154 1 1 0 0 1 1 5 6 2.261650 1 0.090000 1.970000 0.210755 0.770000 0.430000 1.000000 1.000000 0.776363 0.770000 0 0.580000 1.000000 PKDREJ 10343 broad.mit.edu 37 22 46653425 46653425 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr22:46653425G>A ENST00000253255.5 - 1 5794 c.5795C>T c.(5794-5796)tCg>tTg p.S1932L NM_006071.1 NP_006062.1 Q9NTG1 PKDRE_HUMAN polycystin (PKD) family receptor for egg jelly 73 Ovarian(80;0.00965)|all_neural(38;0.0416) AAATATGACCGAAATGCTACA 0.373000 0 SO:0001583 missense ENST00000253255.5 0 1 hg19 CCDS14073.1 . . . . . . . . . . G 11.51 1.660688 0.29515 . . ENSG00000130943 ENST00000253255 T 0.71461 -0.57 5.55 4.52 0.55395 Polycystin cation channel, PKD1/PKD2 (1); 0.000000 0.53938 D 0.000059 T 0.77916 0.4202 L 0.47716 1.5 0.20563 N 0.99989 D 0.89917 1.0 D 0.91635 0.999 T 0.68236 -0.5462 10 0.59425 D 0.04 -21.0782 11.7598 0.51896 0.084:0.0:0.916:0.0 . 1932 Q9NTG1 PKDRE_HUMAN L 1932 ENSP00000253255:S1932L ENSP00000253255:S1932L S - 2 0 PKDREJ 45032089 0.914000 0.31030 0.108000 0.21378 0.096000 0.18686 2.674000 0.46867 2.618000 0.88619 0.455000 0.32223 TCG TCGA-2J-AABR-01A-11D-A40W-08 PKDREJ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318466.1 0 0 0 6 276 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.964652 5 275 0 35 2 -3.091551 1 1 121412 2 33 1 0 0 0 1.906408 0 0.090000 1.970000 0.037139 0.430000 0.180000 0.720000 0.410000 0.449980 0.430000 0 0.290000 0.600000 IL18RAP 8807 broad.mit.edu 37 2 103063588 103063588 + Silent SNP G G C TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr2:103063588G>C ENST00000264260.2 + 10 1720 c.1131G>C c.(1129-1131)gcG>gcC p.A377A IL18RAP_ENST00000409369.1_Silent_p.A235A NM_003853.2 NP_003844.1 O95256 I18RA_HUMAN interleukin 18 receptor accessory protein 37 TGCTGGCGGCGAGTGCCCTCC 0.582000 0 SO:0001819 synonymous_variant ENST00000264260.2 0 1 hg19 CCDS2061.1 TCGA-2J-AABR-01A-11D-A40W-08 IL18RAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253291.2 0 0 0 6 907 1 169 0 6.681461e-05 0 2 1 169 2 0 0 0 0 0 2 0 0.006225 6 893 1 165 19 -2.200819 0 1 0 0 1 1 2 3 2.011385 0 0.090000 1.970000 0.098117 0.170000 0.060000 1.000000 0.150000 0.295668 0.170000 0 0.100000 0.350000 NEB 4703 broad.mit.edu 37 2 152552104 152552104 + Silent SNP A A G TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr2:152552104A>G ENST00000172853.10 - 18 1809 c.1662T>C c.(1660-1662)taT>taC p.Y554Y NEB_ENST00000603639.1_Silent_p.Y554Y|NEB_ENST00000409198.1_Silent_p.Y554Y|NEB_ENST00000427231.2_Silent_p.Y554Y|NEB_ENST00000604864.1_Silent_p.Y554Y|NEB_ENST00000397345.3_Silent_p.Y554Y P20929 NEBU_HUMAN nebulin 301 CACTCAAGTTATAGGCATTGA 0.373000 0 SO:0001819 synonymous_variant ENST00000172853.10 1 1 hg19 TCGA-2J-AABR-01A-11D-A40W-08 NEB-201 KNOWN basic protein_coding protein_coding 0 0 0 5 105 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 0.939019 5 105 0 25 2 -8.516195 1 1 0 0 1 1 2 3 2.011385 0 0.090000 1.970000 0.098117 0.990000 0.420000 1.000000 1.000000 0.898829 0.990000 1 0.710000 1.000000 IRS1 3667 broad.mit.edu 37 2 227660111 227660111 + Missense_Mutation SNP T T C TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr2:227660111T>C ENST00000305123.5 - 1 4364 c.3344A>G c.