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 KIF4B 285643 broad.mit.edu 37 5 154395466 154395466 + Frame_Shift_Del DEL C C - TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr5:154395466delC ENST00000435029.4 + 1 2207 c.2047delC c.(2047-2049)caafs p.Q683fs NM_001099293.1 NP_001092763.1 Q2VIQ3 KIF4B_HUMAN kinesin family member 4B 58 Renal(175;0.00488) Medulloblastoma(196;0.0523) KIRC - Kidney renal clear cell carcinoma(527;0.00112) CCGTAAGAGGCAATATGAGCT 0.423000 0 SO:0001589 frameshift_variant ENST00000435029.4 0 1 hg19 CCDS47324.1 TCGA-RB-AA9M-01A-11D-A397-08 KIF4B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377478.1 1 0 0 32 567 0 96 0 0 0 0 0 0 0 0 0 0 0 0 1 1.000000 32 563 0 96 2 0 0 0 0 0 0 -5.981519 1 1 0 0 1 1 2 3 2.040345 0 0.100001 2 0.114610 0.990000 0.770000 1.000000 1.000000 0.974719 0.990000 1 0.940000 1.000000 C10orf90 118611 broad.mit.edu 37 10 128147750 128147750 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr10:128147750G>A ENST00000284694.7 - 6 1876 c.1756C>T c.(1756-1758)Cgc>Tgc p.R586C C10orf90_ENST00000544758.1_Missense_Mutation_p.R683C|C10orf90_ENST00000480379.1_5'UTR|C10orf90_ENST00000356858.3_Missense_Mutation_p.R539C|C10orf90_ENST00000454341.1_Missense_Mutation_p.R489C NM_001004298.2 NP_001004298.2 Q96M02 CJ090_HUMAN chromosome 10 open reading frame 90 65 all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203) TCTTGTGAGCGAGAAATGAAC 0.498000 0 SO:0001583 missense ENST00000284694.7 1 1 hg19 CCDS31310.1 . . . . . . . . . . G 21.500000 4.160951 0.782260 . . ENSG00000154493 ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642 T;T;T;T 0.29917 1.7;1.81;1.74;1.55 5.010000 5.010000 0.668630 . 0.000000 0.43919 D 0.000518 T 0.53965 0.1829 M 0.65498 2.005 0.807220 D 1.000000 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;0.998 T 0.56475 -0.7973 10 0.87932 D 0 -27.713 15.175300 0.729070 0.0:0.0:1.0:0.0 . 683;586;489 F5GZL2;Q96M02;Q96M02-2 .;CJ090_HUMAN;. C 539;586;489;683;586 ENSP00000284694:R586C;ENSP00000398786:R489C;ENSP00000444369:R683C;ENSP00000405995:R586C ENSP00000284694:R586C R - 1 0 C10orf90 128137740 1 0.714170 1 0.803570 0.977000 0.689770 6.049000 0.710530 2.595000 0.876830 0.655000 0.942530 CGC TCGA-RB-AA9M-01A-11D-A397-08 C10orf90-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 0 24 453 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 22 449 0 71 2 0 0 0 0 0 2 -2.958988 1 1 121412 4 37 1 1 2 3 2.048307 0 0.100001 2 0.116349 0.990000 0.690000 1.000000 1.000000 0.954541 0.990000 1 0.870000 1.000000 MKI67 4288 broad.mit.edu 37 10 129906577 129906577 + Missense_Mutation SNP G G A rs117795868 by1000genomes TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr10:129906577G>A ENST00000368654.3 - 13 3902 c.3527C>T c.(3526-3528)aCg>aTg p.T1176M MKI67_ENST00000368653.3_Missense_Mutation_p.T816M NM_002417.4 NP_002408.3 P46013 KI67_HUMAN marker of proliferation Ki-67 159 all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203) TGGTTTGGGCGTAAGCATGGC 0.463000 0 SO:0001583 missense ENST00000368654.3 0 1 hg19 CCDS7659.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 12.050000 1.822665 0.322370 . . ENSG00000148773 ENST00000368654;ENST00000368653;ENST00000537609 T;T 0.03301 3.98;3.98 2.740000 1.830000 0.252070 . 1.848640 0.03443 N 0.209516 T 0.15998 0.0385 M 0.72118 2.19 0.093100 N 1.000000 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.78314 0.96;0.991;0.989 T 0.06058 -1.0848 10 0.52906 T 0.07 . 5.495500 0.167990 0.1565:0.0:0.8435:0.0 . 1175;816;1176 F5H4V4;P46013-2;P46013 .;.;KI67_HUMAN M 1176;816;1175 ENSP00000357643:T1176M;ENSP00000357642:T816M ENSP00000357642:T816M T - 2 0 MKI67 129796567 5.000000e-03 0.159910 2.000000e-03 0.105220 0.005000 0.049000 0.110000 0.154370 0.740000 0.326510 0.462000 0.415740 ACG TCGA-RB-AA9M-01A-11D-A397-08 MKI67-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050999.1 0 0 0 6 1014 0 140 0 2.300177e-03 0 10 0 140 2 0 0 0 0 0 2 1 0.964138 6 1006 0 140 2 0 0 0 0 0 2 -2.032788 0 1 121412 29 52 1 1 2 3 2.048307 0 0.100001 2 0.116349 0.140000 0.050000 1.000000 0.120000 0.332688 0.140000 0 0.080000 1.000000 RASSF4 83937 broad.mit.edu 37 10 45467292 45467292 + Missense_Mutation SNP G G A rs61759871 TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr10:45467292G>A ENST00000340258.5 + 3 247 c.134G>A c.(133-135)cGt>cAt p.R45H RASSF4_ENST00000374417.2_Missense_Mutation_p.R45H|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000334940.6_Intron|RASSF4_ENST00000472561.1_3'UTR NM_032023.3 NP_114412.2 Q8WYP3 RIN2_HUMAN Ras association (RalGDS/AF-6) domain family member 4 16 CTGAGACACCGTGAGGTGAGC 0.522000 0 SO:0001583 missense ENST00000340258.5 0 1 hg19 CCDS7208.1 . . . . . . . . . . G 19.250000 3.792072 0.704520 0.0 3.49E-4 ENSG00000107551 ENST00000374417;ENST00000374414;ENST00000340258;ENST00000427758;ENST00000428466;ENST00000374411 T;T;T;T 0.29397 1.57;2.37;1.57;1.57 5.270000 5.270000 0.740610 . 0.312435 0.30446 N 0.009610 T 0.28896 0.0717 L 0.49640 1.575 0.807220 D 1.000000 B;B 0.28208 0.203;0.026 B;B 0.21151 0.033;0.008 T 0.03684 -1.1013 10 0.40728 T 0.16 -8.1958 14.764300 0.696260 0.0:0.0:1.0:0.0 rs61759871 136;45 Q59FL4;Q9H2L5 .;RASF4_HUMAN H 45;45;45;45;38;136 ENSP00000363538:R45H;ENSP00000339692:R45H;ENSP00000409767:R45H;ENSP00000413468:R38H ENSP00000339692:R45H R + 2 0 RASSF4 44787298 9.990000e-01 0.422020 9.990000e-01 0.593770 0.615000 0.374170 2.358000 0.441340 2.632000 0.892090 0.655000 0.942530 CGT TCGA-RB-AA9M-01A-11D-A397-08 RASSF4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047745.2 1 0 0 17 223 1 37 0 1.464338e-01 1 76 1 37 9 0 0 0 0 0 2 0 0.346423 17 220 1 36 20 0 0 0 0 0 2 -10.889140 1 1 121400 15 40 1 1 2 3 2.036269 0 0.100001 2 0.113738 0.990000 0.900000 1.000000 1.000000 0.994285 0.990000 1 0.990000 1.000000 C2CD2L 9854 broad.mit.edu 37 11 118984833 118984833 + Missense_Mutation SNP C C T rs148221836 by1000genomes TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr11:118984833C>T ENST00000528586.1 + 9 981 c.911C>T c.(910-912)gCg>gTg p.A304V C2CD2L_ENST00000336702.3_Missense_Mutation_p.A557V O14523 C2C2L_HUMAN C2CD2-like p.A557V(2) 13 CTGGGCTATGCGGCATCCCTG 0.612000 2 Substitution - Missense(2) SO:0001583 missense ENST00000528586.1 0 1 hg19 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 24.600000 4.548263 0.861270 . . ENSG00000172375 ENST00000336702;ENST00000528586 T;T 0.49432 0.78;0.78 5.110000 3.200000 0.367480 . 0.000000 0.85682 D 0.000000 T 0.61438 0.2347 M 0.61703 1.905 0.481350 D 0.999593 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.998 T 0.59490 -0.7445 10 0.46703 T 0.11 1.7815 9.464600 0.388040 0.1429:0.7824:0.0:0.0747 . 556;557 O14523;O14523-2 C2C2L_HUMAN;. V 557;304 ENSP00000338885:A557V;ENSP00000433600:A304V ENSP00000338885:A557V A + 2 0 C2CD2L 118490043 9.960000e-01 0.388240 9.830000e-01 0.444330 0.991000 0.796840 3.316000 0.519600 0.813000 0.343500 0.655000 0.942530 GCG TCGA-RB-AA9M-01A-11D-A397-08 C2CD2L-003 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000388199.2 0 0 0 6 655 0 107 0 1.031172e-01 0 50 0 107 2 0 0 0 0 0 2 1 0.964258 6 650 0 106 2 0 0 0 0 0 2 -1.684191 0 1 121412 5 40 1 1 2 3 2.032382 0 0.100001 2 0.112865 0.220000 0.080000 1.000000 0.180000 0.367732 0.220000 0 0.130000 1.000000 CSTF3 1479 broad.mit.edu 37 11 33120306 33120306 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr11:33120306C>T ENST00000323959.4 - 13 1197 c.1058G>A c.(1057-1059)cGc>cAc p.R353H TCP11L1_ENST00000324357.9_Intron NM_001326.2 NP_001317.1 Q12996 CSTF3_HUMAN cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa 19 ATACTTCATGCGACTCTAAGG 0.398000 0 SO:0001583 missense ENST00000323959.4 0 1 hg19 CCDS7883.1 . . . . . . . . . . C 18.330000 3.599320 0.663320 . . ENSG00000176102 ENST00000323959;ENST00000537832 T 0.35421 1.31 5.710000 4.790000 0.613990 Tetratricopeptide-like helical (1); 0.000000 0.85682 D 0.000000 T 0.40956 0.1138 M 0.84846 2.72 0.807220 D 1.000000 P 0.46457 0.878 B 0.32980 0.156 T 0.55667 -0.8105 10 0.54805 T 0.06 . 