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 PDZD7 79955 broad.mit.edu 37 10 102778797 102778797 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr10:102778797G>A ENST00000370215.3 - 8 1331 c.1106C>T c.(1105-1107)gCc>gTc p.A369V NM_024895.4 NP_079171.1 Q9H5P4 PDZD7_HUMAN PDZ domain containing 7 22 CGTCTGCATGGCTGTGTCCGC 0.741000 OREG0020453 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000370215.3 0 1 hg19 CCDS31269.1 . . . . . . . . . . G 34 5.397005 0.96009 . . ENSG00000186862 ENST00000393462;ENST00000370215 T 0.14266 2.52 5.21 5.21 0.72293 . 0.457692 0.22908 N 0.054180 T 0.37183 0.0994 M 0.61703 1.905 0.54753 D 0.99998 D;D 0.89917 1.0;1.0 D;D 0.87578 0.96;0.998 T 0.03761 -1.1006 10 0.48119 T 0.1 . 18.7565 0.91835 0.0:0.0:1.0:0.0 . 369;369 Q9H5P4;Q9H5P4-2 PDZD7_HUMAN;. V 369 ENSP00000359234:A369V ENSP00000359234:A369V A - 2 0 PDZD7 102768787 1.000000 0.71417 0.997000 0.53966 0.850000 0.48378 8.990000 0.93510 2.433000 0.82419 0.561000 0.74099 GCC TCGA-HZ-8002-01A-11D-2201-08 PDZD7-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049883.1 0 0 0 3 59 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 7.725786e-01 2 53 0 15 2 0 0 0 0 16 2 -8.309006 1 0 116480 2 26 1 0 1 1 1.994749 0 0.100000 2 0.093199 0.940000 0.290000 1.000000 1.000000 0.827207 0.940000 1 0.550000 1.000000 DMBT1 1755 broad.mit.edu 37 10 124399679 124399679 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr10:124399679G>A ENST00000338354.3 + 52 6785 c.6679G>A c.(6679-6681)Gac>Aac p.D2227N DMBT1_ENST00000368909.3_Missense_Mutation_p.D2227N|DMBT1_ENST00000359586.6_Missense_Mutation_p.D947N|DMBT1_ENST00000368955.3_Missense_Mutation_p.D2217N|DMBT1_ENST00000368956.2_Missense_Mutation_p.D1599N|DMBT1_ENST00000344338.3_Missense_Mutation_p.D2217N|DMBT1_ENST00000330163.4_Missense_Mutation_p.D1599N Q9UGM3 DMBT1_HUMAN deleted in malignant brain tumors 1 72 all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238) CACCTGGGTCGACACCATGTA 0.478000 Ovarian(182;93 2026 18125 22222 38972) 0 SO:0001583 missense ENST00000338354.3 0 1 hg19 . . . . . . . . . . G 10.08 1.252436 0.22880 0.0 2.35E-4 ENSG00000187908 ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586 D;D;D;D;D;D;D 0.81821 -1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54 5.53 -11.1 0.00147 Zona pellucida sperm-binding protein (3); 2.913890 0.01909 N 0.039733 T 0.58637 0.2136 N 0.10809 0.05 0.09310 N 1 B;B;B;B;B;B;B 0.24963 0.001;0.115;0.001;0.001;0.001;0.001;0.001 B;B;B;B;B;B;B 0.09377 0.001;0.004;0.0;0.0;0.0;0.0;0.001 T 0.53655 -0.8408 10 0.08599 T 0.76 . 15.5153 0.75818 0.1221:0.2851:0.5928:0.0 . 947;2207;1476;2356;1599;2217;2227 F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3 .;.;.;.;.;.;DMBT1_HUMAN N 2227;2356;2227;2227;2227;2226;1599;2217;1599;1599;2227;2217;1599;373;947 ENSP00000342210:D2227N;ENSP00000343175:D2217N;ENSP00000327747:D1599N;ENSP00000357905:D2227N;ENSP00000357951:D2217N;ENSP00000357952:D1599N;ENSP00000352593:D947N ENSP00000331522:D1599N D + 1 0 DMBT1 124389669 0.000000 0.05858 0.000000 0.03702 0.731000 0.41821 -0.417000 0.07088 -2.593000 0.00455 -1.004000 0.02495 GAC TCGA-HZ-8002-01A-11D-2201-08 DMBT1-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000050792.2 0 0 0 17 816 0 199 1 3.304017e-01 2 53 0 199 2 0 0 0 0 0 2 1 9.999559e-01 17 796 0 199 2 0 0 0 0 199 2 -2.469359 0 1 121092 6 43 1 0 1 1 1.994749 0 0.100000 2 0.093199 0.400000 0.240000 0.620000 0.400000 0.422912 0.400000 0 0.310000 0.520000 ADARB2 105 broad.mit.edu 37 10 1405435 1405435 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr10:1405435C>T ENST00000381312.1 - 3 1190 c.865G>A c.(865-867)Ggg>Agg p.G289R RP11-398B16.2_ENST00000432987.1_RNA NM_018702.3 NP_061172.1 Q9NS39 RED2_HUMAN adenosine deaminase, RNA-specific, B2 (non-functional) p.G289R(1) 41 all_epithelial(10;0.059)|Colorectal(49;0.0815) TAGCGCAGCCCGGCGCGCAGG 0.771000 1 Substitution - Missense(1) SO:0001583 missense ENST00000381312.1 0 1 hg19 CCDS7058.1 . . . . . . . . . . C 19.66 3.869534 0.72065 . . ENSG00000185736 ENST00000381312 T 0.76448 -1.02 5.24 5.24 0.73138 Double-stranded RNA-binding (2);Double-stranded RNA-binding-like (1); 0.000000 0.85682 D 0.000000 D 0.86740 0.6005 L 0.60845 1.875 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.87900 0.2690 10 0.87932 D 0 -37.0365 18.8514 0.92232 0.0:1.0:0.0:0.0 . 289 Q9NS39 RED2_HUMAN R 289 ENSP00000370713:G289R ENSP00000370713:G289R G - 1 0 ADARB2 1395435 1.000000 0.71417 0.875000 0.34327 0.009000 0.06853 7.681000 0.84073 2.445000 0.82738 0.561000 0.74099 GGG TCGA-HZ-8002-01A-11D-2201-08 ADARB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046426.1 1 0 0 5 52 0 11 0 0 0 0 11 2 0 0 0 0 0 2 1 9.376066e-01 5 51 0 10 2 0 0 0 0 11 2 -10.898560 1 1 0 0 1 0 1 1 1.994091 0 0.100000 2 0.093199 0.990000 0.600000 1.000000 1.000000 0.962344 0.990000 1 0.950000 1.000000 MPP7 143098 broad.mit.edu 37 10 28343119 28343119 + Missense_Mutation SNP C C A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr10:28343119C>A ENST00000375732.1 - 17 1865 c.1606G>T c.(1606-1608)Ggt>Tgt p.G536C MPP7_ENST00000540098.1_Missense_Mutation_p.G536C|MPP7_ENST00000337532.5_Missense_Mutation_p.G536C|MPP7_ENST00000375719.3_Missense_Mutation_p.G536C Q5T2T1 MPP7_HUMAN membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7) 22 AAAAGATGACCATATTGACTT 0.318000 0 SO:0001583 missense ENST00000375732.1 0 1 hg19 CCDS7158.1 . . . . . . . . . . C 18.58 3.655017 0.67472 . . ENSG00000150054 ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000441595 T;T;T;T;T 0.44881 0.91;0.91;0.91;0.91;0.91 5.18 5.18 0.71444 Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2); 0.096174 0.64402 D 0.000001 T 0.66790 0.2825 M 0.85777 2.775 0.80722 D 1 D 0.76494 0.999 D 0.80764 0.994 T 0.71879 -0.4459 10 0.66056 D 0.02 . 13.0486 0.58942 0.0:0.9226:0.0:0.0774 . 