(3343-3345)aAc>aGc p.N1115S IRS1_ENST00000498335.1_5'Flank NM_005544.2 NP_005535.1 P35568 IRS1_HUMAN insulin receptor substrate 1 69 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) GGGCACTGTGTTGCCCACCCG 0.617000 0 SO:0001583 missense ENST00000305123.5 1 1 hg19 CCDS2463.1 . . . . . . . . . . T 5.525 0.281845 0.10458 . . ENSG00000169047 ENST00000305123 T 0.56275 0.47 5.81 5.81 0.92471 . 0.174974 0.34268 N 0.004120 T 0.25382 0.0617 N 0.11064 0.09 0.27707 N 0.945585 B 0.31581 0.329 B 0.28849 0.095 T 0.32613 -0.9900 10 0.05436 T 0.98 -25.738 6.918 0.24371 0.0:0.1629:0.0:0.8371 . 1115 P35568 IRS1_HUMAN S 1115 ENSP00000304895:N1115S ENSP00000304895:N1115S N - 2 0 IRS1 227368355 0.000000 0.05858 0.965000 0.40720 0.245000 0.25701 -0.476000 0.06591 2.206000 0.71126 0.533000 0.62120 AAC TCGA-2J-AABR-01A-11D-A40W-08 IRS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256886.3 0 0 0 12 353 0 82 1 3.860067e-01 4 33 0 82 2 0 0 0 0 0 2 1 0.999046 12 346 0 81 2 -12.531370 1 1 0 0 1 1 2 3 2.010203 0 0.090000 1.970000 0.098117 0.790000 0.420000 1.000000 1.000000 0.792332 0.790000 0 0.580000 1.000000 PER2 8864 broad.mit.edu 37 2 239185809 239185809 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr2:239185809C>T ENST00000254657.3 - 3 535 c.256G>A c.(256-258)Gca>Aca p.A86T PER2_ENST00000254658.3_Missense_Mutation_p.A86T|PER2_ENST00000440245.1_Missense_Mutation_p.A86T|PER2_ENST00000355768.2_Missense_Mutation_p.A86T NM_022817.2 NP_073728.1 O15055 PER2_HUMAN period circadian clock 2 p.A86T(1) 37 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244) TCAGATTTTGCCATCATCAGG 0.383000 1 Substitution - Missense(1) SO:0001583 missense ENST00000254657.3 0 1 hg19 CCDS2528.1 . . . . . . . . . . C 0.421 -0.908299 0.02434 . . ENSG00000132326 ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768;ENST00000431832 T;T;T;T;T 0.53423 2.72;0.68;1.71;0.68;0.62 4.96 2.12 0.27331 . 0.345872 0.34110 N 0.004259 T 0.34308 0.0893 L 0.34521 1.04 0.20074 N 0.999938 B;B;B;B 0.10296 0.003;0.0;0.001;0.0 B;B;B;B 0.12837 0.008;0.001;0.005;0.001 T 0.18053 -1.0349 10 0.31617 T 0.26 -1.2378 11.0032 0.47618 0.0:0.7639:0.0:0.2361 . 86;86;86;86 F5GYD5;B4DH14;O15055-2;O15055 .;.;.;PER2_HUMAN T 86 ENSP00000254657:A86T;ENSP00000254658:A86T;ENSP00000397516:A86T;ENSP00000348013:A86T;ENSP00000405891:A86T ENSP00000254657:A86T A - 1 0 PER2 238850548 0.693000 0.27728 0.002000 0.10522 0.041000 0.13682 0.717000 0.25851 -0.004000 0.14419 -0.797000 0.03246 GCA TCGA-2J-AABR-01A-11D-A40W-08 PER2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257167.1 0 0 0 7 1384 1 321 0 8.469510e-03 0 23 1 321 2 0 0 0 0 0 2 0 0.043278 7 1369 1 318 16 -1.735477 0 1 0 0 1 1 2 3 2.010203 0 0.090000 1.970000 0.098117 0.120000 0.040000 1.000000 0.110000 0.260129 0.120000 0 0.080000 0.260000 ARAP2 116984 broad.mit.edu 37 4 36189102 36189102 + Missense_Mutation SNP C C A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr4:36189102C>A ENST00000303965.4 - 8 2138 c.1649G>T c.