15.992000 0.802140 0.1358:0.8642:0.0:0.0 . 353 Q12996 CSTF3_HUMAN H 353;286 ENSP00000315791:R353H ENSP00000315791:R353H R - 2 0 CSTF3 33076882 1 0.714170 1 0.803570 0.965000 0.642790 7.813000 0.861230 1.394000 0.466240 0.650000 0.862430 CGC TCGA-RB-AA9M-01A-11D-A397-08 CSTF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388801.1 0 0 0 5 678 0 108 0 2.085783e-02 0 24 0 108 2 0 0 0 0 0 2 1 0.936529 5 673 0 108 2 0 0 0 0 0 2 -1.898617 0 1 0 0 1 1 2 3 2.032382 0 0.100001 2 0.112865 0.180000 0.060000 1.000000 0.140000 0.338860 0.180000 0 0.100000 1.000000 DDB2 1643 broad.mit.edu 37 11 47259552 47259552 + Splice_Site SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr11:47259552G>A ENST00000256996.4 + 8 1383 c.1188G>A c.(1186-1188)tcG>tcA p.S396S DDB2_ENST00000378600.3_Splice_Site_p.S207S|ACP2_ENST00000525230.1_5'Flank|DDB2_ENST00000378603.3_Splice_Site_p.S332S|DDB2_ENST00000378601.3_3'UTR NM_000107.2 NP_000098.1 Q92466 DDB2_HUMAN damage-specific DNA binding protein 2, 48kDa 17 GCATCAGTTCGGTGAGGCTTG 0.463000 Mis, N skin basal cell, skin squamous cell, melanoma Direct reversal of damage;Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (E) 11 11p12 1643 damage-specific DNA binding protein 2 E 0 SO:0001630 splice_region_variant Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000256996.4 1 0 hg19 CCDS7927.1 TCGA-RB-AA9M-01A-11D-A397-08 DDB2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 0 9 253 0 40 0 7.307775e-01 0 73 0 40 2 0 0 0 0 0 2 1 0.994446 9 253 0 39 2 0 0 0 0 0 2 -2.737534 1 1 121412 2 34 1 1 2 3 2.032382 0 0.100001 2 0.112865 0.790000 0.370000 1.000000 1.000000 0.779574 0.790000 0 0.540000 1.000000 SF3B2 10992 broad.mit.edu 37 11 65820570 65820570 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr11:65820570G>A ENST00000322535.6 + 3 302 c.253G>A c.(253-255)Gca>Aca p.A85T SF3B2_ENST00000528302.1_Missense_Mutation_p.A85T|snoU13_ENST00000459530.1_RNA NM_006842.2 NP_006833.2 Q13435 SF3B2_HUMAN splicing factor 3b, subunit 2, 145kDa 41 TCCCATGTCGGCACAGGTAGG 0.493000 0 SO:0001583 missense ENST00000322535.6 0 1 hg19 CCDS31612.1 . . . . . . . . . . G 12.840000 2.059249 0.363730 . . ENSG00000087365 ENST00000528302;ENST00000322535;ENST00000533595;ENST00000524627;ENST00000355456;ENST00000530322;ENST00000524475 . . . 4.550000 3.640000 0.417300 . 0.317215 0.34291 N 0.004088 T 0.38878 0.1057 N 0.08118 0 0.307480 N 0.745392 D;D 0.57571 0.98;0.98 D;P 0.68192 0.956;0.811 T 0.36529 -0.9744 9 0.52906 T 0.07 -5.6862 8.659800 0.340860 0.1041:0.0:0.8959:0.0 . 85;85 Q13435;E9PJ04 SF3B2_HUMAN;. T 85;85;85;85;87;80;3 . ENSP00000318861:A85T A + 1 0 SF3B2 65577146 9.970000e-01 0.396340 9.940000e-01 0.499520 0.846000 0.480900 5.333000 0.659170 1.270000 0.442970 0.655000 0.942530 GCA TCGA-RB-AA9M-01A-11D-A397-08 SF3B2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391352.2 0 0 0 6 775 0 134 0 3.545936e-01 0 142 0 134 2 0 0 0 0 0 2 1 0.963481 6 764 0 132 2 0 0 0 0 0 2 -2.180734 0 1 0 0 1 1 2 3 2.032382 0 0.100001 2 0.112865 0.180000 0.060000 1.000000 0.160000 0.341978 0.180000 0 0.110000 1.000000 CLEC12A 160364 broad.mit.edu 37 12 10131591 10131591 + Missense_Mutation SNP C C T rs141455664 byFrequency TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr12:10131591C>T ENST00000304361.4 + 2 300 c.118C>T c.(118-120)Cgt>Tgt p.R40C CLEC12A_ENST00000434319.2_Missense_Mutation_p.R40C|CLEC12A_ENST00000355690.4_Missense_Mutation_p.R50C|CLEC12A_ENST00000350667.4_Intron NM_138337.5|NM_201623.3 NP_612210.4|NP_963917.2 Q5QGZ9 CL12A_HUMAN C-type lectin domain family 12, member A 16 TCATGTATGGCGTCCAGCAGC 0.433000 Melanoma(197;1487 2125 16611 22221 34855) 0 SO:0001583 missense ENST00000304361.4 0 1 hg19 CCDS8608.1 . . . . . . . . . . C 11.260000 1.584844 0.282680 0.0 2.33E-4 ENSG00000172322 ENST00000355690;ENST00000396507;ENST00000304361;ENST00000434319 T;T;T;T 0.09163 4.41;3.01;4.43;3.88 4.580000 2.690000 0.318650 . . . . . T 0.13586 0.0329 M 0.84219 2.685 0.199450 N 0.999945 B;B 0.33549 0.293;0.417 B;B 0.25759 0.029;0.063 T 0.15178 -1.0446 9 0.44086 T 0.13 . 6.704900 0.232440 0.0:0.718:0.1808:0.1011 . 40;50 Q5QGZ9;Q5QGZ9-1 CL12A_HUMAN;. C 50;40;40;40 ENSP00000347916:R50C;ENSP00000379764:R40C;ENSP00000302804:R40C;ENSP00000405244:R40C ENSP00000302804:R40C R + 1 0 CLEC12A 10022858 2.500000e-02 0.190820 1.800000e-02 0.162750 0.008000 0.064300 0.136000 0.159740 0.591000 0.297110 0.650000 0.862430 CGT TCGA-RB-AA9M-01A-11D-A397-08 CLEC12A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000399545.1 1 0 0 29 404 1 58 0 0 0 1 1 58 2 0 0 0 0 0 2 1 0.833167 29 401 1 58 23 0 0 0 0 0 2 -3.318739 1 1 121412 8 44 1 1 2 3 2.016832 0 0.100001 2 0.109353 0.990000 0.940000 1.000000 1.000000 0.996545 0.990000 1 0.990000 1.000000 HVCN1 84329 broad.mit.edu 37 12 111088053 111088053 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr12:111088053G>A ENST00000356742.5 - 6 1429 c.676C>T c.(676-678)Cgg>Tgg p.R226W HVCN1_ENST00000548312.1_Missense_Mutation_p.R226W|HVCN1_ENST00000439744.2_Missense_Mutation_p.R206W|HVCN1_ENST00000242607.8_Missense_Mutation_p.R226W Q96D96 HVCN1_HUMAN hydrogen voltage-gated channel 1 19 AAGAGTTGCCGTTCTGAACGT 0.398000 0 SO:0001583 missense ENST00000356742.5 0 1 hg19 CCDS31900.1 . . . . . . . . . . G 15.940000 2.980869 0.538270 . . ENSG00000122986 ENST00000548312;ENST00000242607;ENST00000356742;ENST00000439744 T;T;T;T 0.50813 0.73;0.75;0.75;0.75 6.170000 4.310000 0.513920 . 0.308268 0.36409 N 0.002616 T 0.64768 0.2628 M 0.76574 2.34 0.320530 N 0.596686 B;D 0.76494 0.068;0.999 B;P 0.60886 0.019;0.88 T 0.74870 -0.3517 10 0.87932 D 0 -25.0411 13.914800 0.638900 0.0:0.0:0.7229:0.2771 . 226;226 Q96D96;Q96D96-3 HVCN1_HUMAN;. W 226;226;226;206 ENSP00000449601:R226W;ENSP00000242607:R226W;ENSP00000349181:R226W;ENSP00000412052:R206W ENSP00000242607:R226W R - 1 2 HVCN1 109572436 1 0.714170 1 0.803570 0.987000 0.754690 2.967000 0.492160 0.882000 0.360160 -0.182000 0.129630 CGG TCGA-RB-AA9M-01A-11D-A397-08 HVCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404653.1 0 0 0 5 405 0 73 0 8.453255e-02 0 32 0 73 2 0 0 0 0 0 2 1 0.936693 5 402 0 73 2 0 0 0 0 0 2 -3.140808 1 1 121410 1 32 1 1 2 3 2.007791 0 0.100001 2 0.107144 0.280000 0.100000 1.000000 0.240000 0.377212 0.280000 0 0.170000 0.520000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 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 27.200000 4.808637 0.907070 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.680000 5.680000 0.881260 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.807220 D 1.000000 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 . 18.371900 0.904090 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 0.714170 1 0.803570 0.998000 0.957120 7.743000 0.850200 2.668000 0.907890 0.563000 0.778840 GGT TCGA-RB-AA9M-01A-11D-A397-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 18 311 0 31 1 4.935802e-01 9 20 0 31 2 1 9.999959e-01 11 369 0 770 2 1 0.999982 18 308 0 31 2 1 1 617 7400 2 7998 17 -5.560625 1 1 0 0 1 1 2 3 2.024180 0 0.100001 2 0.111112 0.990000 0.700000 1.000000 1.000000 0.964314 0.990000 1 0.910000 1.000000 ZIC5 85416 broad.mit.edu 37 13 100617645 100617645 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr13:100617645G>A ENST00000267294.4 - 2 2211 c.1978C>T c.(1978-1980)Cgg>Tgg p.R660W NM_033132.3 NP_149123.2 Q96T25 ZIC5_HUMAN Zic family member 5 9 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) TGTATCGTCCGCACAACTTCA 0.483000 0 SO:0001583 missense ENST00000267294.4 0 1 hg19 CCDS9494.2 . . . . . . . . . . G 18.140000 3.556755 0.654250 . . ENSG00000139800 ENST00000267294 T 0.18016 2.24 6.060000 5.140000 0.703340 . . . . . T 0.29321 0.0730 L 0.36672 1.1 0.350970 D 0.764889 D 0.89917 1.0 D 0.69654 0.965 T 0.18335 -1.0340 9 0.87932 D 0 . 11.116300 0.482620 0.0:0.0:0.7346:0.2654 . 