536 Q5T2T1 MPP7_HUMAN C 536;536;536;536;297 ENSP00000364884:G536C;ENSP00000337907:G536C;ENSP00000438693:G536C;ENSP00000364871:G536C;ENSP00000398319:G297C ENSP00000337907:G536C G - 1 0 MPP7 28383125 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 1.634000 0.37123 2.395000 0.81488 0.591000 0.81541 GGT TCGA-HZ-8002-01A-11D-2201-08 MPP7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047345.1 1 0 0 4 71 0 26 0 1.646381e-01 0 11 0 26 2 0 0 0 0 0 2 1 8.824205e-01 3 69 0 26 2 0 0 0 0 26 2 -4.123378 1 0 0 0 1 0 1 1 1.994091 0 0.100000 2 0.093199 0.990000 0.370000 1.000000 1.000000 0.869253 0.990000 1 0.640000 1.000000 MADD 8567 broad.mit.edu 37 11 47296667 47296667 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr11:47296667C>T ENST00000311027.5 + 3 781 c.616C>T c.(616-618)Cgc>Tgc p.R206C MADD_ENST00000402192.2_Missense_Mutation_p.R206C|MADD_ENST00000395344.3_Missense_Mutation_p.R206C|MADD_ENST00000349238.3_Missense_Mutation_p.R206C|MADD_ENST00000395336.3_Missense_Mutation_p.R206C|MADD_ENST00000402799.1_Missense_Mutation_p.R206C|MADD_ENST00000342922.4_Missense_Mutation_p.R206C|MADD_ENST00000407859.3_Missense_Mutation_p.R206C|MADD_ENST00000406482.1_Missense_Mutation_p.R206C NM_003682.3 NP_003673.3 MAP-kinase activating death domain 84 CTGTAGTGAGCGCCTTCTGGG 0.522000 0 SO:0001583 missense ENST00000311027.5 0 1 hg19 CCDS7930.1 . . . . . . . . . . C 19.75 3.885704 0.72410 . . ENSG00000110514 ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192 T;T;T;T;T;T;T;T;T 0.07908 3.26;3.15;3.15;3.26;3.27;3.17;3.16;3.26;3.26 5.81 3.84 0.44239 DENN (3); 0.057038 0.64402 D 0.000002 T 0.27731 0.0682 M 0.73598 2.24 0.80722 D 1 D;P;D;D;D;D;D;D;D;D 0.89917 1.0;0.948;1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0 D;P;D;D;D;D;D;D;D;D 0.91635 0.994;0.791;0.992;0.981;0.981;0.981;0.988;0.999;0.993;0.988 T 0.02661 -1.1127 9 . . . -6.6138 14.1753 0.65537 0.487:0.513:0.0:0.0 . 206;206;206;206;206;206;206;206;206;206 B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3 .;.;.;.;.;.;.;.;MADD_HUMAN;. C 206 ENSP00000343902:R206C;ENSP00000385585:R206C;ENSP00000384435:R206C;ENSP00000304505:R206C;ENSP00000310933:R206C;ENSP00000384204:R206C;ENSP00000378753:R206C;ENSP00000378745:R206C;ENSP00000384287:R206C . R + 1 0 MADD 47253243 1.000000 0.71417 0.788000 0.31933 0.970000 0.65996 3.083000 0.50136 1.409000 0.46915 0.655000 0.94253 CGC TCGA-HZ-8002-01A-11D-2201-08 MADD-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000317746.1 0 0 0 13 523 0 108 1 5.465036e-01 4 67 0 108 2 0 0 0 0 0 2 1 9.994934e-01 13 515 0 106 2 0 0 0 0 108 2 -10.762330 1 1 0 0 1 1 2 3 2.029215 0 0.100000 2 0.111988 0.540000 0.280000 1.000000 0.480000 0.610401 0.540000 0 0.390000 1.000000 TMEM132B 114795 broad.mit.edu 37 12 126138387 126138387 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr12:126138387G>A ENST00000299308.3 + 9 2376 c.2368G>A c.(2368-2370)Gaa>Aaa p.E790K TMEM132B_ENST00000535886.1_Missense_Mutation_p.E302K NM_052907.2 NP_443139.2 Q14DG7 T132B_HUMAN transmembrane protein 132B p.E790K(1) 107 all_neural(191;0.101)|Medulloblastoma(191;0.163) GGTCAAATTCGAACCAAGTAG 0.423000 1 Substitution - Missense(1) SO:0001583 missense ENST00000299308.3 1 1 hg19 CCDS41859.1 . . . . . . . . . . G 14.92 2.678338 0.47886 . . ENSG00000139364 ENST00000299308;ENST00000535886 T;T 0.13538 2.58;2.58 5.53 5.53 0.82687 . 0.479442 0.20533 N 0.090474 T 0.11580 0.0282 L 0.34521 1.04 0.40552 D 0.981121 P 0.47106 0.89 B 0.33295 0.161 T 0.10660 -1.0620 10 0.41790 T 0.15 . 19.4753 0.94985 0.0:0.0:1.0:0.0 . 790 Q14DG7 T132B_HUMAN K 790;302 ENSP00000299308:E790K;ENSP00000440436:E302K ENSP00000299308:E790K E + 1 0 TMEM132B 124704340 1.000000 0.71417 0.343000 0.25615 0.598000 0.36846 6.179000 0.71974 2.596000 0.87737 0.650000 0.86243 GAA TCGA-HZ-8002-01A-11D-2201-08 TMEM132B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000400043.1 1 0 0 13 320 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 9.994030e-01 11 307 0 94 2 0 0 0 0 94 2 -4.016711 1 1 121028 1 32 1 0 1 1 1.998225 0 0.100000 2 0.094112 0.780000 0.440000 1.000000 1.000000 0.782626 0.780000 0 0.590000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D 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 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D 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-HZ-8002-01A-11D-2201-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 9 113 0 24 0 4.941126e-01 0 20 0 24 2 1 9.999998e-01 44 555 0 402 2 1 9.941519e-01 9 110 0 24 2 1 1 840 7114 0 24 2 -5.707509 1 1 121404 2 44 1 0 1 1 1.998225 0 0.100000 2 0.094112 0.990000 0.700000 1.000000 1.000000 0.975434 0.990000 1 0.990000 1.000000 KCNA1 3736 broad.mit.edu 37 12 5021748 5021748 + Silent SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr12:5021748C>T ENST00000382545.3 + 2 2311 c.1204C>T c.(1204-1206)Ctg>Ttg p.L402L KCNA1_ENST00000543874.2_Intron NM_000217.2 NP_000208.2 Q09470 KCNA1_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia) 63 Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236) AACAATTGCCCTGCCCGTACC 0.517000 0 SO:0001819 synonymous_variant ENST00000382545.3 1 1 hg19 CCDS8535.1 TCGA-HZ-8002-01A-11D-2201-08 KCNA1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000103343.2 1 0 0 123 2339 0 474 0 0 0 0 474 2 0 0 0 0 0 2 1 1 120 2280 0 465 2 0 0 0 0 474 2 -9.441565 1 1 0 0 1 1 2 3 2.012033 0 0.100000 2 0.108470 0.990000 0.840000 1.000000 1.000000 0.974911 0.990000 1 0.920000 1.000000 TIMELESS 8914 broad.mit.edu 37 12 56825369 56825369 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr12:56825369C>T ENST00000553532.1 - 8 857 c.707G>A c.(706-708)gGa>gAa p.G236E TIMELESS_ENST00000229201.4_Missense_Mutation_p.G235E|TIMELESS_ENST00000554616.1_Missense_Mutation_p.G236E timeless circadian clock 49 CTGCCCTACTCCCGCCAGCTG 0.547000 0 SO:0001583 missense ENST00000553532.1 1 1 hg19 CCDS8918.1 . . . . . . . . . . C 2.672 -0.277284 0.05679 . . ENSG00000111602 ENST00000229201;ENST00000553532;ENST00000554616 T;T;T 0.39056 1.1;1.1;1.1 5.42 3.49 0.39957 Timeless protein (1); 0.470219 0.24623 N 0.036943 T 0.18923 0.0454 N 0.04508 -0.205 0.09310 N 1 B;B 0.24675 0.089;0.109 B;B 0.30943 0.075;0.122 T 0.22800 -1.0206 10 0.11182 T 0.66 -0.0727 8.6066 0.33778 0.1394:0.5219:0.3387:0.0 . 