(1648-1650)aGa>aTa p.R550I NM_015230.3 NP_056045.2 Q8WZ64 ARAP2_HUMAN ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 82 AACAAAAGTTCTTTGTGTTGT 0.299000 0 SO:0001583 missense ENST00000303965.4 0 1 hg19 CCDS3441.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 28.9 4.962860 0.92791 0.0 1.16E-4 ENSG00000047365 ENST00000303965 T 0.18338 2.22 5.91 5.91 0.95273 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.000000 0.85682 D 0.000000 T 0.54127 0.1839 M 0.91090 3.175 0.80722 D 1 D;D 0.89917 1.0;0.998 D;D 0.87578 0.998;0.998 T 0.62492 -0.6843 10 0.87932 D 0 . 19.8836 0.96906 0.0:1.0:0.0:0.0 . 480;550 A7E2A5;Q8WZ64 .;ARAP2_HUMAN I 550 ENSP00000302895:R550I ENSP00000302895:R550I R - 2 0 ARAP2 35865497 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.860000 0.69546 2.791000 0.96007 0.650000 0.86243 AGA TCGA-2J-AABR-01A-11D-A40W-08 ARAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215074.2 0 0 0 11 301 0 48 0 6.667203e-02 1 10 0 48 2 0 0 0 0 0 2 1 0.998292 11 297 0 48 2 -11.968510 1 1 0 0 1 1 2 3 2.014557 0 0.090000 1.970000 0.098921 0.860000 0.440000 1.000000 1.000000 0.829332 0.860000 1 0.620000 1.000000 TSPAN5 10098 broad.mit.edu 37 4 99407920 99407920 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr4:99407920G>A ENST00000305798.3 - 3 650 c.248C>T c.(247-249)gCg>gTg p.A83V TSPAN5_ENST00000509168.1_5'UTR|TSPAN5_ENST00000505184.1_Missense_Mutation_p.A12V NM_005723.3 NP_005714.2 P62079 TSN5_HUMAN tetraspanin 5 14 TTCCCGTAGCGCTCCAATGCA 0.478000 0 SO:0001583 missense ENST00000305798.3 1 1 hg19 CCDS3646.1 . . . . . . . . . . G 18.26 3.584361 0.65992 . . ENSG00000168785 ENST00000305798;ENST00000505184;ENST00000515287;ENST00000511651 D;D;D;D 0.83837 -1.77;-1.77;-1.77;-1.77 5.51 5.51 0.81932 Tetraspanin, conserved site (1); 0.096844 0.64402 D 0.000001 D 0.93203 0.7835 M 0.92026 3.265 0.80722 D 1 D 0.89917 1.0 D 0.72982 0.979 D 0.93958 0.7238 10 0.87932 D 0 . 19.614 0.95622 0.0:0.0:1.0:0.0 . 83 P62079 TSN5_HUMAN V 83;12;12;12 ENSP00000307701:A83V;ENSP00000423916:A12V;ENSP00000423504:A12V;ENSP00000426248:A12V ENSP00000307701:A83V A - 2 0 TSPAN5 99626943 1.000000 0.71417 0.973000 0.42090 0.986000 0.74619 9.454000 0.97621 2.873000 0.98535 0.561000 0.74099 GCG TCGA-2J-AABR-01A-11D-A40W-08 TSPAN5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253641.2 0 0 0 18 581 0 102 1 2.558038e-02 3 5 0 102 2 0 0 0 0 0 2 1 0.999980 16 575 0 100 2 -3.238237 1 1 0 0 1 1 2 3 2.014557 0 0.090000 1.970000 0.098921 0.720000 0.420000 1.000000 1.000000 0.745266 0.720000 0 0.550000 1.000000 CHSY3 337876 broad.mit.edu 37 5 129519959 129519959 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr5:129519959G>A ENST00000305031.4 + 3 1482 c.1124G>A c.(1123-1125)cGg>cAg p.R375Q CHSY3_ENST00000507545.1_3'UTR NM_175856.4 NP_787052.3 Q70JA7 CHSS3_HUMAN chondroitin sulfate synthase 3 28 all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GAACACAATCGGAAGGGTTAC 0.343000 0 SO:0001583 missense ENST00000305031.4 1 1 hg19 CCDS34223.1 . . . . . . . . . . G 21.6 4.168044 0.78339 . . ENSG00000198108 ENST00000305031 T 0.16196 2.36 4.46 3.59 0.41128 . 0.455483 0.18240 N 0.147272 T 0.19644 0.0472 L 0.43152 1.355 0.36257 D 0.854274 D 0.54047 0.964 P 0.46796 0.527 T 0.19582 -1.0301 9 . . . 