660 Q96T25 ZIC5_HUMAN W 660 ENSP00000267294:R660W ENSP00000267294:R660W R - 1 2 ZIC5 99415646 9.980000e-01 0.408360 9.970000e-01 0.539660 0.991000 0.796840 2.915000 0.488050 2.871000 0.984540 0.655000 0.942530 CGG TCGA-RB-AA9M-01A-11D-A397-08 ZIC5-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000045623.3 0 0 0 5 437 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 0.935995 5 432 0 65 2 0 0 0 0 0 2 -2.212733 0 1 121412 10 40 1 1 2 3 2.022375 0 0.100001 2 0.110673 0.270000 0.090000 1.000000 0.220000 0.395986 0.270000 0 0.160000 1.000000 COL4A1 1282 broad.mit.edu 37 13 110822921 110822921 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr13:110822921C>T ENST00000375820.4 - 42 3836 c.3715G>A c.(3715-3717)Gga>Aga p.G1239R NM_001845.4 NP_001836.2 P02462 CO4A1_HUMAN collagen, type IV, alpha 1 105 all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604) Breast(118;0.2) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145) CCCTGAGGTCCGCGGTCTCCT 0.627000 0 SO:0001583 missense ENST00000375820.4 0 1 hg19 CCDS9511.1 . . . . . . . . . . C 27.800000 4.862753 0.915110 . . ENSG00000187498 ENST00000375815;ENST00000375820;ENST00000397198 D 0.99637 -6.29 4.790000 4.790000 0.613990 . 0.057832 0.64402 D 0.000002 D 0.99813 0.9918 H 0.98089 4.145 0.807220 D 1.000000 D 0.89917 1.0 D 0.85130 0.997 D 0.96593 0.9439 10 0.87932 D 0 . 17.916800 0.889540 0.0:1.0:0.0:0.0 . 1239 P02462 CO4A1_HUMAN R 882;1239;888 ENSP00000364979:G1239R ENSP00000364973:G882R G - 1 0 COL4A1 109620922 1 0.714170 5.410000e-01 0.281020 0.929000 0.565000 7.171000 0.775950 2.198000 0.705610 0.650000 0.862430 GGA TCGA-RB-AA9M-01A-11D-A397-08 COL4A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045759.3 0 0 0 4 101 0 20 0 9.999345e-01 0 899 0 20 2 0 0 0 0 0 2 1 0.891773 4 101 0 20 2 0 0 0 0 0 2 -7.366885 1 1 0 0 1 1 2 3 2.022375 0 0.100001 2 0.110673 0.920000 0.300000 1.000000 1.000000 0.814044 0.920000 1 0.540000 1.000000 RNF17 56163 broad.mit.edu 37 13 25435469 25435469 + Silent SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr13:25435469C>T ENST00000255324.5 + 27 3890 c.3838C>T c.(3838-3840)Ctg>Ttg p.L1280L RNF17_ENST00000339524.3_Silent_p.L332L|RNF17_ENST00000381921.1_Silent_p.L1280L NM_001184993.1|NM_031277.2 NP_001171922.1|NP_112567.2 Q9BXT8 RNF17_HUMAN ring finger protein 17 36 Lung SC(185;0.0225)|Breast(139;0.077) CCCTATTTTGCTGTATCCTGA 0.318000 0 SO:0001819 synonymous_variant ENST00000255324.5 1 1 hg19 CCDS9308.2 TCGA-RB-AA9M-01A-11D-A397-08 RNF17-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044217.1 1 0 0 46 960 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 46 951 0 147 2 0 0 0 0 0 2 -5.239360 1 1 0 0 1 1 2 3 2.036290 0 0.100001 2 0.113738 0.970000 0.700000 1.000000 1.000000 0.928698 0.970000 1 0.820000 1.000000 PLEKHG3 26030 broad.mit.edu 37 14 65197580 65197580 + Silent SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr14:65197580G>A ENST00000394691.1 + 6 777 c.630G>A c.(628-630)cgG>cgA p.R210R PLEKHG3_ENST00000247226.7_Silent_p.R154R A1L390 PKHG3_HUMAN pleckstrin homology domain containing, family G (with RhoGef domain) member 3 29 TTCGGGACCGGCAGGAGCTGC 0.642000 0 SO:0001819 synonymous_variant ENST00000394691.1 0 1 hg19 TCGA-RB-AA9M-01A-11D-A397-08 PLEKHG3-010 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000412028.1 0 0 0 4 170 0 31 0 5.303362e-01 0 67 0 31 2 0 0 0 0 0 2 1 0.885772 4 166 0 31 2 0 0 0 0 0 2 -3.543912 1 1 0 0 1 1 2 3 2.033040 0 0.100001 2 0.112865 0.580000 0.180000 1.000000 1.000000 0.633416 0.580000 0 0.330000 1.000000 AQR 9716 broad.mit.edu 37 15 35202432 35202432 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr15:35202432C>T ENST00000156471.5 - 17 1792 c.1567G>A c.(1567-1569)Gcc>Acc p.A523T NM_014691.2 NP_055506.1 O60306 AQR_HUMAN aquarius intron-binding spliceosomal factor 57 Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08) TTGGGTTTGGCCACTTCAACG 0.473000 0 SO:0001583 missense ENST00000156471.5 0 1 hg19 CCDS42013.1 . . . . . . . . . . C 36.000000 5.798913 0.969600 . . ENSG00000021776 ENST00000156471;ENST00000543879 D 0.93953 -3.32 5.730000 5.730000 0.898150 . 0.000000 0.85682 D 0.000000 D 0.96800 0.8955 M 0.91249 3.19 0.807220 D 1.000000 D 0.54772 0.968 P 0.54664 0.758 D 0.96700 0.9517 10 0.52906 T 0.07 -13.1707 19.911200 0.970250 0.0:1.0:0.0:0.0 . 523 O60306 AQR_HUMAN T 523 ENSP00000156471:A523T ENSP00000156471:A523T A - 1 0 AQR 32989724 1 0.714170 1 0.803570 0.952000 0.607820 7.696000 0.842700 2.718000 0.929930 0.585000 0.799380 GCC TCGA-RB-AA9M-01A-11D-A397-08 AQR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417526.2 0 0 0 7 528 0 74 0 1.695721e-01 0 49 0 74 2 0 0 0 0 0 2 1 0.980204 7 524 0 73 2 0 0 0 0 0 2 -2.026521 0 1 0 0 1 1 2 3 2.030819 0 0.100001 2 0.112427 0.310000 0.120000 1.000000 0.250000 0.433652 0.310000 0 0.200000 1.000000 INO80 54617 broad.mit.edu 37 15 41341604 41341604 + Silent SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr15:41341604C>T ENST00000361937.3 - 21 2881 c.2457G>A c.(2455-2457)ccG>ccA p.P819P INO80_ENST00000401393.3_Silent_p.P819P Q9ULG1 INO80_HUMAN INO80 complex subunit 49 CAAATAACTCCGGGTGATTAC 0.408000 0 SO:0001819 synonymous_variant ENST00000361937.3 1 1 hg19 CCDS10071.1 TCGA-RB-AA9M-01A-11D-A397-08 INO80-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252527.2 1 0 0 20 340 0 47 1 5.510321e-01 4 28 0 47 2 0 0 0 0 0 2 1 0.999996 19 339 0 47 2 0 0 0 0 0 2 -3.075967 1 1 121412 3 35 1 1 2 3 2.030819 0 0.100001 2 0.112427 0.990000 0.730000 1.000000 1.000000 0.971056 0.990000 1 0.930000 1.000000 SEMA6D 80031 broad.mit.edu 37 15 48056428 48056428 + Silent SNP A A G TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr15:48056428A>G ENST00000316364.5 + 11 1462 c.1023A>G c.(1021-1023)aaA>aaG p.K341K SEMA6D_ENST00000355997.3_Silent_p.K341K|SEMA6D_ENST00000358066.4_Silent_p.K341K|SEMA6D_ENST00000389428.3_Silent_p.K341K|SEMA6D_ENST00000389433.2_Silent_p.K341K|SEMA6D_ENST00000537942.1_Silent_p.K341K|SEMA6D_ENST00000389432.2_Silent_p.K341K|SEMA6D_ENST00000536845.2_Silent_p.K341K|SEMA6D_ENST00000558816.1_Silent_p.K341K|SEMA6D_ENST00000558014.1_Silent_p.K341K|SEMA6D_ENST00000354744.4_Silent_p.K341K|SEMA6D_ENST00000389425.3_Silent_p.K341K NM_153618.1 NP_705871.1 Q8NFY4 SEM6D_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D 77 all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18) AAGTATTCAAAGGACGGTTTA 0.413000 0 SO:0001819 synonymous_variant ENST00000316364.5 1 1 hg19 CCDS32225.1 TCGA-RB-AA9M-01A-11D-A397-08 SEMA6D-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416868.1 1 0 0 24 388 0 50 0 3.316428e-02 0 5 0 50 2 0 0 0 0 0 2 1 1.000000 24 385 0 49 2 0 0 0 0 0 2 -6.077965 1 1 0 0 1 1 2 3 2.030819 0 0.100001 2 0.112427 0.990000 0.790000 1.000000 1.000000 0.982951 0.990000 1 0.990000 1.000000 POLG 5428 broad.mit.edu 37 15 89864367 89864367 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr15:89864367G>A ENST00000268124.5 - 17 3056 c.2723C>T c.(2722-2724)gCc>gTc p.A908V POLG_ENST00000442287.2_Missense_Mutation_p.A908V NM_001126131.1|NM_002693.2 NP_001119603.1|NP_002684.1 P54098 DPOG1_HUMAN polymerase (DNA directed), gamma 33 Lung NSC(78;0.0472)|all_lung(78;0.089) STAD - Stomach adenocarcinoma(125;0.165) ATGCATGCCGGCAAAGTGGGC 0.582000 DNA polymerases (catalytic subunits) Colon(73;648 1203 11348 18386 27782) 0 SO:0001583 missense ENST00000268124.5 0 1 hg19 CCDS10350.1 . . . . . . . . . . G 25.600000 4.651395 0.880560 . . ENSG00000140521 ENST00000268124;ENST00000442287 D;D 0.96716 -4.1;-4.1 5.240000 4.310000 0.513920 DNA-directed DNA polymerase, family A, palm domain (2); 0.050208 0.85682 D 0.000000 D 0.97343 0.9131 L 0.58583 1.82 0.584320 D 0.999999 D 0.89917 1.0 D 0.87578 0.998 D 0.97312 0.9938 10 0.51188 T 0.08 -3.644 15.200400 0.731320 0.0:0.0:0.858:0.142 . 908 P54098 DPOG1_HUMAN V 908 ENSP00000268124:A908V;ENSP00000399851:A908V ENSP00000268124:A908V A - 2 0 POLG 87665371 1 0.714170 4.510000e-01 0.269820 0.989000 0.773840 7.638000 0.833280 1.184000 0.429570 0.655000 0.942530 GCC TCGA-RB-AA9M-01A-11D-A397-08 POLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000312854.2 0 0 0 6 659 0 109 0 2.191350e-01 0 83 0 109 2 0 0 0 0 0 2 1 0.964262 6 654 0 109 2 0 0 0 0 0 2 -2.004086 0 1 0 0 1 1 2 3 2.030819 0 0.100001 2 0.112427 0.220000 0.080000 1.000000 0.180000 0.363205 0.220000 0 0.130000 1.000000 KIAA0556 23247 broad.mit.edu 37 16 27761391 27761391 + Missense_Mutation SNP G G T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr16:27761391G>T ENST00000261588.4 + 16 3129 c.3110G>T c.