235;236 Q9UNS1-2;Q9UNS1 .;TIM_HUMAN E 235;236;236 ENSP00000229201:G235E;ENSP00000450607:G236E;ENSP00000450848:G236E ENSP00000229201:G236E G - 2 0 TIMELESS 55111636 0.077000 0.21312 0.764000 0.31436 0.291000 0.27294 2.205000 0.42770 2.715000 0.92844 0.655000 0.94253 GGA TCGA-HZ-8002-01A-11D-2201-08 TIMELESS-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000409771.1 1 0 0 19 366 0 73 1 6.312343e-01 7 34 0 73 2 0 0 0 0 0 2 1 9.999878e-01 19 352 0 71 2 0 0 0 0 73 2 -3.227970 1 1 0 0 1 0 1 1 1.998225 0 0.100000 2 0.094112 0.970000 0.610000 1.000000 1.000000 0.914543 0.970000 1 0.780000 1.000000 NALCN 259232 broad.mit.edu 37 13 102047562 102047562 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr13:102047562G>A ENST00000251127.6 - 3 344 c.263C>T c.(262-264)gCa>gTa p.A88V NALCN_ENST00000376200.5_Missense_Mutation_p.A88V|NALCN_ENST00000376196.3_Missense_Mutation_p.A88V|NALCN_ENST00000470333.1_5'UTR NM_052867.2 NP_443099.1 Q8IZF0 NALCN_HUMAN sodium leak channel, non-selective 177 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184) GTGCATTTTTGCTATCATCTC 0.388000 0 SO:0001583 missense ENST00000251127.6 0 1 hg19 CCDS9498.1 . . . . . . . . . . G 12.55 1.972746 0.34848 . . ENSG00000102452 ENST00000251127;ENST00000376196;ENST00000376200;ENST00000449582 D;D;D 0.98105 -4.72;-4.72;-4.72 5.59 5.59 0.84812 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.92861 0.7729 N 0.08118 0 0.80722 D 1 B;B 0.32526 0.374;0.328 B;B 0.35039 0.194;0.194 D 0.91202 0.4992 10 0.02654 T 1 . 19.5954 0.95535 0.0:0.0:1.0:0.0 . 88;88 F2Z323;Q8IZF0 .;NALCN_HUMAN V 88 ENSP00000251127:A88V;ENSP00000365367:A88V;ENSP00000365373:A88V ENSP00000251127:A88V A - 2 0 NALCN 100845563 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.476000 0.97823 2.635000 0.89317 0.563000 0.77884 GCA TCGA-HZ-8002-01A-11D-2201-08 NALCN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045663.2 0 0 0 7 386 0 96 0 2.560592e-02 0 12 0 96 2 0 0 0 0 0 2 1 9.789733e-01 7 376 0 95 2 0 0 0 0 96 2 -6.628334 1 0 0 0 1 1 2 3 2.015544 0 0.100000 2 0.108911 0.410000 0.170000 1.000000 0.350000 0.491448 0.410000 0 0.270000 0.790000 ARHGEF7 8874 broad.mit.edu 37 13 111870079 111870079 + Silent SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr13:111870079C>T ENST00000375741.2 + 6 835 c.585C>T c.(583-585)ttC>ttT p.F195F ARHGEF7_ENST00000375737.5_Silent_p.F92F|ARHGEF7_ENST00000426073.2_Silent_p.F17F|ARHGEF7_ENST00000317133.5_Silent_p.F174F|ARHGEF7_ENST00000375739.2_Silent_p.F145F|ARHGEF7_ENST00000375736.4_Silent_p.F17F|ARHGEF7_ENST00000544132.1_5'UTR|ARHGEF7_ENST00000375723.1_Silent_p.F17F|ARHGEF7_ENST00000370623.3_Silent_p.F102F|ARHGEF7_ENST00000218789.5_Silent_p.F17F NM_001113511.1|NM_145735.2 NP_001106983.1|NP_663788.1 Q14155 ARHG7_HUMAN Rho guanine nucleotide exchange factor (GEF) 7 41 all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163) BRCA - Breast invasive adenocarcinoma(86;0.188) AGTTTAACTTCCAGCAGACCA 0.478000 0 SO:0001819 synonymous_variant ENST00000375741.2 1 1 hg19 CCDS45068.1 TCGA-HZ-8002-01A-11D-2201-08 ARHGEF7-204 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 16 572 0 131 1 4.448522e-01 3 50 0 131 2 0 0 0 0 0 2 1 9.999196e-01 15 561 0 130 2 0 0 0 0 131 2 -2.939235 1 1 0 0 1 1 2 3 2.015544 0 0.100000 2 0.108911 0.580000 0.330000 1.000000 0.550000 0.638330 0.580000 0 0.440000 0.940000 ZC3H13 23091 broad.mit.edu 37 13 46543773 46543773 + Missense_Mutation SNP T T A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr13:46543773T>A ENST00000242848.4 - 14 3254 c.2906A>T c.(2905-2907)aAa>aTa p.K969I ZC3H13_ENST00000378921.2_5'UTR|ZC3H13_ENST00000282007.3_Missense_Mutation_p.K969I Q5T200 ZC3HD_HUMAN zinc finger CCCH-type containing 13 79 Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) CTCTTTCTTTTTCTTAATTGG 0.363000 Esophageal Squamous(187;747 2077 11056 31291 44172) 0 SO:0001583 missense ENST00000242848.4 0 1 hg19 . . . . . . . . . . T 11.21 1.572751 0.28092 . . ENSG00000123200 ENST00000242848;ENST00000282007 T;T 0.49139 1.81;0.79 5.78 2.02 0.26589 . 0.257379 0.33515 N 0.004827 T 0.56790 0.2009 M 0.62723 1.935 0.80722 D 1 P;D 0.54397 0.943;0.966 P;P 0.58266 0.69;0.836 T 0.56220 -0.8015 10 0.51188 T 0.08 . 10.1538 0.42809 0.0:0.1986:0.0:0.8014 . 969;969 Q5T200;Q5T200-2 ZC3HD_HUMAN;. I 969 ENSP00000242848:K969I;ENSP00000282007:K969I ENSP00000242848:K969I K - 2 0 ZC3H13 45441774 1.000000 0.71417 1.000000 0.80357 0.931000 0.56810 3.762000 0.55250 0.543000 0.28864 0.533000 0.62120 AAA TCGA-HZ-8002-01A-11D-2201-08 ZC3H13-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000044789.1 0 0 0 10 401 0 169 0 8.305532e-01 1 131 0 169 2 0 0 0 0 0 2 1 9.965579e-01 9 392 0 165 2 0 0 0 0 169 2 -10.142810 1 0 0 0 1 1 2 3 2.015544 0 0.100000 2 0.108911 0.540000 0.260000 1.000000 0.490000 0.598604 0.540000 0 0.380000 0.960000 HS3ST3B1 9953 broad.mit.edu 37 17 14205111 14205111 + Silent SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr17:14205111G>A ENST00000360954.2 + 1 712 c.276G>A c.(274-276)gcG>gcA p.A92A RP11-214O1.2_ENST00000583262.1_lincRNA NM_006041.1 NP_006032.1 Q9Y662 HS3SB_HUMAN heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 7 CGTTCCGGGCGCCGCCAGCCA 0.751000 0 SO:0001819 synonymous_variant ENST00000360954.2 0 1 hg19 CCDS11167.1 TCGA-HZ-8002-01A-11D-2201-08 HS3ST3B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000129998.1 0 0 0 3 44 0 10 0 0 0 0 10 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 10 2 -8.814529 1 0 0 0 1 0 1 1 1.988506 0 0.100000 2 0.091826 0.990000 0.360000 1.000000 1.000000 0.884753 0.990000 1 0.670000 1.000000 RECQL5 9400 broad.mit.edu 37 17 73624802 73624802 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr17:73624802G>A ENST00000317905.5 - 17 2689 c.2530C>T c.