0.1414 13.2683 0.60146 0.0779:0.0:0.9221:0.0 . 375 Q70JA7 CHSS3_HUMAN Q 375 ENSP00000302629:R375Q . R + 2 0 CHSY3 129547858 0.973000 0.33851 0.789000 0.31954 0.998000 0.95712 3.393000 0.52544 1.477000 0.48234 0.644000 0.83932 CGG TCGA-2J-AABR-01A-11D-A40W-08 CHSY3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371453.1 0 0 0 16 396 0 59 0 1.004716e-02 0 4 0 59 2 0 0 0 0 0 2 1 0.999931 17 391 0 56 2 -2.494159 0 1 0 0 1 1 2 3 2.010253 0 0.090000 1.970000 0.098117 0.920000 0.530000 1.000000 1.000000 0.875938 0.920000 1 0.700000 1.000000 FAT2 2196 broad.mit.edu 37 5 150911532 150911532 + Splice_Site SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr5:150911532C>T ENST00000261800.5 - 13 9440 c.e13-1 NM_001447.2 NP_001438.1 Q9NYQ8 FAT2_HUMAN FAT atypical cadherin 2 196 Medulloblastoma(196;0.0912)|all_hematologic(541;0.104) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) GCATTGGCGCCTGGCAGGGAG 0.652000 0 SO:0001630 splice_region_variant ENST00000261800.5 1 1 hg19 CCDS4317.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 12.87|12.87 2.067656|2.067656 0.36470|0.36470 .|. .|. ENSG00000086570|ENSG00000086570 ENST00000261800|ENST00000520200 .|. .|. .|. 5.43|5.43 5.43|5.43 0.79202|0.79202 .|. .|. .|. .|. .|. .|T .|0.73760 .|0.3628 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.72337 .|-0.4324 .|4 .|. .|. .|. .|. 17.4335|17.4335 0.87545|0.87545 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|. .|. .|. .|K -1|1 .|. .|. .|R -|- .|2 .|0 FAT2|FAT2 150891725|150891725 1.000000|1.000000 0.71417|0.71417 0.897000|0.897000 0.35233|0.35233 0.240000|0.240000 0.25518|0.25518 5.591000|5.591000 0.67536|0.67536 2.557000|2.557000 0.86248|0.86248 0.557000|0.557000 0.71058|0.71058 .|AGG TCGA-2J-AABR-01A-11D-A40W-08 FAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252434.1 1 0 0 20 362 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 0.999996 20 361 0 60 2 -5.402922 1 1 0 0 1 1 2 3 2.010253 0 0.090000 1.970000 0.098117 0.990000 0.750000 1.000000 1.000000 0.976844 0.990000 1 0.960000 1.000000 NUP155 9631 broad.mit.edu 37 5 37370977 37370977 + Missense_Mutation SNP G G C TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr5:37370977G>C ENST00000231498.3 - 1 306 c.103C>G c.(103-105)Caa>Gaa p.Q35E NUP155_ENST00000381843.2_5'Flank|NUP155_ENST00000513532.1_Missense_Mutation_p.Q35E NM_153485.1 NP_705618.1 O75694 NU155_HUMAN nucleoporin 155kDa 62 all_lung(31;0.000137) COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) CGGTCCTCTTGCAACTGACGG 0.582000 0 SO:0001583 missense ENST00000231498.3 1 1 hg19 CCDS3921.1 . . . . . . . . . . G 13.87 2.366755 0.41902 . . ENSG00000113569 ENST00000231498;ENST00000513532 T;T 0.77877 -1.12;-1.13 4.28 3.38 0.38709 . 0.056570 0.64402 N 0.000001 T 0.69975 0.3171 L 0.57536 1.79 0.50039 D 0.999841 B;B 0.30146 0.0;0.27 B;B 0.31442 0.0;0.13 T 0.63959 -0.6519 10 0.02654 T 1 . 14.0155 0.64521 0.0:0.1524:0.8476:0.0 . 