(3109-3111)gGg>gTg p.G1037V NM_015202.2 NP_056017.2 O60303 K0556_HUMAN KIAA0556 76 CTCATCGACGGGGTGAACAGG 0.552000 0 SO:0001583 missense ENST00000261588.4 1 1 hg19 CCDS32415.1 . . . . . . . . . . G 20.100000 3.936532 0.734420 . . ENSG00000047578 ENST00000261588 T 0.24908 1.83 5.220000 5.220000 0.725690 . 0.052178 0.85682 D 0.000000 T 0.64681 0.2620 H 0.94698 3.57 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 T 0.75869 -0.3165 10 0.87932 D 0 -20.8399 18.760800 0.918490 0.0:0.0:1.0:0.0 . 1037 O60303 K0556_HUMAN V 1037 ENSP00000261588:G1037V ENSP00000261588:G1037V G + 2 0 KIAA0556 27668892 1 0.714170 9.950000e-01 0.509660 0.686000 0.399770 7.850000 0.869150 2.578000 0.870160 0.655000 0.942530 GGG TCGA-RB-AA9M-01A-11D-A397-08 KIAA0556-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433724.1 1 0 1 15 230 0 49 1 2.302530e-01 5 9 0 49 2 0 0 0 0 0 2 1 0.999883 15 229 0 49 2 0 0 0 0 0 2 -2.842415 1 1 0 0 1 1 2 3 2.057098 0 0.100001 2 0.118081 0.990000 0.760000 1.000000 1.000000 0.981608 0.990000 1 0.990000 1.000000 SRL 6345 broad.mit.edu 37 16 4253174 4253174 + Missense_Mutation SNP C C G rs74003216 by1000genomes TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr16:4253174C>G ENST00000399609.3 - 3 264 c.252G>C c.(250-252)gaG>gaC p.E84D SRL_ENST00000537996.1_Missense_Mutation_p.E42D NM_001098814.1 NP_001092284.1 Q86TD4 SRCA_HUMAN sarcalumenin 21 TACCTGTGATCTCATGCTGCC 0.597000 0 SO:0001583 missense ENST00000399609.3 1 0 hg19 CCDS42113.1 14 0.00641025641025641 13 0.026422764227642278 1 0.0027624309392265192 0 0.0 0 0.0 C 10.720000 1.428480 0.257260 0.017607 2.38E-4 ENSG00000185739 ENST00000399609;ENST00000330063;ENST00000537996 D;D 0.95447 -3.71;-3.71 4.140000 4.140000 0.485510 . 0.000000 0.64402 U 0.000001 D 0.83110 0.5183 L 0.53249 1.67 0.547530 D 0.999989 B 0.27559 0.181 B 0.26864 0.074 D 0.83958 0.0320 10 0.21540 T 0.41 -19.3002 10.604400 0.453860 0.0:0.9102:0.0:0.0898 . 84 Q86TD4-2 . D 84;542;42 ENSP00000382518:E84D;ENSP00000440350:E42D ENSP00000333285:E542D E - 3 2 SRL 4193175 1 0.714170 1 0.803570 0.989000 0.773840 3.559000 0.537560 2.277000 0.760200 0.650000 0.862430 GAG TCGA-RB-AA9M-01A-11D-A397-08 SRL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438087.1 1 0 0 60 721 0 119 0 0 0 0 119 2 0 0 0 0 0 2 1 1.000000 59 718 0 119 2 0 0 0 0 0 2 -13.426180 1 1 121008 210 56 1 1 2 3 2.057098 0 0.100001 2 0.118081 0.990000 0.990000 1.000000 1.000000 0.999989 0.990000 1 0.990000 1.000000 TP53 7157 broad.mit.edu 37 17 7577082 7577082 + Nonsense_Mutation SNP C C A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr17:7577082C>A ENST00000269305.4 - 8 1045 c.856G>T c.(856-858)Gaa>Taa p.E286* TP53_ENST00000445888.2_Nonsense_Mutation_p.E286*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.E286*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E286*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E286*|TP53_ENST00000413465.2_Intron 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.E286K(58)|p.E286*(22)|p.0?(8)|p.E286Q(5)|p.?(2)|p.E286fs*59(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.G279fs*59(1)|p.R283fs*59(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) AGATTCTCTTCCTCTGTGCGC 0.557000 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 112 Substitution - Missense(63)|Substitution - Nonsense(22)|Deletion - Frameshift(11)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(2) GRCh37 CM076567 TP53 M SO:0001587 stop_gained 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 0 1 hg19 CCDS11118.1 . . . . . . . . . . C 31.000000 5.072281 0.939500 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 . . . 4.990000 4.990000 0.663350 . 0.000000 0.85682 D 0.000000 . . . . . . 0.807220 A 1.000000 . . . . . . . . . . 0.87932 D 0 -23.2961 15.807000 0.785200 0.0:1.0:0.0:0.0 . . . . X 286;286;286;286;286;275;154 . ENSP00000269305:E286X E - 1 0 TP53 7517807 1 0.714170 9.720000e-01 0.419010 0.455000 0.324080 7.587000 0.826130 2.579000 0.870560 0.462000 0.415740 GAA TCGA-RB-AA9M-01A-11D-A397-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 14 154 0 30 0 9.780873e-01 1 72 0 30 2 1 1 76 1091 0 2302 2 1 0.999778 14 152 0 27 2 0 0 0 0 0 2 -7.026286 1 1 0 0 1 0 1 1 1.915075 0 0.100001 2 0.052632 0.900000 0.640000 1.000000 0.990000 0.888564 0.900000 1 0.780000 0.980000 ZNF773 374928 broad.mit.edu 37 19 58017973 58017973 + Silent SNP G G A rs149516480 TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr19:58017973G>A ENST00000282292.4 + 4 650 c.510G>A c.(508-510)acG>acA p.T170T ZNF773_ENST00000598770.1_Silent_p.T169T|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron NM_198542.1 NP_940944.1 Q6PK81 ZN773_HUMAN zinc finger protein 773 22 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221) TGACTCACACGGGAGAGAAGT 0.488000 0 SO:0001819 synonymous_variant ENST00000282292.4 0 1 hg19 CCDS33134.1 TCGA-RB-AA9M-01A-11D-A397-08 ZNF773-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000466475.1 1 0 1 21 150 0 23 0 1.735482e-01 0 6 0 23 2 0 0 0 0 0 2 1 0.999998 21 146 0 23 2 0 0 0 0 0 2 -2.923011 1 1 121412 19 41 1 0 3 3 2.057200 1 0.100001 2 0.142450 0.990000 0.990000 1.000000 1.000000 0.999997 0.990000 1 0.990000 1.000000 FNDC5 252995 broad.mit.edu 37 1 33330257 33330257 + Missense_Mutation SNP G G T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr1:33330257G>T ENST00000496770.1 - 5 629 c.416C>A c.(415-417)gCa>gAa p.A139E FNDC5_ENST00000481487.1_Intron|FNDC5_ENST00000373471.3_Intron|FNDC5_ENST00000609187.1_Intron NM_001171941.1 NP_001165412.1 Q8NAU1 FNDC5_HUMAN fibronectin type III domain containing 5 5 Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186) CCCAGGTCTTGCCCTCACCTT 0.602000 0 SO:0001583 missense ENST00000496770.1 0 1 hg19 TCGA-RB-AA9M-01A-11D-A397-08 FNDC5-006 PUTATIVE basic protein_coding protein_coding OTTHUMT00000011472.2 0 0 0 4 245 0 42 0 0 0 1 0 42 2 0 0 0 0 0 2 1 0.889202 4 243 0 41 2 0 0 0 0 0 2 -3.275825 1 1 0 0 1 0 1 1 1.914001 0 0.100001 2 0.052632 0.320000 0.110000 0.670000 0.290000 0.350674 0.320000 0 0.190000 0.490000 PRKACB 5567 broad.mit.edu 37 1 84668430 84668430 + Missense_Mutation SNP A A G TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr1:84668430A>G ENST00000370689.2 + 8 971 c.707A>G c.(706-708)tAt>tGt p.Y236C PRKACB_ENST00000370688.3_Missense_Mutation_p.Y236C|PRKACB_ENST00000370682.3_Missense_Mutation_p.Y240C|PRKACB_ENST00000370685.3_Missense_Mutation_p.Y283C|PRKACB_ENST00000370680.1_Missense_Mutation_p.Y242C|PRKACB_ENST00000394838.2_Missense_Mutation_p.Y243C|PRKACB_ENST00000394839.2_Missense_Mutation_p.Y206C NM_001242862.1|NM_002731.2 NP_001229791.1|NP_002722.1 P22694 KAPCB_HUMAN protein kinase, cAMP-dependent, catalytic, beta 16 GCAGCTGGCTATCCCCCATTC 0.368000 0 SO:0001583 missense ENST00000370689.2 1 1 hg19 CCDS691.1 . . . . . . . . . . A 24.700000 4.558215 0.862310 . . ENSG00000142875 ENST00000370689;ENST00000370688;ENST00000370685;ENST00000370684;ENST00000394838;ENST00000370682;ENST00000370679;ENST00000370680;ENST00000394839;ENST00000370681 T;T;T;T;T;T;T;T 0.65178 -0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14 5.540000 5.540000 0.830590 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.61677 0.2366 N 0.21545 0.675 0.807220 D 1.000000 D;D;D;D;D;D;D;D;D;D;D 0.89917 1.0;0.998;0.999;0.996;0.991;0.999;0.995;0.999;0.994;1.0;0.99 D;D;D;D;P;D;D;D;D;D;D 0.91635 0.999;0.957;0.972;0.972;0.886;0.953;0.953;0.953;0.972;0.999;0.933 T 0.69767 -0.5056 10 0.87932 D 0 -9.6973 15.980100 0.801020 1.0:0.0:0.0:0.0 . 