(2530-2532)Ccc>Tcc p.P844S RECQL5_ENST00000443199.2_5'UTR|RECQL5_ENST00000423245.2_Missense_Mutation_p.P817S NM_004259.6 NP_004250.4 O94762 RECQ5_HUMAN RecQ protein-like 5 36 all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09) all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112) GCAGGGGTGGGCTGGACTTCA 0.652000 Other identified genes with known or suspected DNA repair function 0 SO:0001583 missense ENST00000317905.5 1 1 hg19 CCDS42380.1 . . . . . . . . . . G 10.20 1.285118 0.23478 . . ENSG00000108469 ENST00000443199;ENST00000423245;ENST00000317905 T;T 0.59638 0.25;0.43 5.15 4.19 0.49359 . 1.175340 0.06100 N 0.665238 T 0.48786 0.1519 L 0.35723 1.085 0.47153 D 0.999332 B;B;B 0.22909 0.013;0.013;0.077 B;B;B 0.26094 0.003;0.003;0.066 T 0.12630 -1.0540 10 0.07813 T 0.8 -1.086 11.4825 0.50333 0.0879:0.0:0.9121:0.0 . 844;817;40 O94762;Q6P4G0;Q6FIC9 RECQ5_HUMAN;.;. S 439;844;844 ENSP00000394820:P844S;ENSP00000317636:P844S ENSP00000317636:P844S P - 1 0 RECQL5 71136397 0.049000 0.20398 0.010000 0.14722 0.558000 0.35554 1.541000 0.36126 1.180000 0.42898 0.563000 0.77884 CCC TCGA-HZ-8002-01A-11D-2201-08 RECQL5-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448207.1 0 0 0 12 454 0 73 0 2.243800e-01 0 32 0 73 2 0 0 0 0 0 2 1 9.990415e-01 12 446 0 72 2 0 0 0 0 73 2 -3.769229 1 1 0 0 1 0 1 1 1.988972 0 0.100000 2 0.091826 0.510000 0.280000 0.830000 0.510000 0.538603 0.510000 0 0.380000 0.680000 NOL4 8715 broad.mit.edu 37 18 31538336 31538336 + Missense_Mutation SNP C C G TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr18:31538336C>G ENST00000261592.5 - 7 1400 c.1103G>C c.(1102-1104)aGt>aCt p.S368T NOL4_ENST00000535384.1_Missense_Mutation_p.S83T|NOL4_ENST00000269185.4_Missense_Mutation_p.S254T|NOL4_ENST00000589544.1_Missense_Mutation_p.S368T|NOL4_ENST00000538587.1_Missense_Mutation_p.S294T|NOL4_ENST00000535475.1_Missense_Mutation_p.S213T NM_001198546.1|NM_003787.4 NP_001185475.1|NP_003778.2 O94818 NOL4_HUMAN nucleolar protein 4 51 TCGGTCTACACTCTCATTTTT 0.443000 0 SO:0001583 missense ENST00000261592.5 1 1 hg19 CCDS11907.2 . . . . . . . . . . C 9.460 1.092768 0.20471 . . ENSG00000101746 ENST00000261592;ENST00000269185;ENST00000399171;ENST00000535384;ENST00000535475;ENST00000538587 D;D;T;D;T 0.84442 -1.85;-1.85;-1.29;-1.85;-1.29 5.64 5.64 0.86602 . 0.188941 0.47093 D 0.000242 D 0.83792 0.5331 L 0.40543 1.245 0.41127 D 0.985853 P;B;B;B;B;B;B;B 0.41450 0.75;0.449;0.066;0.136;0.449;0.066;0.017;0.136 B;B;B;B;B;B;B;B 0.42827 0.399;0.215;0.061;0.143;0.143;0.061;0.043;0.061 D 0.84778 0.0771 10 0.54805 T 0.06 -5.3095 19.7023 0.96060 0.0:1.0:0.0:0.0 . 254;117;83;294;368;83;368;213 B4DLW2;F8W825;B7Z3Z7;B4DSQ0;O94818;F5H1E3;O94818-2;B3KRF4 .;.;.;.;NOL4_HUMAN;.;.;. T 368;254;117;83;213;294 ENSP00000261592:S368T;ENSP00000269185:S254T;ENSP00000445733:S83T;ENSP00000438190:S213T;ENSP00000443472:S294T ENSP00000261592:S368T S - 2 0 NOL4 29792334 1.000000 0.71417 0.971000 0.41717 0.099000 0.18886 5.673000 0.68109 2.639000 0.89480 0.557000 0.71058 AGT TCGA-HZ-8002-01A-11D-2201-08 NOL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255386.1 0 0 0 26 853 0 211 0 1.330580e-02 0 6 0 211 2 0 0 0 0 0 2 1 9.999999e-01 24 834 0 209 2 0 0 0 0 211 2 -3.461704 1 1 0 0 1 1 2 3 2.003108 0 0.100000 2 0.106256 0.610000 0.400000 1.000000 0.590000 0.654632 0.610000 0 0.490000 0.810000 KCNA10 3744 broad.mit.edu 37 1 111060380 111060380 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr1:111060380G>A ENST00000369771.2 - 1 1417 c.1030C>T c.(1030-1032)Cgc>Tgc p.R344C NM_005549.2 NP_005540.1 Q16322 KCA10_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 10 p.R344C(1) 35 all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301) Dalfampridine(DB06637) CTCACCAGGCGGATGATCCTC 0.577000 1 Substitution - Missense(1) SO:0001583 missense ENST00000369771.2 0 1 hg19 CCDS826.1 . . . . . . . . . . G 21.9 4.215244 0.79352 2.27E-4 0.0 ENSG00000143105 ENST00000369771 D 0.99259 -5.64 5.63 5.63 0.86233 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.99832 0.9924 H 0.99900 4.915 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.96505 0.9374 10 0.87932 D 0 . 18.3064 0.90184 0.0:0.0:1.0:0.0 . 344 Q16322 KCA10_HUMAN C 344 ENSP00000358786:R344C ENSP00000358786:R344C R - 1 0 KCNA10 110861903 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 6.505000 0.73708 2.676000 0.91093 0.558000 0.71614 CGC TCGA-HZ-8002-01A-11D-2201-08 KCNA10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059081.1 0 0 0 16 1078 0 196 0 0 0 0 196 2 0 0 0 0 0 2 1 9.999150e-01 16 1050 0 195 2 0 0 0 0 196 2 -2.308347 0 1 121412 2 40 1 0 1 1 1.999258 0 0.100000 2 0.094112 0.290000 0.170000 0.450000 0.290000 0.305492 0.290000 0 0.220000 0.380000 PBXIP1 57326 broad.mit.edu 37 1 154920764 154920764 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr1:154920764C>T ENST00000368463.3 - 6 559 c.488G>A c.(487-489)cGg>cAg p.R163Q PBXIP1_ENST00000368460.3_Missense_Mutation_p.R163Q|PBXIP1_ENST00000368465.1_Missense_Mutation_p.R134Q|PBXIP1_ENST00000498553.1_5'UTR|PBXIP1_ENST00000539880.1_Intron|PBXIP1_ENST00000542459.1_Missense_Mutation_p.R8Q NM_020524.2 NP_065385.2 Q96AQ6 PBIP1_HUMAN pre-B-cell leukemia homeobox interacting protein 1 24 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) CTCCCGGCCCCGCCGTCTCCG 0.687000 0 SO:0001583 missense ENST00000368463.3 0 1 hg19 CCDS1074.1 . . . . . . . . . . C 13.67 2.305987 0.40795 . . ENSG00000163346 ENST00000368465;ENST00000368463;ENST00000351146;ENST00000542459;ENST00000368460 T;T;T;T 0.15256 2.44;2.44;2.44;2.44 4.64 3.73 0.42828 . 0.381252 0.23284 N 0.049879 T 0.07098 0.0180 M 0.65975 2.015 0.25005 N 0.991446 B 0.27498 0.18 B 0.17722 0.019 T 0.18241 -1.0343 10 0.66056 D 0.02 -7.6894 6.8497 0.24008 0.0:0.7955:0.0:0.2045 . 