35;35 E9PF10;O75694 .;NU155_HUMAN E 35 ENSP00000231498:Q35E;ENSP00000422019:Q35E ENSP00000231498:Q35E Q - 1 0 NUP155 37406734 1.000000 0.71417 0.999000 0.59377 0.996000 0.88848 5.782000 0.68973 0.985000 0.38656 0.650000 0.86243 CAA TCGA-2J-AABR-01A-11D-A40W-08 NUP155-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207593.2 0 0 0 17 512 0 84 0 6.905859e-03 0 4 0 84 2 0 0 0 0 0 2 1 0.999961 17 504 0 81 2 -3.703665 1 1 0 0 1 1 2 3 2.018212 0 0.090000 1.970000 0.099723 0.770000 0.450000 1.000000 1.000000 0.785584 0.770000 0 0.590000 1.000000 BVES 11149 broad.mit.edu 37 6 105573335 105573335 + Missense_Mutation SNP T T C TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr6:105573335T>C ENST00000314641.5 - 4 686 c.470A>G c.(469-471)aAg>aGg p.K157R BVES_ENST00000446408.2_Missense_Mutation_p.K157R|BVES_ENST00000336775.5_Missense_Mutation_p.K157R NM_001199563.1 NP_001186492.1 Q8NE79 POPD1_HUMAN blood vessel epicardial substance p.K157R(1) 21 all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238) AGTTTGGCCCTTTTTCAAGGT 0.438000 1 Substitution - Missense(1) SO:0001583 missense ENST00000314641.5 0 1 hg19 CCDS5051.1 . . . . . . . . . . T 11.10 1.540510 0.27563 0.0 1.16E-4 ENSG00000112276 ENST00000314641;ENST00000336775;ENST00000446408 T;T;T 0.31510 1.49;1.49;1.49 5.76 3.34 0.38264 Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1); 0.130282 0.64402 N 0.000002 T 0.07638 0.0192 L 0.31845 0.965 0.39124 D 0.961725 B 0.14438 0.01 B 0.13407 0.009 T 0.12528 -1.0544 10 0.13470 T 0.59 -15.0112 6.8871 0.24208 0.0:0.148:0.1607:0.6914 . 157 Q8NE79 POPD1_HUMAN R 157 ENSP00000313172:K157R;ENSP00000337259:K157R;ENSP00000397310:K157R ENSP00000313172:K157R K - 2 0 BVES 105680028 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 2.676000 0.46883 1.016000 0.39470 0.533000 0.62120 AAG TCGA-2J-AABR-01A-11D-A40W-08 BVES-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406075.1 0 0 0 6 844 1 159 0 4.558606e-04 0 4 1 159 2 0 0 0 0 0 2 0 0.000334 6 831 2 155 25 -1.630380 0 1 121412 4 44 1 1 2 3 2.009004 0 0.090000 1.970000 0.097715 0.180000 0.060000 1.000000 0.160000 0.301090 0.180000 0 0.110000 0.360000 KCNH2 3757 broad.mit.edu 37 7 150656780 150656780 + Nonsense_Mutation SNP C C A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr7:150656780C>A ENST00000262186.5 - 3 753 c.352G>T c.(352-354)Gag>Tag p.E118* KCNH2_ENST00000392968.2_Nonsense_Mutation_p.E22*|KCNH2_ENST00000430723.3_Nonsense_Mutation_p.E118* NM_000238.3 NP_000229.1 Q12809 KCNH2_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 2 42 all_neural(206;0.219) OV - Ovarian serous cystadenocarcinoma(82;0.0121) Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661) GCCCCATCCTCGTTCTTCACG 0.597000 GBM(137;110 1844 13671 20123 45161) 0 SO:0001587 stop_gained ENST00000262186.5 0 1 hg19 CCDS5910.1 . . . . . . . . . . c 42 9.256142 0.99117 . . ENSG00000055118 ENST00000392968;ENST00000262186;ENST00000430723 . . . 4.71 4.71 0.59529 . 0.000000 0.64402 D 0.000012 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.72032 D 0.01 . 