236;224;243;242;206;242;240;283;283;236;236 B2RB89;P22694-3;B4DKB0;B1APG3;B1APG4;P22694-6;P22694-7;P22694-2;B4E2L0;P22694;P22694-8 .;.;.;.;.;.;.;.;.;KAPCB_HUMAN;. C 236;236;283;224;243;240;242;242;206;198 ENSP00000359723:Y236C;ENSP00000359722:Y236C;ENSP00000359719:Y283C;ENSP00000359718:Y224C;ENSP00000378314:Y243C;ENSP00000359716:Y240C;ENSP00000359714:Y242C;ENSP00000378315:Y206C ENSP00000359713:Y242C Y + 2 0 PRKACB 84441018 1 0.714170 1 0.803570 0.993000 0.825480 9.229000 0.952730 2.230000 0.728870 0.528000 0.532280 TAT TCGA-RB-AA9M-01A-11D-A397-08 PRKACB-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000027641.1 0 0 0 36 484 0 92 0 9.846336e-01 0 90 0 92 2 0 0 0 0 0 2 1 1.000000 36 483 0 92 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.914001 0 0.100001 2 0.052632 0.940000 0.770000 1.000000 0.990000 0.931798 0.940000 1 0.860000 0.990000 ZNF831 128611 broad.mit.edu 37 20 57767447 57767447 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr20:57767447C>T ENST00000371030.2 + 1 1373 c.1373C>T c.(1372-1374)gCg>gTg p.A458V NM_178457.1 NP_848552.1 Q5JPB2 ZN831_HUMAN zinc finger protein 831 125 all_lung(29;0.0085) GACATCCGCGCGCTGGAGCCA 0.677000 0 SO:0001583 missense ENST00000371030.2 0 1 hg19 CCDS42894.1 . . . . . . . . . . C 12.150000 1.850162 0.326990 . . ENSG00000124203 ENST00000371030 T 0.04809 3.55 5.210000 5.210000 0.722930 . . . . . T 0.14013 0.0339 L 0.47716 1.5 0.093100 N 0.999997 D 0.76494 0.999 P 0.56788 0.806 T 0.03060 -1.1077 9 0.62326 D 0.03 -11.9417 17.743900 0.884140 0.0:1.0:0.0:0.0 . 458 Q5JPB2 ZN831_HUMAN V 458 ENSP00000360069:A458V ENSP00000360069:A458V A + 2 0 ZNF831 57200842 9.100000e-01 0.309200 2.570000e-01 0.244040 0.026000 0.113680 4.059000 0.574700 2.423000 0.821700 0.655000 0.942530 GCG TCGA-RB-AA9M-01A-11D-A397-08 ZNF831-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000079916.2 1 0 0 12 165 0 20 0 0 0 0 20 2 0 0 0 0 0 2 1 0.999133 12 162 0 19 2 0 0 0 0 0 2 -16.253660 1 1 0 0 1 1 2 3 2.029886 0 0.100001 2 0.111989 0.990000 0.780000 1.000000 1.000000 0.985185 0.990000 1 0.990000 1.000000 PCNT 5116 broad.mit.edu 37 21 47856946 47856946 + Silent SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr21:47856946C>T ENST00000359568.5 + 40 9158 c.9051C>T c.(9049-9051)caC>caT p.H3017H PCNT_ENST00000480896.1_3'UTR NM_006031.5 NP_006022.3 O95613 PCNT_HUMAN pericentrin 104 Breast(49;0.112) CTTTACTGCACACGTTGGAGG 0.557000 0 SO:0001819 synonymous_variant ENST00000359568.5 1 1 hg19 CCDS33592.1 TCGA-RB-AA9M-01A-11D-A397-08 PCNT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207336.1 1 0 0 28 424 0 64 1 3.893809e-01 2 19 0 64 2 0 0 0 0 0 2 1 1.000000 28 420 0 63 2 0 0 0 0 0 2 -6.990694 1 1 0 0 1 1 2 3 2.033801 0 0.100001 2 0.112865 0.990000 0.870000 1.000000 1.000000 0.992200 0.990000 1 0.990000 1.000000 ZNF70 7621 broad.mit.edu 37 22 24087156 24087156 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr22:24087156C>T ENST00000341976.3 - 2 632 c.172G>A c.(172-174)Gaa>Aaa p.E58K NM_021916.2 NP_068735.1 Q9UC06 ZNF70_HUMAN zinc finger protein 70 21 TCATTTTCTTCGTCCTGCTCA 0.507000 0 SO:0001583 missense ENST00000341976.3 1 1 hg19 CCDS13812.1 . . . . . . . . . . C 4.116000 0.019653 0.080060 . . ENSG00000187792 ENST00000341976 T 0.06294 3.32 3.260000 0.946000 0.195490 . . . . . T 0.05044 0.0135 L 0.36672 1.1 0.093100 N 1.000000 B 0.24132 0.098 B 0.12837 0.008 T 0.38499 -0.9658 9 0.87932 D 0 . 3.585700 0.079700 0.4283:0.437:0.0:0.1346 . 58 Q9UC06 ZNF70_HUMAN K 58 ENSP00000339314:E58K ENSP00000339314:E58K E - 1 0 ZNF70 22417156 3.900000e-02 0.199470 0 0.037020 0.011000 0.076110 0.251000 0.182570 0.324000 0.233330 0.650000 0.862430 GAA TCGA-RB-AA9M-01A-11D-A397-08 ZNF70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319881.1 1 0 0 31 419 0 85 0 2.794341e-02 0 4 0 85 2 0 0 0 0 0 2 1 1.000000 31 417 0 84 2 0 0 0 0 0 2 -7.704658 1 1 121412 1 30 1 0 1 1 1.925720 0 0.100001 2 0.069768 0.990000 0.870000 1.000000 1.000000 0.991638 0.990000 1 0.990000 1.000000 TTN 7273 broad.mit.edu 37 2 179430078 179430078 + Silent SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:179430078G>A ENST00000591111.1 - 276 76082 c.75858C>T c.(75856-75858)aaC>aaT p.N25286N TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Silent_p.N24359N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.N17862N|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Silent_p.N26927N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Silent_p.N18054N|TTN_ENST00000359218.5_Silent_p.N17987N|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTTCTTCAACGTTTACTCTTG 0.393000 0 SO:0001819 synonymous_variant ENST00000591111.1 1 1 hg19 TCGA-RB-AA9M-01A-11D-A397-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 39 670 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 39 669 0 108 2 0 0 0 0 0 2 -6.449671 1 1 120816 1 35 1 1 2 3 2.030298 0 0.100001 2 0.112427 0.990000 0.820000 1.000000 1.000000 0.983014 0.990000 1 0.970000 1.000000 TTN 7273 broad.mit.edu 37 2 179483095 179483095 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:179483095C>T ENST00000591111.1 - 202 42391 c.42167G>A c.(42166-42168)cGt>cAt p.R14056H TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R13129H|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R6632H|TTN_ENST00000589042.1_Missense_Mutation_p.R15697H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R6824H|TTN_ENST00000359218.5_Missense_Mutation_p.R6757H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTTAATGTCACGTCTTTCAAC 0.438000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 15.850000 2.955264 0.532930 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.59502 0.26;0.26;0.26;0.26 5.750000 5.750000 0.904690 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . D 0.82499 0.5050 M 0.91140 3.18 0.584320 D 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.999;0.999;0.999 D 0.85254 0.1046 9 0.87932 D 0 . 20.304600 0.986210 0.0:1.0:0.0:0.0 . 6632;6757;6824;14056 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN H 13129;6632;6824;6757;6632 ENSP00000343764:R13129H;ENSP00000434586:R6632H;ENSP00000340554:R6824H;ENSP00000352154:R6757H ENSP00000340554:R6824H R - 2 0 TTN 179191340 1 0.714170 1 0.803570 0.995000 0.863560 7.776000 0.855600 2.878000 0.986340 0.650000 0.862430 CGT TCGA-RB-AA9M-01A-11D-A397-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 11 258 0 44 0 6.087837e-03 0 3 0 44 2 0 0 0 0 0 2 1 0.998362 11 256 0 42 2 0 0 0 0 0 2 -3.902299 1 1 120812 4 37 1 1 2 3 2.030298 0 0.100001 2 0.112427 0.920000 0.460000 1.000000 1.000000 0.856392 0.920000 1 0.650000 1.000000 DNAH7 56171 broad.mit.edu 37 2 196825327 196825327 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:196825327G>A ENST00000312428.6 - 18 2648 c.2548C>T c.(2548-2550)Cgc>Tgc p.R850C NM_018897.2 NP_061720.2 Q8WXX0 DYH7_HUMAN dynein, axonemal, heavy chain 7 p.R850C(1) 205 TGCCTGGGGCGCAAACCAGGA 0.453000 1 Substitution - Missense(1) SO:0001583 missense ENST00000312428.6 0 1 hg19 CCDS42794.1 . . . . . . . . . . G 15.840000 2.952760 0.532930 . . ENSG00000118997 ENST00000312428 T 0.63417 -0.04 5.740000 5.740000 0.901520 Dynein heavy chain, domain-2 (1); 0.125121 0.53938 D 0.000044 D 0.84392 0.5462 M 0.93375 3.41 0.807220 D 1.000000 D 0.76494 0.999 D 0.64877 0.93 D 0.87323 0.2319 10 0.59425 D 0.04 . 19.919600 0.970820 0.0:0.0:1.0:0.0 . 850 Q8WXX0 DYH7_HUMAN C 850 ENSP00000311273:R850C ENSP00000311273:R850C R - 1 0 DNAH7 196533572 1 0.714170 1 0.803570 0.963000 0.636630 4.626000 0.612690 2.708000 0.925220 0.650000 0.862430 CGC TCGA-RB-AA9M-01A-11D-A397-08 DNAH7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335202.3 0 0 0 5 465 0 79 0 0 0 1 0 79 2 0 0 0 0 0 2 1 0.937501 5 464 0 78 2 0 0 0 0 0 2 -1.784081 0 1 120856 4 40 1 1 2 3 2.036327 0 0.100001 2 0.113738 0.270000 0.090000 1.000000 0.210000 0.407629 0.270000 0 0.160000 1.000000 MAP2 4133 broad.mit.edu 37 2 210558569 210558569 + Missense_Mutation SNP G G C TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:210558569G>C ENST00000360351.4 + 7 2181 c.1675G>C c.