163 Q96AQ6 PBIP1_HUMAN Q 134;163;163;8;163 ENSP00000357450:R134Q;ENSP00000357448:R163Q;ENSP00000438584:R8Q;ENSP00000357445:R163Q ENSP00000295523:R163Q R - 2 0 PBXIP1 153187388 0.841000 0.29509 0.988000 0.46212 0.773000 0.43773 2.101000 0.41787 1.163000 0.42636 0.563000 0.77884 CGG TCGA-HZ-8002-01A-11D-2201-08 PBXIP1-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090943.1 0 0 0 6 111 0 18 0 5.506923e-01 1 32 0 18 2 0 0 0 0 0 2 1 9.569276e-01 6 102 0 18 2 0 0 0 0 18 2 -9.940429 1 1 121304 2 26 1 1 2 3 2.000801 0 0.100000 2 0.105812 0.990000 0.460000 1.000000 1.000000 0.903023 0.990000 1 0.720000 1.000000 TAGLN2 8407 broad.mit.edu 37 1 159888604 159888604 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr1:159888604G>A ENST00000368097.4 - 5 896 c.586C>T c.(586-588)Cgc>Tgc p.R196C TAGLN2_ENST00000478033.1_5'UTR|TAGLN2_ENST00000368096.1_Missense_Mutation_p.R217C|TAGLN2_ENST00000320307.4_Missense_Mutation_p.R196C NM_001277223.1|NM_003564.1 NP_001264152.1|NP_003555.1 P37802 TAGL2_HUMAN transgelin 2 9 all_hematologic(112;0.0597) BRCA - Breast invasive adenocarcinoma(70;0.111) AGGATCTGGCGTGGCATCCCG 0.552000 0 SO:0001583 missense ENST00000368097.4 1 1 hg19 CCDS1189.1 . . . . . . . . . . G 18.91 3.724566 0.68959 . . ENSG00000158710 ENST00000368097;ENST00000368096;ENST00000320307 D;D;D 0.91631 -2.88;-2.88;-2.88 4.65 2.68 0.31781 Calponin homology domain (1); 0.407364 0.15695 U 0.249233 D 0.92945 0.7755 H 0.97611 4.04 0.58432 D 0.999999 P 0.39060 0.657 B 0.40228 0.323 D 0.92678 0.6156 9 . . . -12.6358 10.6602 0.45698 0.0:0.0:0.4966:0.5034 . 196 P37802 TAGL2_HUMAN C 196;217;196 ENSP00000357077:R196C;ENSP00000357076:R217C;ENSP00000357075:R196C . R - 1 0 TAGLN2 158155228 1.000000 0.71417 0.975000 0.42487 0.996000 0.88848 3.226000 0.51254 0.628000 0.30357 0.655000 0.94253 CGC TCGA-HZ-8002-01A-11D-2201-08 TAGLN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059105.1 0 0 1 21 884 0 126 1 1 328 2041 0 126 2 0 0 0 0 0 2 1 9.999965e-01 20 859 0 126 2 0 0 0 0 126 2 -14.823980 1 1 0 0 1 1 2 3 2.000801 0 0.100000 2 0.105812 0.480000 0.300000 1.000000 0.470000 0.537529 0.480000 0 0.380000 0.650000 RPL11 6135 broad.mit.edu 37 1 24022341 24022341 + Nonsense_Mutation SNP C C A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr1:24022341C>A ENST00000374550.3 + 5 495 c.450C>A c.(448-450)tgC>tgA p.C150* RPL11_ENST00000482370.1_3'UTR NM_000975.3|NM_001199802.1 NP_000966.2|NP_001186731.1 P62913 RL11_HUMAN ribosomal protein L11 6 Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255) GGACAGGCTGCATTGGGGCCA 0.517000 0 SO:0001587 stop_gained ENST00000374550.3 0 1 hg19 CCDS238.1 . . . . . . . . . . C 22.9 4.354407 0.82243 . . ENSG00000142676 ENST00000374550;ENST00000458455 . . . 5.7 3.82 0.43975 . 0.218912 0.49305 D 0.000147 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.27785 T 0.31 -16.091 7.4225 0.27079 0.1337:0.7263:0.0:0.14 . . . . X 150;148 . ENSP00000363676:C150X C + 3 2 RPL11 23894928 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 2.446000 0.44908 1.417000 0.47077 -0.218000 0.12543 TGC TCGA-HZ-8002-01A-11D-2201-08 RPL11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008168.1 0 0 0 3 74 0 19 1 1 3 7669 0 19 2 0 0 0 0 0 2 1 8.041530e-01 2 73 0 19 2 0 0 0 0 19 2 -6.410007 1 0 0 0 1 0 1 1 1.999258 0 0.100000 2 0.094112 0.800000 0.240000 1.000000 1.000000 0.761606 0.800000 0 0.460000 1.000000 LEPR 3953 broad.mit.edu 37 1 66036155 66036155 + Splice_Site SNP G G T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr1:66036155G>T ENST00000349533.6 + 4 225 c.e4-1 LEPR_ENST00000371058.1_Splice_Site|snoU13_ENST00000459362.1_RNA|LEPR_ENST00000406510.3_Splice_Site|LEPR_ENST00000371060.3_Splice_Site|LEPR_ENST00000462765.1_Splice_Site|LEPR_ENST00000344610.8_Splice_Site|LEPR_ENST00000371059.3_Splice_Site NM_002303.5 NP_002294.2 O15243 OBRG_HUMAN leptin receptor p.?(2) 36 TATCCTAACAGAATTTATTTA 0.299000 2 Unknown(2) SO:0001630 splice_region_variant ENST00000349533.6 0 1 hg19 CCDS631.1 . . . . . . . . . . G 9.738 1.163980 0.21538 . . ENSG00000116678 ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058 . . . 5.56 5.56 0.83823 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.0325 0.71720 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . LEPR 65808743 1.000000 0.71417 0.995000 0.50966 0.077000 0.17291 5.008000 0.63991 2.619000 0.88677 0.460000 0.39030 . TCGA-HZ-8002-01A-11D-2201-08 LEPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025275.1 0 0 0 5 156 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 9.321202e-01 5 150 0 70 2 0 0 0 0 70 2 -7.362274 1 0 0 0 1 0 1 1 1.999258 0 0.100000 2 0.094112 0.640000 0.250000 1.000000 1.000000 0.663998 0.640000 0 0.410000 0.940000 LPPR4 0 broad.mit.edu 37 1 99772446 99772446 + Silent SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr1:99772446C>T ENST00000370185.3 + 7 2669 c.2172C>T c.(2170-2172)cgC>cgT p.R724R LPPR4_ENST00000370184.1_Silent_p.R566R|LPPR4_ENST00000457765.1_Silent_p.R666R NM_014839.4 NP_055654.2 Q7Z2D5 LPPR4_HUMAN 72 all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202) CTTCTTCCCGCGACTCCACCC 0.507000 0 SO:0001819 synonymous_variant ENST00000370185.3 1 1 hg19 CCDS757.1 TCGA-HZ-8002-01A-11D-2201-08 LPPR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029670.2 1 0 0 15 266 0 70 0 2.491065e-01 0 17 0 70 2 0 0 0 0 0 2 1 9.998702e-01 14 263 0 70 2 0 0 0 0 70 2 -17.161540 1 1 0 0 1 0 1 1 1.999258 0 0.100000 2 0.094112 0.990000 0.620000 1.000000 1.000000 0.935565 0.990000 1 0.820000 1.000000 SIGLEC1 6614 broad.mit.edu 37 20 3670268 3670268 + Missense_Mutation SNP A A G TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr20:3670268A>G ENST00000344754.4 - 19 4975 c.4976T>C c.(4975-4977)cTg>cCg p.L1659P SIGLEC1_ENST00000202578.4_Missense_Mutation_p.L1659P NM_023068.3 NP_075556.1 Q9BZZ2 SN_HUMAN sialic acid binding Ig-like lectin 1, sialoadhesin 70 GCAGGCCCCCAGGCCCAACAG 0.652000 0 SO:0001583 missense ENST00000344754.4 0 1 hg19 CCDS13060.1 . . . . . . . . . . A 14.89 2.670089 0.47677 . . ENSG00000088827 ENST00000344754;ENST00000202578 T;T 0.27104 1.72;1.69 5.39 5.39 0.77823 . 