15.2258 0.73352 0.0:1.0:0.0:0.0 . . . . X 22;118;118 . ENSP00000262186:E118X E - 1 0 KCNH2 150287713 1.000000 0.71417 0.995000 0.50966 0.995000 0.86356 7.258000 0.78371 2.183000 0.69458 0.436000 0.28706 GAG TCGA-2J-AABR-01A-11D-A40W-08 KCNH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350741.2 0 0 0 4 259 0 42 0 0 0 1 0 42 2 0 0 0 0 0 2 1 0.889278 4 257 0 40 2 -4.063491 1 1 0 0 1 1 2 3 2.016032 0 0.090000 1.970000 0.099322 0.420000 0.130000 1.000000 0.320000 0.508372 0.420000 0 0.240000 1.000000 TAF6 6878 broad.mit.edu 37 7 99707631 99707631 + Silent SNP G G A rs148894017 TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr7:99707631G>A ENST00000344095.4 - 12 1749 c.1224C>T c.(1222-1224)gaC>gaT p.D408D TAF6_ENST00000437822.2_Silent_p.D445D|AP4M1_ENST00000421755.1_Intron|TAF6_ENST00000453269.2_Silent_p.D408D|TAF6_ENST00000472509.1_Silent_p.D465D|TAF6_ENST00000452041.1_Silent_p.D408D|TAF6_ENST00000418432.2_Silent_p.D332D NM_005641.3 NP_005632.1 P49848 TAF6_HUMAN TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa 26 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) GCACAGGGCCGTCCAGCACAC 0.587000 0 SO:0001819 synonymous_variant ENST00000344095.4 0 1 hg19 CCDS5686.1 TCGA-2J-AABR-01A-11D-A40W-08 TAF6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000337024.2 0 0 0 5 349 0 40 0 5.510637e-01 0 117 0 40 2 0 0 0 0 0 2 1 0.934638 5 342 0 40 2 -2.651826 1 1 121412 2 39 1 1 2 3 2.016796 0 0.090000 1.970000 0.099322 0.380000 0.130000 1.000000 0.320000 0.475282 0.380000 0 0.230000 1.000000 SPATC1 375686 broad.mit.edu 37 8 145094826 145094826 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr8:145094826G>A ENST00000377470.3 + 2 330 c.228G>A c.(226-228)ccG>ccA p.P76P SPATC1_ENST00000447830.2_Silent_p.P76P NM_198572.2 NP_940974.2 Q76KD6 SPERI_HUMAN spermatogenesis and centriole associated 1 15 all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105) TCCTGCCCCCGTCCCCAGCAG 0.632000 0 SO:0001819 synonymous_variant ENST00000377470.3 0 1 hg19 CCDS6413.2 TCGA-2J-AABR-01A-11D-A40W-08 SPATC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000346926.1 0 0 0 10 438 0 79 0 6.504065e-04 0 2 0 79 2 0 0 0 0 0 2 1 0.996697 10 431 0 77 2 -3.022936 1 1 121412 5 39 1 1 2 3 2.017190 0 0.090000 1.970000 0.099322 0.550000 0.270000 1.000000 0.500000 0.615312 0.550000 0 0.390000 1.000000 RNF20 56254 broad.mit.edu 37 9 104324559 104324559 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr9:104324559G>A ENST00000389120.3 + 20 2873 c.2783G>A c.(2782-2784)cGt>cAt p.R928H NM_019592.5 NP_062538.5 Q5VTR2 BRE1A_HUMAN ring finger protein 20, E3 ubiquitin protein ligase 54 all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255) TGTAACATGCGTAAAAAGGAT 0.418000 0 SO:0001583 missense ENST00000389120.3 0 1 hg19 CCDS35084.1 . . . . . . . . . . G 20.7 4.027440 0.75390 . . ENSG00000155827 ENST00000389120 D 0.86297 -2.1 5.87 4.98 0.66077 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1); 0.000000 0.85682 D 0.000000 D 0.90249 0.6951 L 0.56340 1.77 0.80722 D 1 D 0.62365 0.991 P 0.58620 0.842 D 0.91247 0.5026 10 0.72032 D 0.01 -9.7351 15.166 0.72825 0.0684:0.0:0.9316:0.0 . 