(1675-1677)Gat>Cat p.D559H MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.D555H|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron NM_002374.3 NP_002365.3 P11137 MTAP2_HUMAN microtubule-associated protein 2 124 Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202) Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229) AGCTGAGCTTGATATGCCATT 0.368000 Pancreas(27;423 979 28787 29963) 0 SO:0001583 missense ENST00000360351.4 1 1 hg19 CCDS2384.1 . . . . . . . . . . G 10.480000 1.362979 0.246840 . . ENSG00000078018 ENST00000360351;ENST00000447185 T;T 0.19938 2.11;2.11 6.160000 5.270000 0.740610 MAP2/Tau projection (1); 0.357573 0.27451 N 0.019304 T 0.30230 0.0758 L 0.50333 1.59 0.093100 N 0.999995 P;P 0.50819 0.925;0.939 P;P 0.54499 0.639;0.754 T 0.18209 -1.0344 10 0.87932 D 0 -4.3757 7.785100 0.290870 0.129:0.2609:0.6101:0.0 . 555;559 P11137-3;P11137 .;MAP2_HUMAN H 559;555 ENSP00000353508:D559H;ENSP00000392164:D555H ENSP00000353508:D559H D + 1 0 MAP2 210266814 3.580000e-01 0.249470 8.090000e-01 0.324080 0.394000 0.305680 1.674000 0.375440 1.561000 0.495840 0.650000 0.862430 GAT TCGA-RB-AA9M-01A-11D-A397-08 MAP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256521.2 1 0 0 23 388 0 57 0 3.509141e-03 0 2 0 57 2 0 0 0 0 0 2 1 0.999999 23 386 0 56 2 0 0 0 0 0 2 -5.963975 1 1 0 0 1 1 2 3 2.036327 0 0.100001 2 0.113738 0.990000 0.760000 1.000000 1.000000 0.976339 0.990000 1 0.950000 1.000000 C2orf44 80304 broad.mit.edu 37 2 24262247 24262247 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:24262247G>A ENST00000295148.4 - 2 175 c.118C>T c.(118-120)Cgg>Tgg p.R40W C2orf44_ENST00000406895.3_Missense_Mutation_p.R40W NM_025203.2 NP_079479.1 Q9H6R7 CB044_HUMAN chromosome 2 open reading frame 44 C2orf44/ALK(2) 24 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CTGTGAAGCCGCAAATCAGTT 0.507000 T ALK NSCLC Dom yes 2 2p23.3 80304 chromosome 2 open reading frame 44 E 0 SO:0001583 missense ENST00000295148.4 0 1 hg19 CCDS1705.1 . . . . . . . . . . G 8.548000 0.874935 0.173950 . . ENSG00000163026 ENST00000295148;ENST00000406895;ENST00000443232 T;T;T 0.43688 3.4;3.4;0.94 5.240000 3.370000 0.385960 . 0.488094 0.24352 N 0.039266 T 0.20740 0.0499 N 0.08118 0 0.093100 N 1.000000 P;P 0.49447 0.61;0.924 B;B 0.40782 0.275;0.34 T 0.05209 -1.0899 10 0.39692 T 0.17 2.1853 7.507200 0.275510 0.1561:0.0:0.7084:0.1355 . 40;40 Q9H6R7-2;Q9H6R7 .;CB044_HUMAN W 40 ENSP00000295148:R40W;ENSP00000385816:R40W;ENSP00000413426:R40W ENSP00000295148:R40W R - 1 2 C2orf44 24115751 9.730000e-01 0.338510 3.360000e-01 0.255220 0.420000 0.313550 1.353000 0.340450 0.660000 0.309640 0.655000 0.942530 CGG TCGA-RB-AA9M-01A-11D-A397-08 C2orf44-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000246825.1 0 0 0 5 397 0 50 0 2.467431e-03 0 5 0 50 2 0 0 0 0 0 2 1 0.936677 5 394 0 49 2 0 0 0 0 0 2 -1.887659 0 1 121412 9 42 1 1 2 3 2.031292 0 0.100001 2 0.112427 0.310000 0.100000 1.000000 0.250000 0.431727 0.310000 0 0.180000 1.000000 SOCS5 9655 broad.mit.edu 37 2 46986955 46986955 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:46986955G>A ENST00000306503.5 + 2 1458 c.1286G>A c.(1285-1287)cGa>cAa p.R429Q SOCS5_ENST00000394861.2_Missense_Mutation_p.R429Q NM_014011.4 NP_054730.1 O75159 SOCS5_HUMAN suppressor of cytokine signaling 5 p.R429L(1)|p.R429Q(1) 22 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) LUSC - Lung squamous cell carcinoma(58;0.114) CTGCATGCCCGAATTGAGCAG 0.498000 2 Substitution - Missense(2) SO:0001583 missense ENST00000306503.5 1 1 hg19 CCDS1830.1 . . . . . . . . . . G 16.210000 3.060002 0.553250 . . ENSG00000171150 ENST00000306503;ENST00000394861 D;D 0.89270 -2.49;-2.49 5.430000 3.640000 0.417300 SH2 motif (4); 0.056973 0.64402 D 0.000001 D 0.93916 0.8053 M 0.82716 2.605 0.807220 D 1.000000 D 0.89917 1.0 D 0.76575 0.988 D 0.93888 0.7177 10 0.87932 D 0 -11.2549 11.823900 0.522560 0.1425:0.0:0.8575:0.0 . 429 O75159 SOCS5_HUMAN Q 429 ENSP00000305133:R429Q;ENSP00000378330:R429Q ENSP00000305133:R429Q R + 2 0 SOCS5 46840459 1 0.714170 7.150000e-01 0.305520 0.898000 0.525720 9.657000 0.985540 0.867000 0.356540 -0.136000 0.146810 CGA TCGA-RB-AA9M-01A-11D-A397-08 SOCS5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250791.2 0 0 0 15 750 0 92 1 2.267176e-01 2 41 0 92 2 0 0 0 0 0 2 1 0.999867 15 747 0 92 2 0 0 0 0 0 2 -2.519424 1 1 0 0 1 1 2 3 2.031292 0 0.100001 2 0.112427 0.430000 0.240000 1.000000 0.390000 0.531238 0.430000 0 0.320000 1.000000 TSPYL6 388951 broad.mit.edu 37 2 54482353 54482353 + Silent SNP C C A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr2:54482353C>A ENST00000317802.7 - 1 1056 c.936G>T c.(934-936)gtG>gtT p.V312V ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000303536.4_Intron NM_001003937.2 NP_001003937.2 Q8N831 TSYL6_HUMAN TSPY-like 6 20 TGACCTCATACACCTTTACAA 0.473000 0 SO:0001819 synonymous_variant ENST00000317802.7 0 1 hg19 CCDS42682.1 TCGA-RB-AA9M-01A-11D-A397-08 TSPYL6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324069.3 0 0 0 5 605 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 0.937769 5 604 0 89 2 0 0 0 0 0 2 -3.111406 1 1 0 0 1 1 2 3 2.031292 0 0.100001 2 0.112427 0.200000 0.060000 1.000000 0.160000 0.351871 0.200000 0 0.120000 1.000000 ARHGAP31 57514 broad.mit.edu 37 3 119101232 119101232 + Silent SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr3:119101232G>A ENST00000264245.4 + 5 1057 c.525G>A c.(523-525)gcG>gcA p.A175A NM_020754.2 NP_065805.2 Q2M1Z3 RHG31_HUMAN Rho GTPase activating protein 31 67 TGGTGTGGGCGCCAAACCTCC 0.557000 Pancreas(7;176 297 5394 51128 51241) 0 SO:0001819 synonymous_variant ENST00000264245.4 0 1 hg19 CCDS43135.1 TCGA-RB-AA9M-01A-11D-A397-08 ARHGAP31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354942.2 0 0 0 5 297 0 34 0 4.772194e-02 0 17 0 34 2 0 0 0 0 0 2 1 0.938047 5 297 0 34 2 0 0 0 0 0 2 -2.420032 0 1 0 0 1 1 2 3 2.030482 0 0.100001 2 0.112427 0.410000 0.140000 1.000000 0.320000 0.507849 0.410000 0 0.240000 1.000000 CNTN4 152330 broad.mit.edu 37 3 2861248 2861248 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr3:2861248C>T ENST00000397461.1 + 6 821 c.437C>T c.(436-438)cCg>cTg p.P146L CNTN4_ENST00000418658.1_Missense_Mutation_p.P146L|CNTN4_ENST00000427331.1_Missense_Mutation_p.P146L NM_001206955.1 NP_001193884.1 Q8IWV2 CNTN4_HUMAN contactin 4 61 Ovarian(110;0.156) CTGTGTGGCCCGCCACCCCAT 0.448000 0 SO:0001583 missense ENST00000397461.1 1 1 hg19 CCDS43041.1 . . . . . . . . . . C 26.100000 4.708348 0.890180 . . ENSG00000144619 ENST00000418658;ENST00000397461;ENST00000427331 T;T;T 0.65178 -0.14;-0.14;-0.14 5.860000 5.860000 0.939800 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 D 0.82641 0.5081 M 0.88979 2.995 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.79108 0.992;0.982 D 0.85330 0.1089 10 0.87932 D 0 . 17.104400 0.866580 0.0:1.0:0.0:0.0 . 146;146 B3KTK4;Q8IWV2 .;CNTN4_HUMAN L 146 ENSP00000396010:P146L;ENSP00000380602:P146L;ENSP00000413642:P146L ENSP00000380602:P146L P + 2 0 CNTN4 2836248 1 0.714170 8.720000e-01 0.342170 0.971000 0.663760 5.939000 0.701790 2.765000 0.950210 0.655000 0.942530 CCG TCGA-RB-AA9M-01A-11D-A397-08 CNTN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239236.2 1 0 0 14 212 0 42 0 2.112637e-01 0 13 0 42 2 0 0 0 0 0 2 1 0.999761 14 209 0 41 2 0 0 0 0 0 2 -2.490115 0 1 0 0 1 0 1 1 1.898297 1 0.100001 2 0.052632 0.860000 0.570000 1.000000 0.990000 0.850821 0.860000 1 0.720000 0.970000 ZBTB47 92999 broad.mit.edu 37 3 42703100 42703100 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr3:42703100G>A ENST00000232974.6 + 3 1878 c.1597G>A c.(1597-1599)Gcc>Acc p.A533T ZBTB47_ENST00000505904.1_Missense_Mutation_p.A79T|ZBTB47_ENST00000457842.3_Missense_Mutation_p.A157T Q9UFB7 ZBT47_HUMAN zinc finger and BTB domain containing 47 13 CTACACCATGGCCCACGTGCG 0.522000 0 SO:0001583 missense ENST00000232974.6 1 1 hg19 CCDS46805.2 . . . . . . . . . . G 22.600000 4.313988 0.813580 . . ENSG00000114853 ENST00000232974;ENST00000542870;ENST00000457842;ENST00000505904 T;T;T 0.07567 3.18;3.18;3.18 4.840000 4.840000 0.625910 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 T 0.30541 0.0768 M 0.75447 2.3 0.807220 D 1.000000 D 0.89917 1.0 D 0.83275 0.996 T 0.03514 -1.1029 10 0.52906 T 0.07 -29.8628 17.928600 0.889910 0.0:0.0:1.0:0.0 . 