0.000000 0.30060 N 0.010502 T 0.37293 0.0998 L 0.34521 1.04 0.58432 D 0.999999 D;D 0.89917 0.999;1.0 D;D 0.85130 0.997;0.987 T 0.05733 -1.0867 10 0.28530 T 0.3 . 12.0747 0.53636 1.0:0.0:0.0:0.0 . 1659;1659 Q9BZZ2;Q9BZZ2-3 SN_HUMAN;. P 1659 ENSP00000341141:L1659P;ENSP00000202578:L1659P ENSP00000202578:L1659P L - 2 0 SIGLEC1 3618268 0.998000 0.40836 1.000000 0.80357 0.103000 0.19146 4.194000 0.58393 2.162000 0.67917 0.533000 0.62120 CTG TCGA-HZ-8002-01A-11D-2201-08 SIGLEC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077761.2 1 0 0 3 61 0 11 0 8.948709e-02 0 8 0 11 2 0 0 0 0 0 2 1 7.970732e-01 3 58 0 11 2 0 0 0 0 11 2 -6.872078 1 1 0 0 1 1 2 3 2.023883 0 0.100000 2 0.110672 0.990000 0.320000 1.000000 1.000000 0.867233 0.990000 1 0.620000 1.000000 CBS 875 broad.mit.edu 37 21 44479374 44479374 + Silent SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr21:44479374G>A ENST00000398165.3 - 13 1444 c.1185C>T c.(1183-1185)ggC>ggT p.G395G CBS_ENST00000398158.1_Silent_p.G395G|CBS_ENST00000398168.1_Silent_p.G395G|CBS_ENST00000359624.3_Silent_p.G395G|CBS_ENST00000544202.1_Silent_p.G307G|CBS_ENST00000352178.5_Silent_p.G395G NM_000071.2 NP_000062.1 P35520 CBS_HUMAN cystathionine-beta-synthase 17 L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118) CCTTCAGAAAGCCCTTCTGCA 0.677000 0 SO:0001819 synonymous_variant ENST00000398165.3 1 1 hg19 CCDS13693.1 . . . . . . . . . . G 6.771 0.511235 0.12883 . . ENSG00000160200 ENST00000430013 . . . 4.63 2.54 0.30619 . . . . . T 0.44329 0.1288 . . . 0.80722 D 1 . . . . . . T 0.33292 -0.9874 4 . . . -36.0301 2.2239 0.03979 0.108:0.212:0.462:0.2179 . . . . V 49 . . A - 2 0 CBS 43352443 0.981000 0.34729 1.000000 0.80357 0.499000 0.33736 0.337000 0.19841 0.911000 0.36747 0.563000 0.77884 GCT TCGA-HZ-8002-01A-11D-2201-08 CBS-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195525.1 0 0 0 17 618 0 131 0 1.582446e-01 1 24 0 131 2 0 0 0 0 0 2 1 9.999580e-01 17 604 0 128 2 0 0 0 0 131 2 -3.120661 1 1 0 0 1 0 0 0 1.953017 0 0.100000 2 0.072165 0.520000 0.310000 0.780000 0.510000 0.537062 0.520000 0 0.400000 0.660000 FAM19A5 25817 broad.mit.edu 37 22 49042501 49042501 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr22:49042501G>A ENST00000402357.1 + 2 338 c.205G>A c.(205-207)Gcg>Acg p.A69T FAM19A5_ENST00000358295.5_Missense_Mutation_p.A62T|FAM19A5_ENST00000473898.1_Intron NM_001082967.1 NP_001076436.1 Q7Z5A7 F19A5_HUMAN family with sequence similarity 19 (chemokine (C-C motif)-like), member A5 7 all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195) CGCCCGCTGTGCGTGTAGAAA 0.706000 0 SO:0001583 missense ENST00000402357.1 0 1 hg19 CCDS46728.1 . . . . . . . . . . G 23.7 4.446877 0.84101 . . ENSG00000219438 ENST00000402357;ENST00000336769;ENST00000358295 . . . 5.2 5.2 0.72013 . . . . . T 0.75474 0.3854 M 0.62723 1.935 0.80722 D 1 D;D 0.62365 0.975;0.991 P;P 0.62382 0.591;0.901 T 0.78409 -0.2215 8 0.87932 D 0 . 17.3357 0.87280 0.0:0.0:1.0:0.0 . 62;69 Q7Z5A7-2;Q7Z5A7 .;F19A5_HUMAN T 69;69;62 . ENSP00000336812:A69T A + 1 0 FAM19A5 47428937 1.000000 0.71417 0.125000 0.21846 0.391000 0.30476 8.827000 0.92041 2.417000 0.82017 0.655000 0.94253 GCG TCGA-HZ-8002-01A-11D-2201-08 FAM19A5-003 PUTATIVE basic|CCDS protein_coding protein_coding OTTHUMT00000317504.1 0 0 0 6 188 0 35 0 2.393978e-01 0 26 0 35 2 0 0 0 0 0 2 1 9.582568e-01 6 176 0 33 2 0 0 0 0 35 2 -8.606893 1 0 0 0 1 0 0 0 1.960641 0 0.100000 2 0.075975 0.610000 0.260000 1.000000 1.000000 0.638900 0.610000 0 0.410000 0.870000 MAP3K2 10746 broad.mit.edu 37 2 128065382 128065382 + Splice_Site SNP T T C TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr2:128065382T>C ENST00000409947.1 - 17 1917 c.e17-2 MAP3K2_ENST00000344908.5_Splice_Site Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 2 7 Colorectal(110;0.1) Bosutinib(DB06616) GCAACACTCCTGAAAAGAAAC 0.368000 0 SO:0001630 splice_region_variant ENST00000409947.1 0 0 hg19 CCDS46404.1 . . . . . . . . . . T 19.09 3.760741 0.69763 . . ENSG00000169967 ENST00000409947;ENST00000344908 . . . 5.56 5.56 0.83823 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 16.0018 0.80297 0.0:0.0:0.0:1.0 . . . . . -1 . . . - . . MAP3K2 127781852 1.000000 0.71417 0.979000 0.43373 0.879000 0.50718 7.997000 0.88414 2.226000 0.72624 0.528000 0.53228 . TCGA-HZ-8002-01A-11D-2201-08 MAP3K2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331014.1 1 0 1 2 37 0 9 0 0 0 0 9 2 0 0 0 0 0 2 1 6.515365e-01 2 34 0 9 2 0 0 0 0 9 2 -4.067877 1 0 0 0 1 1 2 3 2.032224 0 0.100000 2 0.112863 0.990000 0.280000 1.000000 1.000000 0.876247 0.990000 1 0.630000 1.000000 MYO7B 4648 broad.mit.edu 37 2 128350393 128350393 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr2:128350393C>T ENST00000409816.2 + 16 2049 c.2017C>T c.(2017-2019)Cgg>Tgg p.R673W MYO7B_ENST00000428314.1_Missense_Mutation_p.R673W|MYO7B_ENST00000389524.4_Missense_Mutation_p.R673W Q6PIF6 MYO7B_HUMAN myosin VIIB 75 Colorectal(110;0.1) GCTGTGCCTGCGGCAGCTGCG 0.672000 0 SO:0001583 missense ENST00000409816.2 0 1 hg19 CCDS46405.1 . . . . . . . . . . C 21.0 4.086081 0.76642 . . ENSG00000169994 ENST00000389524;ENST00000428314;ENST00000409816 T;T;T 0.72394 -0.65;-0.65;-0.65 4.93 4.04 0.47022 Myosin head, motor domain (2); 0.419727 0.22981 N 0.053306 D 0.84705 0.5531 M 0.91612 3.225 0.40257 D 0.978134 D 0.76494 0.999 D 0.65987 0.94 D 0.86786 0.1982 10 0.87932 D 0 . 9.7827 0.40658 0.1463:0.777:0.0:0.0767 . 