928 Q5VTR2 BRE1A_HUMAN H 928 ENSP00000373772:R928H ENSP00000373772:R928H R + 2 0 RNF20 103364380 1.000000 0.71417 1.000000 0.80357 0.583000 0.36354 7.601000 0.82783 1.628000 0.50416 -0.150000 0.13652 CGT TCGA-2J-AABR-01A-11D-A40W-08 RNF20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356402.1 0 0 0 5 471 0 85 0 8.045950e-02 0 36 0 85 2 0 0 0 0 0 2 1 0.936454 5 467 0 82 2 -2.554803 1 1 0 0 1 0 1 1 2.002265 0 0.090000 1.970000 0.055576 0.230000 0.090000 0.480000 0.220000 0.259197 0.230000 0 0.150000 0.360000 ANAPC2 29882 broad.mit.edu 37 9 140080689 140080689 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chr9:140080689C>T ENST00000323927.2 - 3 864 c.860G>A c.(859-861)cGt>cAt p.R287H SSNA1_ENST00000322310.5_5'Flank NM_013366.3 NP_037498.1 Q9UJX6 ANC2_HUMAN anaphase promoting complex subunit 2 15 all_cancers(76;0.0926) STAD - Stomach adenocarcinoma(284;0.0698) GTGGAACTCACGCAGGAAGGA 0.642000 0 SO:0001583 missense ENST00000323927.2 0 1 hg19 CCDS7033.1 . . . . . . . . . . C 11.01 1.512989 0.27123 0.0 1.16E-4 ENSG00000176248 ENST00000323927 T 0.03181 4.02 3.7 2.7 0.31948 . 0.867499 0.10426 N 0.676110 T 0.02807 0.0084 N 0.12182 0.205 0.09310 N 1 B;B 0.22851 0.046;0.076 B;B 0.17433 0.008;0.018 T 0.38564 -0.9655 10 0.48119 T 0.1 -16.0898 10.9309 0.47217 0.0:0.8075:0.1925:0.0 . 287;287 Q9UJX6;Q9UJX6-2 ANC2_HUMAN;. H 287 ENSP00000314004:R287H ENSP00000314004:R287H R - 2 0 ANAPC2 139200510 0.002000 0.14202 0.973000 0.42090 0.917000 0.54804 0.301000 0.19174 2.059000 0.61396 0.555000 0.69702 CGT TCGA-2J-AABR-01A-11D-A40W-08 ANAPC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055315.1 0 0 0 4 182 0 32 0 1.762531e-01 0 28 0 32 2 0 0 0 0 0 2 1 0.888714 4 180 0 31 2 -3.317274 1 1 121340 17 41 1 1 2 3 2.005350 0 0.090000 1.970000 0.127684 0.560000 0.190000 1.000000 1.000000 0.592863 0.560000 0 0.340000 0.880000 BEX2 84707 broad.mit.edu 37 X 102564580 102564580 + Missense_Mutation SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chrX:102564580G>A ENST00000372677.3 - 3 592 c.325C>T c.(325-327)Cgg>Tgg p.R109W BEX2_ENST00000372674.1_Missense_Mutation_p.R109W|BEX2_ENST00000536889.1_Missense_Mutation_p.R141W NM_032621.3 NP_116010.1 Q9BXY8 BEX2_HUMAN brain expressed X-linked 2 3 CTGACTGCCCGCAAACTATGA 0.507000 0 SO:0001583 missense ENST00000372677.3 0 1 hg19 CCDS14505.1 . . . . . . . . . . G 14.93 2.681005 0.47886 . . ENSG00000133134 ENST00000372677;ENST00000536889;ENST00000372674 T;T;T 0.15952 2.42;2.38;2.42 4.29 2.44 0.29823 . 0.162857 0.29253 N 0.012700 T 0.38161 0.1030 M 0.83953 2.67 0.28106 N 0.931193 D;D 0.89917 0.999;1.0 D;D 0.68483 0.91;0.958 T 0.15780 -1.0425 10 0.44086 T 0.13 . 8.329 0.32175 0.0:0.0:0.5702:0.4298 . 109;141 Q9BXY8;F5H7H5 BEX2_HUMAN;. W 109;141;109 ENSP00000361762:R109W;ENSP00000442521:R141W;ENSP00000361759:R109W ENSP00000361759:R109W R - 1 2 BEX2 102451236 0.638000 0.27225 0.551000 0.28230 0.784000 0.44337 0.741000 0.26202 0.518000 0.28383 0.600000 0.82982 CGG TCGA-2J-AABR-01A-11D-A40W-08 BEX2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057702.1 0 0 0 9 820 0 161 0 1.374317e-01 0 53 0 161 2 0 0 0 0 0 2 1 0.993736 9 805 0 155 2 -1.947661 0 1 0 0 1 0 1 1 0.090000 1.970000 0.090000 0.240000 0.120000 0.430000 0.240000 0.264143 0.240000 0 0.170000 0.340000 IGSF1 3547 broad.mit.edu 37 X 130416639 130416639 + Missense_Mutation SNP C C T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chrX:130416639C>T ENST00000361420.3 - 7 1104 c.1025G>A c.