157 Q9UFB7 ZBT47_HUMAN T 533;432;157;79 ENSP00000232974:A533T;ENSP00000411491:A157T;ENSP00000420968:A79T ENSP00000232974:A533T A + 1 0 ZBTB47 42678104 1 0.714170 1 0.803570 0.806000 0.455450 9.785000 0.990420 2.230000 0.728870 0.561000 0.740990 GCC TCGA-RB-AA9M-01A-11D-A397-08 ZBTB47-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000343485.3 1 0 0 17 192 0 35 1 7.763571e-01 4 30 0 35 2 0 0 0 0 0 2 1 0.999970 17 191 0 35 2 0 0 0 0 0 2 -3.221917 1 1 0 0 1 0 1 1 1.898297 1 0.100001 2 0.052632 0.910000 0.670000 1.000000 0.990000 0.901181 0.910000 1 0.810000 0.980000 FAM71B 153745 broad.mit.edu 37 5 156590151 156590151 + Silent SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr5:156590151C>T ENST00000302938.4 - 2 1220 c.1125G>A c.(1123-1125)gcG>gcA p.A375A NM_130899.2 NP_570969.2 Q8TC56 FA71B_HUMAN family with sequence similarity 71, member B 68 Renal(175;0.00212) Medulloblastoma(196;0.0523)|all_neural(177;0.21) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) TGCCTGCAAACGCCGCACTCA 0.582000 0 SO:0001819 synonymous_variant ENST00000302938.4 0 1 hg19 CCDS4335.1 TCGA-RB-AA9M-01A-11D-A397-08 FAM71B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252570.2 1 0 0 15 214 1 34 0 0 0 1 34 2 0 0 0 0 0 2 0 0.181686 15 212 1 32 21 0 0 0 0 0 2 -19.136370 1 0 121412 11 41 1 1 2 3 2.040345 0 0.100001 2 0.114610 0.990000 0.810000 1.000000 1.000000 0.987494 0.990000 1 0.990000 1.000000 FLT4 2324 broad.mit.edu 37 5 180048549 180048549 + Silent SNP C C G TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr5:180048549C>G ENST00000261937.6 - 13 2091 c.2013G>C c.(2011-2013)tcG>tcC p.S671S FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.S671S|FLT4_ENST00000393347.3_Silent_p.S671S NM_182925.4 NP_891555.2 P35916 VGFR3_HUMAN fms-related tyrosine kinase 4 71 all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268) CACCCTGCACCGACAGGTACT 0.672000 Colon(97;1075 1466 27033 27547 35871) 0 SO:0001819 synonymous_variant ENST00000261937.6 1 1 hg19 CCDS4457.1 TCGA-RB-AA9M-01A-11D-A397-08 FLT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253527.4 1 0 0 12 211 0 40 0 7.694994e-02 0 8 0 40 2 0 0 0 0 0 2 1 0.999098 12 207 0 39 2 0 0 0 0 0 2 -2.929030 1 1 0 0 1 1 2 3 2.040345 0 0.100001 2 0.114610 0.990000 0.630000 1.000000 1.000000 0.952241 0.990000 1 0.870000 1.000000 PDZD2 23037 broad.mit.edu 37 5 32108081 32108081 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr5:32108081C>T ENST00000438447.1 + 25 8748 c.8360C>T c.(8359-8361)gCg>gTg p.A2787V PDZD2_ENST00000282493.3_Missense_Mutation_p.A2787V|CTD-2152M20.2_ENST00000503441.1_RNA|PDZD2_ENST00000513490.1_3'UTR O15018 PDZD2_HUMAN PDZ domain containing 2 148 GTAGGTGGTGCGGCTGAACAA 0.348000 0 SO:0001583 missense ENST00000438447.1 0 1 hg19 CCDS34137.1 . . . . . . . . . . C 25.100000 4.600307 0.870550 . . ENSG00000133401 ENST00000438447;ENST00000382161;ENST00000282493 T;T 0.37411 1.2;1.2 5.880000 5.880000 0.946010 PDZ/DHR/GLGF (4); 0.000000 0.56097 D 0.000030 T 0.51890 0.1701 L 0.39898 1.24 0.525010 D 0.999956 D 0.89917 1.0 D 0.97110 1.0 T 0.30149 -0.9988 10 0.29301 T 0.29 . 17.721800 0.883530 0.0:1.0:0.0:0.0 . 2787 O15018 PDZD2_HUMAN V 2787;2588;2787 ENSP00000402033:A2787V;ENSP00000282493:A2787V ENSP00000282493:A2787V A + 2 0 PDZD2 32143838 1 0.714170 9.990000e-01 0.593770 0.597000 0.368140 6.955000 0.760070 2.778000 0.955600 0.655000 0.942530 GCG TCGA-RB-AA9M-01A-11D-A397-08 PDZD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366608.1 0 0 0 6 478 0 60 0 1.384985e-03 0 4 0 60 2 0 0 0 0 0 2 1 0.964273 6 474 0 60 2 0 0 0 0 0 2 -1.894700 0 1 121412 2 39 1 1 2 3 2.040345 0 0.100001 2 0.114610 0.300000 0.110000 1.000000 0.250000 0.439996 0.300000 0 0.190000 1.000000 FYB 2533 broad.mit.edu 37 5 39127879 39127879 + Missense_Mutation SNP A A T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr5:39127879A>T ENST00000351578.6 - 11 2061 c.1871T>A c.(1870-1872)aTt>aAt p.I624N FYB_ENST00000505428.1_Missense_Mutation_p.I624N|FYB_ENST00000515010.1_Missense_Mutation_p.I624N|FYB_ENST00000540520.1_Missense_Mutation_p.I634N|FYB_ENST00000512982.1_Missense_Mutation_p.I624N NM_199335.3 NP_955367.1 O15117 FYB_HUMAN FYN binding protein 45 all_lung(31;0.000343) Epithelial(62;0.235) CCCATCATAAATGTCATCATC 0.328000 0 SO:0001583 missense ENST00000351578.6 0 1 hg19 CCDS47200.1 . . . . . . . . . . A 15.210000 2.765303 0.495740 . . ENSG00000082074 ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542 T;T;T;T;T 0.37915 1.47;1.47;1.17;1.17;1.17 5.380000 5.380000 0.774910 . 0.067000 0.64402 D 0.000010 T 0.54208 0.1844 L 0.49126 1.545 0.439420 D 0.996602 D;D 0.76494 0.999;0.998 D;D 0.83275 0.996;0.995 T 0.56038 -0.8045 10 0.66056 D 0.02 -13.8248 14.257900 0.660650 1.0:0.0:0.0:0.0 . 634;624 B4DLN2;O15117 .;FYB_HUMAN N 624;624;624;624;634;624 ENSP00000316460:I624N;ENSP00000426346:I624N;ENSP00000425845:I624N;ENSP00000427114:I624N;ENSP00000442840:I634N ENSP00000316460:I624N I - 2 0 FYB 39163636 1 0.714170 1 0.803570 0.994000 0.842990 6.035000 0.709400 2.164000 0.680740 0.477000 0.441520 ATT TCGA-RB-AA9M-01A-11D-A397-08 FYB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000367098.1 1 0 0 15 152 0 19 0 2.448651e-01 0 10 0 19 2 0 0 0 0 0 2 1 0.999897 15 152 0 19 2 0 0 0 0 0 2 -19.982870 1 1 0 0 1 1 2 3 2.040345 0 0.100001 2 0.114610 0.990000 0.990000 1.000000 1.000000 0.998882 0.990000 1 0.990000 1.000000 CMYA5 202333 broad.mit.edu 37 5 79032394 79032394 + Silent SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr5:79032394C>T ENST00000446378.2 + 2 7837 c.7806C>T c.(7804-7806)ctC>ctT p.L2602L NM_153610.3 NP_705838.3 Q8N3K9 CMYA5_HUMAN cardiomyopathy associated 5 128 Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262) AAGCCATGCTCGCAGAGGCTC 0.398000 0 SO:0001819 synonymous_variant ENST00000446378.2 1 1 hg19 CCDS47238.1 TCGA-RB-AA9M-01A-11D-A397-08 CMYA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369497.1 1 0 0 18 173 0 32 0 0 0 1 0 32 2 0 0 0 0 0 2 1 0.999986 18 173 0 32 2 0 0 0 0 0 2 -3.221906 1 1 0 0 1 1 2 3 2.040345 0 0.100001 2 0.114610 0.990000 0.990000 1.000000 1.000000 0.999654 0.990000 1 0.990000 1.000000 GRIK2 2898 broad.mit.edu 37 6 102516294 102516294 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr6:102516294C>T ENST00000421544.1 + 16 3125 c.2635C>T c.(2635-2637)Cca>Tca p.P879S GRIK2_ENST00000369138.1_3'UTR|GRIK2_ENST00000413795.1_3'UTR|GRIK2_ENST00000369137.3_Missense_Mutation_p.P803S|GRIK2_ENST00000369134.4_Missense_Mutation_p.P830S NM_021956.4 NP_068775.1 Q13002 GRIK2_HUMAN glutamate receptor, ionotropic, kainate 2 83 all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599) AAAACATAAGCCACAGGCCCC 0.423000 0 SO:0001583 missense ENST00000421544.1 1 1 hg19 CCDS5048.1 . . . . . . . . . . C 15.620000 2.886211 0.519080 . . ENSG00000164418 ENST00000421544;ENST00000369137;ENST00000369134 T;T;T 0.10288 2.89;3.11;2.9 5.790000 5.790000 0.918170 . 0.049332 0.85682 D 0.000000 T 0.07863 0.0197 L 0.53249 1.67 0.584320 D 0.999999 B 0.16396 0.017 B 0.15484 0.013 T 0.10847 -1.0612 10 0.33141 T 0.24 . 20.036100 0.975580 0.0:1.0:0.0:0.0 . 879 Q13002 GRIK2_HUMAN S 879;803;830 ENSP00000397026:P879S;ENSP00000358133:P803S;ENSP00000358130:P830S ENSP00000358130:P830S P + 1 0 GRIK2 102622987 1 0.714170 1 0.803570 0.982000 0.717510 7.463000 0.808690 2.745000 0.941140 0.462000 0.415740 CCA TCGA-RB-AA9M-01A-11D-A397-08 GRIK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043718.1 1 0 0 22 300 0 51 0 1.492248e-02 0 3 0 51 2 0 0 0 0 0 2 1 0.999999 22 296 0 51 2 0 0 0 0 0 2 -7.060106 1 1 0 0 1 0 0 0 1.920210 0 0.100001 2 0.056604 0.970000 0.720000 1.000000 1.000000 0.942193 0.970000 1 0.850000 1.000000 GRM1 2911 broad.mit.edu 37 6 146480607 146480607 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr6:146480607G>A ENST00000282753.1 + 2 1059 c.824G>A c.