673 Q6PIF6 MYO7B_HUMAN W 673 ENSP00000374175:R673W;ENSP00000415090:R673W;ENSP00000386461:R673W ENSP00000374175:R673W R + 1 2 MYO7B 128066863 0.096000 0.21769 0.486000 0.27416 0.986000 0.74619 2.109000 0.41863 1.198000 0.43158 0.655000 0.94253 CGG TCGA-HZ-8002-01A-11D-2201-08 MYO7B-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000331124.3 0 0 0 5 137 0 20 0 1.198744e-01 0 14 0 20 2 0 0 0 0 0 2 1 9.244901e-01 5 126 0 19 2 0 0 0 0 20 2 -7.526299 1 1 0 0 1 1 2 3 2.032224 0 0.100000 2 0.112863 0.850000 0.310000 1.000000 1.000000 0.793415 0.850000 1 0.520000 1.000000 COL5A2 1290 broad.mit.edu 37 2 189927907 189927907 + Missense_Mutation SNP T T A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr2:189927907T>A ENST00000374866.3 - 27 2134 c.1860A>T c.(1858-1860)aaA>aaT p.K620N NM_000393.3 NP_000384.2 P05997 CO5A2_HUMAN collagen, type V, alpha 2 95 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127) CACTGCTACCTTTGGGGCCTG 0.502000 0 SO:0001583 missense ENST00000374866.3 1 1 hg19 CCDS33350.1 . . . . . . . . . . T 17.21 3.330784 0.60853 . . ENSG00000204262 ENST00000374866;ENST00000452536 D 0.94184 -3.37 4.57 3.4 0.38934 . 0.000000 0.50627 D 0.000104 D 0.95686 0.8597 M 0.80616 2.505 0.58432 D 0.999999 D;D 0.71674 0.998;0.974 D;P 0.73708 0.981;0.831 D 0.94257 0.7499 9 . . . . 8.2608 0.31783 0.0:0.181:0.0:0.819 . 260;620 Q5PR22;P05997 .;CO5A2_HUMAN N 620;260 ENSP00000364000:K620N . K - 3 2 COL5A2 189636152 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 1.183000 0.32041 0.711000 0.32018 0.383000 0.25322 AAA TCGA-HZ-8002-01A-11D-2201-08 COL5A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313523.1 0 0 0 26 981 0 216 1 9.999999e-01 9 981 0 216 2 0 0 0 0 0 2 1 9.999999e-01 26 954 0 216 2 0 0 0 0 216 2 -3.142539 1 1 0 0 1 1 2 3 2.032224 0 0.100000 2 0.112863 0.560000 0.350000 1.000000 0.520000 0.630023 0.560000 0 0.440000 1.000000 AGAP1 116987 broad.mit.edu 37 2 236957825 236957825 + Missense_Mutation SNP G G A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr2:236957825G>A ENST00000304032.8 + 16 2594 c.2014G>A c.(2014-2016)Gag>Aag p.E672K AGAP1_ENST00000336665.5_Missense_Mutation_p.E619K|AGAP1_ENST00000409538.1_Missense_Mutation_p.E884K|AGAP1_ENST00000428334.2_Missense_Mutation_p.E511K NM_001037131.2 NP_001032208.1 Q9UPQ3 AGAP1_HUMAN ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 41 CTGGCCAGTCGAGCTCATCAA 0.582000 0 SO:0001583 missense ENST00000304032.8 0 1 hg19 CCDS33408.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 36|36 5.882175|5.882175 0.97062|0.97062 .|. .|. ENSG00000157985|ENSG00000157985 ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334|ENST00000418654;ENST00000453371 T;T;T;T|. 0.45668|. 0.89;0.89;0.89;0.89|. 5.49|5.49 5.49|5.49 0.81192|0.81192 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.81772|0.81772 0.4893|0.4893 M|M 0.81239|0.81239 2.535|2.535 0.80722|0.80722 D|D 1|1 D;D|. 0.89917|. 1.0;0.999|. D;D|. 0.80764|. 0.992;0.994|. T|T 0.82232|0.82232 -0.0559|-0.0559 10|5 0.56958|. D|. 0.05|. .|. 19.3968|19.3968 0.94610|0.94610 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 619;672|. Q9UPQ3-2;Q9UPQ3|. .;AGAP1_HUMAN|. K|Q 672;619;884;511|224;73 ENSP00000307634:E672K;ENSP00000338378:E619K;ENSP00000386897:E884K;ENSP00000411824:E511K|. ENSP00000307634:E672K|. E|R +|+ 1|2 0|0 AGAP1|AGAP1 236622564|236622564 1.000000|1.000000 0.71417|0.71417 0.954000|0.954000 0.39281|0.39281 0.981000|0.981000 0.71138|0.71138 9.722000|9.722000 0.98770|0.98770 2.565000|2.565000 0.86533|0.86533 0.655000|0.655000 0.94253|0.94253 GAG|CGA TCGA-HZ-8002-01A-11D-2201-08 AGAP1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000257076.2 0 0 0 12 698 0 122 1 3.042277e-01 4 57 0 122 2 0 0 0 0 0 2 1 9.990402e-01 13 687 0 122 2 0 0 0 0 122 2 -2.881783 1 1 121412 1 34 1 1 2 3 2.032224 0 0.100000 2 0.112863 0.380000 0.190000 1.000000 0.340000 0.491801 0.380000 0 0.270000 1.000000 COLQ 8292 broad.mit.edu 37 3 15495398 15495398 + Missense_Mutation SNP C C A TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr3:15495398C>A ENST00000383788.5 - 16 1361 c.1236G>T c.(1234-1236)gaG>gaT p.E412D COLQ_ENST00000383785.2_3'UTR|COLQ_ENST00000435459.2_Missense_Mutation_p.E402D|COLQ_ENST00000383781.4_Missense_Mutation_p.E402D|COLQ_ENST00000603808.1_Missense_Mutation_p.E413D|COLQ_ENST00000383786.5_Missense_Mutation_p.E378D|COLQ_ENST00000383787.2_Missense_Mutation_p.E403D|EAF1-AS1_ENST00000608408.1_RNA NM_005677.3 NP_005668.2 Q9Y215 COLQ_HUMAN collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase 19 CCTCCACACCCTCATGCCGGT 0.587000 0 SO:0001583 missense ENST00000383788.5 0 1 hg19 CCDS33709.1 . . . . . . . . . . C 11.18 1.563678 0.27915 . . ENSG00000206561 ENST00000383787;ENST00000383781;ENST00000435459;ENST00000383788;ENST00000420589;ENST00000454772;ENST00000383786 D;D;D;D;D 0.91295 -2.64;-2.82;-2.77;-2.77;-2.79 5.3 2.12 0.27331 . 0.637835 0.16393 N 0.216367 D 0.87767 0.6260 L 0.48642 1.525 0.80722 D 1 P;B;P;P 0.44044 0.683;0.024;0.555;0.825 B;B;B;P 0.46026 0.212;0.033;0.17;0.501 D 0.84958 0.0875 10 0.72032 D 0.01 0.0611 7.265 0.26224 0.0:0.5012:0.0:0.4988 . 378;403;412;402 Q9Y215-3;Q9Y215-5;Q9Y215;Q9Y215-2 .;.;COLQ_HUMAN;. D 403;402;402;412;402;413;378 ENSP00000373297:E403D;ENSP00000373291:E402D;ENSP00000402511:E402D;ENSP00000373298:E412D;ENSP00000373296:E378D ENSP00000373291:E402D E - 3 2 COLQ 15470402 0.005000 0.15991 0.679000 0.29978 0.987000 0.75469 -0.179000 0.09768 0.637000 0.30526 -0.369000 0.07265 GAG TCGA-HZ-8002-01A-11D-2201-08 COLQ-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000343575.1 0 0 0 4 158 0 21 0 3.953641e-02 0 10 0 21 2 0 0 0 0 0 2 1 8.774925e-01 2 152 0 20 2 0 0 0 0 21 2 -6.152182 1 0 0 0 1 1 2 3 2.010426 0 0.100000 2 0.108028 0.590000 0.190000 1.000000 1.000000 0.632125 0.590000 0 0.350000 1.000000 DOCK2 1794 broad.mit.edu 37 5 169098083 169098083 + Splice_Site SNP A A T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr5:169098083A>T ENST00000256935.8 + 5 306 c.226A>T c.(226-228)Aat>Tat p.N76Y NM_004946.2 NP_004937.1 Q92608 DOCK2_HUMAN dedicator of cytokinesis 2 160 Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) CTTAAATAGAAATACTGAGAA 0.443000 0 SO:0001630 splice_region_variant ENST00000256935.8 0 1 hg19 CCDS4371.1 . . . . . . . . . . A 12.60 1.986874 0.35036 . . ENSG00000134516 ENST00000256935 T 0.50001 0.76 5.67 5.67 0.87782 . 