(1024-1026)cGg>cAg p.R342Q IGSF1_ENST00000370903.3_Missense_Mutation_p.R342Q|IGSF1_ENST00000370904.1_Missense_Mutation_p.R333Q|IGSF1_ENST00000370910.1_Missense_Mutation_p.R333Q Q8N6C5 IGSF1_HUMAN immunoglobulin superfamily, member 1 78 TCCTCGACACCGTAGGCTCAC 0.498000 0 SO:0001583 missense ENST00000361420.3 1 1 hg19 CCDS14629.1 . . . . . . . . . . C 1.457 -0.563461 0.03939 . . ENSG00000147255 ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903 T;T;T;T 0.12774 2.65;2.65;2.65;2.65 4.78 -0.153 0.13403 Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1); 1.769840 0.02967 N 0.143897 T 0.07954 0.0199 N 0.17872 0.535 0.09310 N 1 B;B 0.06786 0.001;0.0 B;B 0.04013 0.001;0.001 T 0.26985 -1.0087 10 0.21014 T 0.42 . 0.7403 0.00972 0.1686:0.3668:0.1618:0.3028 . 333;342 Q8N6C5-2;Q8N6C5 .;IGSF1_HUMAN Q 333;342;333;342 ENSP00000359947:R333Q;ENSP00000355010:R342Q;ENSP00000359941:R333Q;ENSP00000359940:R342Q ENSP00000355010:R342Q R - 2 0 IGSF1 130244320 0.000000 0.05858 0.000000 0.03702 0.047000 0.14425 -0.077000 0.11394 -0.295000 0.08960 0.594000 0.82650 CGG TCGA-2J-AABR-01A-11D-A40W-08 IGSF1-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000058288.1 0 0 0 13 381 0 71 0 0 0 1 0 71 2 0 0 0 0 0 2 1 0.999512 13 376 0 67 2 -2.555299 1 1 121410 5 38 1 0 1 1 0.090000 1.970000 0.090000 0.740000 0.410000 1.000000 1.000000 0.750082 0.740000 0 0.560000 0.950000 PLXNB3 5365 broad.mit.edu 37 X 153036266 153036266 + Silent SNP A A T TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chrX:153036266A>T ENST00000361971.5 + 11 2178 c.2064A>T c.(2062-2064)gcA>gcT p.A688A PLXNB3_ENST00000538282.1_Silent_p.A298A|PLXNB3_ENST00000538776.1_Silent_p.A341A|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538966.1_Silent_p.A711A NM_005393.2 NP_005384.2 Q9ULL4 PLXB3_HUMAN plexin B3 32 all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05) AAGGCCTGGCAGGTCCCCACC 0.622000 0 SO:0001819 synonymous_variant ENST00000361971.5 0 1 hg19 CCDS14729.1 TCGA-2J-AABR-01A-11D-A40W-08 PLXNB3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000061063.1 0 0 0 6 271 0 44 1 9.802928e-03 4 2 0 44 2 0 0 0 0 0 2 1 0.961730 6 262 0 43 2 -7.081947 1 1 0 0 1 0 1 1 0.090000 1.970000 0.090000 0.500000 0.210000 0.950000 1.000000 0.534601 0.500000 0 0.330000 0.720000 PGAM4 441531 broad.mit.edu 37 X 77224488 77224488 + Silent SNP G G A TCGA-2J-AABR-01A-11D-A40W-08 TCGA-2J-AABR-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 534d051f-0b40-486a-8f77-646bf003d3d0 4c28dd95-5359-4c03-b338-7038de30008f g.chrX:77224488G>A ENST00000458128.1 - 1 647 c.648C>T c.(646-648)atC>atT p.I216I ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Intron|ATP7A_ENST00000341514.6_Intron NM_001029891.2 NP_001025062.1 Q8N0Y7 PGAM4_HUMAN phosphoglycerate mutase family member 4 6 ATTCATAGACGATGGGAATAC 0.537000 0 SO:0001819 synonymous_variant ENST00000458128.1 0 1 hg19 CCDS35338.1 TCGA-2J-AABR-01A-11D-A40W-08 PGAM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128371.2 0 0 0 7 745 0 176 0 0 0 0 176 2 0 0 0 0 0 2 1 0.974229 7 688 0 177 2 -2.114288 0 1 0 0 1 0 1 1 0.090000 1.970000 0.090000 0.210000 0.090000 0.400000 0.200000 0.232598 0.210000 0 0.140000 0.310000