0.145914 0.64402 D 0.000012 T 0.30008 0.0751 N 0.22421 0.69 0.80722 D 1 P 0.45902 0.868 B 0.34038 0.174 T 0.13845 -1.0494 10 0.41790 T 0.15 . 12.6492 0.56751 0.8529:0.1471:0.0:0.0 . 76 Q92608 DOCK2_HUMAN Y 76 ENSP00000256935:N76Y ENSP00000256935:N76Y N + 1 0 DOCK2 169030661 1.000000 0.71417 0.979000 0.43373 0.981000 0.71138 3.543000 0.53633 2.158000 0.67659 0.460000 0.39030 AAT TCGA-HZ-8002-01A-11D-2201-08 DOCK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252828.2 0 0 0 6 272 0 60 0 1.508191e-01 0 27 0 60 2 0 0 0 0 0 2 1 9.612907e-01 6 262 0 60 2 0 0 0 0 60 2 -3.453223 1 1 0 0 1 0 1 1 1.993919 0 0.100000 2 0.092742 0.450000 0.180000 0.850000 0.420000 0.477812 0.450000 0 0.290000 0.640000 KCNV1 27012 broad.mit.edu 37 8 110984838 110984838 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr8:110984838C>T ENST00000524391.1 - 3 1672 c.640G>A c.(640-642)Gtc>Atc p.V214I KCNV1_ENST00000297404.1_Missense_Mutation_p.V214I|RP11-696P8.2_ENST00000530667.1_RNA Q6PIU1 KCNV1_HUMAN potassium channel, subfamily V, member 1 p.V214I(1) 37 all_neural(195;0.219) OV - Ovarian serous cystadenocarcinoma(57;5.35e-13) ATGGAGATGACGCCAAAGATA 0.517000 1 Substitution - Missense(1) SO:0001583 missense ENST00000524391.1 0 1 hg19 CCDS6314.1 . . . . . . . . . . C 0.164 -1.078020 0.01903 . . ENSG00000164794 ENST00000524391;ENST00000297404;ENST00000545728 D;D 0.97328 -4.34;-4.34 5.35 4.35 0.52113 . 0.306903 0.28109 N 0.016564 D 0.88566 0.6471 N 0.12569 0.235 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.75539 -0.3282 10 0.02654 T 1 . 3.8825 0.09083 0.0:0.6825:0.0:0.3175 . 214 Q6PIU1 KCNV1_HUMAN I 214;214;90 ENSP00000435954:V214I;ENSP00000297404:V214I ENSP00000297404:V214I V - 1 0 KCNV1 111054014 0.994000 0.37717 0.994000 0.49952 0.610000 0.37248 2.694000 0.47035 2.499000 0.84300 0.557000 0.71058 GTC TCGA-HZ-8002-01A-11D-2201-08 KCNV1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385525.1 0 0 0 11 355 0 93 0 0 0 1 0 93 2 0 0 0 0 0 2 1 9.981255e-01 9 347 0 91 2 0 0 0 0 93 2 -3.693547 1 1 121412 1 30 1 1 2 3 2.050326 0 0.100000 2 0.116781 0.700000 0.340000 1.000000 1.000000 0.727123 0.700000 0 0.490000 1.000000 ZFHX4 79776 broad.mit.edu 37 8 77766675 77766675 + Silent SNP A A G TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr8:77766675A>G ENST00000521891.2 + 10 7966 c.7518A>G c.(7516-7518)gaA>gaG p.E2506E ZFHX4_ENST00000518282.1_Silent_p.E2480E|ZFHX4_ENST00000050961.6_Silent_p.E2461E|ZFHX4_ENST00000455469.2_Silent_p.E2461E NM_024721.4 NP_078997.4 Q86UP3 ZFHX4_HUMAN zinc finger homeobox 4 432 BRCA - Breast invasive adenocarcinoma(89;0.0895) CAACTCTGGAACTCTGGCAGG 0.478000 HNSCC(33;0.089) 0 SO:0001819 synonymous_variant ENST00000521891.2 1 1 hg19 CCDS47878.2 TCGA-HZ-8002-01A-11D-2201-08 ZFHX4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000379197.2 0 0 0 23 866 0 170 0 9.333394e-02 0 19 0 170 2 0 0 0 0 0 2 1 9.999991e-01 25 845 0 167 2 0 0 0 0 170 2 -3.359118 1 1 0 0 1 1 2 3 2.050326 0 0.100000 2 0.116781 0.570000 0.350000 1.000000 0.520000 0.648164 0.570000 0 0.440000 1.000000 KIAA1045 23349 broad.mit.edu 37 9 34976561 34976561 + Missense_Mutation SNP C C T TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chr9:34976561C>T ENST00000242315.3 + 5 755 c.673C>T c.(673-675)Cgt>Tgt p.R225C KIAA1045_ENST00000544237.1_Missense_Mutation_p.R225C|KIAA1045_ENST00000476115.2_3'UTR NM_015297.1 NP_056112.1 Q9UPV7 K1045_HUMAN KIAA1045 19 LUSC - Lung squamous cell carcinoma(32;0.00575) GGACTTTCTGCGTTACCGCCA 0.647000 0 SO:0001583 missense ENST00000242315.3 1 1 hg19 CCDS43796.1 . . . . . . . . . . C 28.3 4.906243 0.92107 0.0 1.18E-4 ENSG00000122733 ENST00000544237;ENST00000242315 T;T 0.21932 1.98;1.98 4.92 4.92 0.64577 EF-hand-like domain (1); 0.137454 0.51477 D 0.000087 T 0.27278 0.0669 N 0.24115 0.695 0.54753 D 0.999985 D 0.76494 0.999 P 0.56700 0.804 T 0.03829 -1.1000 10 0.66056 D 0.02 . 15.2674 0.73672 0.0:1.0:0.0:0.0 . 225 Q9UPV7 K1045_HUMAN C 225 ENSP00000444138:R225C;ENSP00000242315:R225C ENSP00000242315:R225C R + 1 0 KIAA1045 34966561 1.000000 0.71417 1.000000 0.80357 0.884000 0.51177 4.116000 0.57871 2.282000 0.76494 0.561000 0.74099 CGT TCGA-HZ-8002-01A-11D-2201-08 KIAA1045-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052256.2 1 0 0 25 414 0 86 0 3.141406e-02 0 5 0 86 2 0 0 0 0 0 2 1 9.999998e-01 24 408 0 85 2 0 0 0 0 86 2 -6.325333 1 1 121060 1 29 1 0 0 0 1.960936 0 0.100000 2 0.075975 0.990000 0.730000 1.000000 1.000000 0.962536 0.990000 1 0.890000 1.000000 PFKFB1 5207 broad.mit.edu 37 X 54987327 54987327 + Nonsense_Mutation SNP G G A rs147665375 TCGA-HZ-8002-01A-11D-2201-08 TCGA-HZ-8002-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a094025-0de4-477e-853d-0bb1808e24b5 44e758af-a0d1-4d6f-addc-33ec19fd1be3 g.chrX:54987327G>A ENST00000375006.3 - 3 317 c.247C>T c.(247-249)Cga>Tga p.R83* PFKFB1_ENST00000545676.1_Nonsense_Mutation_p.R18*|PFKFB1_ENST00000374992.2_Intron NM_002625.2 NP_002616.2 P16118 F261_HUMAN 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 24 ACTGCCTCTCGTCGATACTGG 0.468000 0 SO:0001587 stop_gained ENST00000375006.3 0 1 hg19 CCDS14364.1 . . . . . . . . . . G 35 5.525944 0.96431 2.61E-4 1.49E-4 ENSG00000158571 ENST00000375006;ENST00000545676 . . . 4.89 2.9 0.33743 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -7.2486 12.3398 0.55087 0.0:0.0:0.6625:0.3375 . . . . X 83;18 . ENSP00000364145:R83X R - 1 2 PFKFB1 55004052 0.984000 0.35163 1.000000 0.80357 0.995000 0.86356 1.625000 0.37029 0.359000 0.24239 0.594000 0.82650 CGA TCGA-HZ-8002-01A-11D-2201-08 PFKFB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056847.1 0 0 0 6 178 0 40 0 1.592900e-03 0 2 0 40 2 0 0 0 0 0 2 1 9.633227e-01 6 174 0 40 2 0 0 0 0 40 2 -3.812622 1 1 121402 7 40 1 0 1 1 0.100000 2 0.100000 0.330000 0.140000 0.630000 0.310000 0.357935 0.330000 0 0.220000 0.480000