(823-825)cGc>cAc p.R275H GRM1_ENST00000492807.2_Missense_Mutation_p.R275H|GRM1_ENST00000355289.4_Missense_Mutation_p.R275H|GRM1_ENST00000507907.1_Missense_Mutation_p.R275H|GRM1_ENST00000361719.2_Missense_Mutation_p.R275H|GRM1_ENST00000392299.2_Missense_Mutation_p.R275H Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 p.R275H(1) 126 Ovarian(120;0.0387) CGACTCTTGCGCAAACTCCGA 0.577000 1 Substitution - Missense(1) SO:0001583 missense ENST00000282753.1 0 1 hg19 CCDS5209.1 . . . . . . . . . . G 27.500000 4.838921 0.911170 . . ENSG00000152822 ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907 D;D;D;D;D;D 0.83419 -1.72;-1.72;-1.72;-1.72;-1.72;-1.72 5.320000 5.320000 0.756190 Extracellular ligand-binding receptor (1); 0.053988 0.64402 D 0.000002 D 0.82398 0.5028 L 0.53671 1.685 0.536880 D 0.999976 P;D;P;P 0.64830 0.932;0.994;0.945;0.932 P;P;P;P 0.58780 0.537;0.845;0.667;0.537 D 0.84833 0.0803 10 0.72032 D 0.01 . 9.669800 0.400060 0.1545:0.0:0.8455:0.0 . 275;275;270;275 F8W805;Q13255;Q59HC2;Q13255-2 .;GRM1_HUMAN;.;. H 275 ENSP00000354896:R275H;ENSP00000376119:R275H;ENSP00000424095:R275H;ENSP00000282753:R275H;ENSP00000347437:R275H;ENSP00000425599:R275H ENSP00000282753:R275H R + 2 0 GRM1 146522300 1 0.714170 1 0.803570 0.994000 0.842990 6.432000 0.734000 2.495000 0.841800 0.655000 0.942530 CGC TCGA-RB-AA9M-01A-11D-A397-08 GRM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042574.1 0 0 0 4 215 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.890095 4 214 0 30 2 0 0 0 0 0 2 -2.674040 1 1 121410 5 38 1 0 0 0 1.920210 0 0.100001 2 0.056604 0.360000 0.120000 0.760000 0.330000 0.397873 0.360000 0 0.220000 0.560000 SCAND3 0 broad.mit.edu 37 6 28543263 28543263 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr6:28543263G>A ENST00000452236.2 - 3 1836 c.1219C>T c.(1219-1221)Cgg>Tgg p.R407W SCAND3_ENST00000530247.1_5'Flank NM_052923.1 NP_443155.1 71 TTTAATGACCGCAAAAAAGTT 0.373000 0 SO:0001583 missense ENST00000452236.2 0 1 hg19 CCDS34355.1 . . . . . . . . . . G 15.120000 2.739153 0.490450 . . ENSG00000232040 ENST00000452236 T 0.41065 1.01 3.450000 1.470000 0.227460 Integrase, catalytic core (2);Ribonuclease H-like (1); . . . . T 0.45538 0.1347 M 0.71581 2.175 0.278850 N 0.939548 D 0.89917 1.0 D 0.75020 0.985 T 0.29027 -1.0025 9 0.87932 D 0 . 9.152700 0.369730 0.0:0.0:0.3848:0.6152 . 407 Q6R2W3 SCND3_HUMAN W 407 ENSP00000395259:R407W ENSP00000395259:R407W R - 1 2 SCAND3 28651242 4.900000e-01 0.260120 9.990000e-01 0.593770 0.981000 0.711380 0.152000 0.163020 0.208000 0.206260 0.655000 0.942530 CGG TCGA-RB-AA9M-01A-11D-A397-08 SCAND3-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000043551.3 0 0 0 5 334 0 57 0 3.601379e-04 0 2 0 57 2 0 0 0 0 0 2 1 0.937987 5 334 0 57 2 0 0 0 0 0 2 -2.441249 0 1 0 0 1 1 2 3 2.021921 0 0.100001 2 0.110233 0.360000 0.120000 1.000000 0.290000 0.457661 0.360000 0 0.210000 1.000000 MUC17 140453 broad.mit.edu 37 7 100677537 100677537 + Missense_Mutation SNP C C G TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr7:100677537C>G ENST00000306151.4 + 3 2904 c.2840C>G c.(2839-2841)aCt>aGt p.T947S NM_001040105.1 NP_001035194.1 Q685J3 MUC17_HUMAN mucin 17, cell surface associated 343 Lung NSC(181;0.136)|all_lung(186;0.182) CTTTCAGCAACTCCTGTTGAC 0.507000 0 SO:0001583 missense ENST00000306151.4 1 1 hg19 CCDS34711.1 . . . . . . . . . . C 2.823000 -0.244331 0.059060 . . ENSG00000169876 ENST00000306151 T 0.02323 4.34 0.942000 -0.333000 0.126710 . . . . . T 0.01730 0.0055 N 0.19112 0.55 0.093100 N 1.000000 B 0.20459 0.045 B 0.08055 0.003 T 0.49062 -0.8978 9 0.08179 T 0.78 . 6.466400 0.219830 0.0:0.6919:0.3081:0.0 . 947 Q685J3 MUC17_HUMAN S 947 ENSP00000302716:T947S ENSP00000302716:T947S T + 2 0 MUC17 100464257 5.000000e-03 0.159910 0 0.037020 0.038000 0.132790 1.904000 0.398680 -0.070000 0.129080 0.134000 0.158780 ACT TCGA-RB-AA9M-01A-11D-A397-08 MUC17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347161.1 0 0 0 84 1970 0 334 0 0 0 0 334 2 0 0 0 0 0 2 1 1.000000 80 1725 0 350 2 0 0 0 0 0 2 -5.239423 1 1 0 0 1 1 2 3 2.042720 0 0.100001 2 0.115045 0.860000 0.670000 1.000000 0.820000 0.871606 0.860000 1 0.750000 1.000000 KIAA0895 23366 broad.mit.edu 37 7 36374693 36374693 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr7:36374693C>T ENST00000297063.6 - 4 1012 c.962G>A c.(961-963)cGt>cAt p.R321H KIAA0895_ENST00000436884.1_Missense_Mutation_p.R218H|KIAA0895_ENST00000480192.1_5'UTR|KIAA0895_ENST00000440378.1_Missense_Mutation_p.R318H|KIAA0895_ENST00000317020.6_Missense_Mutation_p.R270H|Y_RNA_ENST00000364562.1_RNA|KIAA0895_ENST00000453212.1_Missense_Mutation_p.R76H|KIAA0895_ENST00000338533.5_Missense_Mutation_p.R308H NM_001100425.1 NP_001093895.1 Q8NCT3 K0895_HUMAN KIAA0895 26 CCAATGCTCACGTGCAGTGGA 0.433000 0 SO:0001583 missense ENST00000297063.6 1 1 hg19 CCDS43570.1 . . . . . . . . . . C 35.000000 5.530230 0.964460 . . ENSG00000164542 ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000453212;ENST00000431396 . . . 5.840000 5.840000 0.934240 . 0.000000 0.85682 D 0.000000 D 0.83413 0.5249 M 0.77313 2.365 0.807220 D 1.000000 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 1.0;1.0;1.0;0.999;0.999 D 0.84184 0.0441 9 0.72032 D 0.01 -11.6493 20.142000 0.980610 0.0:1.0:0.0:0.0 . 318;218;321;308;270 B7ZLT4;B4DF35;Q8NCT3;Q8NCT3-2;Q8NCT3-3 .;.;K0895_HUMAN;.;. H 321;308;270;318;218;76;76 . ENSP00000297063:R321H R - 2 0 KIAA0895 36341218 1 0.714170 9.940000e-01 0.499520 0.962000 0.633680 7.393000 0.798510 2.754000 0.945170 0.655000 0.942530 CGT TCGA-RB-AA9M-01A-11D-A397-08 KIAA0895-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000337717.1 1 0 1 24 474 0 69 1 3.378364e-01 5 19 0 69 2 0 0 0 0 0 2 1 1.000000 24 471 0 69 2 0 0 0 0 0 2 -4.886812 1 1 0 0 1 1 2 3 2.033721 0 0.100001 2 0.112865 0.990000 0.660000 1.000000 1.000000 0.937439 0.990000 1 0.820000 1.000000 HGF 3082 broad.mit.edu 37 7 81358937 81358937 + Nonsense_Mutation SNP C C A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr7:81358937C>A ENST00000222390.5 - 8 1250 c.1024G>T c.(1024-1026)Gaa>Taa p.E342* HGF_ENST00000457544.2_Nonsense_Mutation_p.E337* NM_000601.4 NP_000592.3 P14210 HGF_HUMAN hepatocyte growth factor (hepapoietin A; scatter factor) 75 TTGAAATTTTCAGGAGTCATG 0.418000 0 SO:0001587 stop_gained ENST00000222390.5 0 1 hg19 CCDS5597.1 . . . . . . . . . . C 38.000000 6.828463 0.978690 . . ENSG00000019991 ENST00000222390;ENST00000457544 . . . 5.760000 5.760000 0.907990 . 0.095331 0.64402 D 0.000001 . . . . . . 0.807220 D 1.000000 . . . . . . . . . . 0.44086 T 0.13 . 19.976700 0.973120 0.0:1.0:0.0:0.0 . . . . X 342;337 . ENSP00000222390:E342X E - 1 0 HGF 81196873 9.820000e-01 0.348650 1 0.803570 0.997000 0.918780 2.444000 0.448900 2.702000 0.922790 0.655000 0.942530 GAA TCGA-RB-AA9M-01A-11D-A397-08 HGF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253315.2 0 0 0 5 326 0 53 0 7.323604e-03 0 7 0 53 2 0 0 0 0 0 2 1 0.937503 5 325 0 53 2 0 0 0 0 0 2 -5.424809 1 1 0 0 1 1 2 3 2.042720 0 0.100001 2 0.115045 0.380000 0.130000 1.000000 0.300000 0.497041 0.380000 0 0.230000 1.000000 FER1L6 654463 broad.mit.edu 37 8 125035751 125035751 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr8:125035751G>A ENST00000522917.1 + 18 2407 c.2201G>A c.(2200-2202)cGc>cAc p.R734H FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.R734H NM_001039112.2 NP_001034201.2 Q2WGJ9 FR1L6_HUMAN fer-1-like family member 6 118 Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741) STAD - Stomach adenocarcinoma(47;0.00186) GCCTATGCCCGCATCGCCTCC 0.527000 0 SO:0001583 missense ENST00000522917.1 0 1 hg19 CCDS43767.1 . . . . . . . . . . G 29.000000 4.971850 0.929190 0.0 1.2E-4 ENSG00000214814 ENST00000522917;ENST00000399018 T;T 0.79352 -1.26;-1.26 5.810000 5.810000 0.924710 Ferlin B-domain (1); 0.162857 0.34435 U 0.003970 D 0.89550 0.6747 M 0.91663 3.23 0.584320 D 0.999998 D 0.76494 0.999 D 0.70935 0.971 D 0.91017 0.4854 10 0.72032 D 0.01 . 12.885100 0.580380 0.0779:0.0:0.9221:0.0 . 734 Q2WGJ9 FR1L6_HUMAN H 734 ENSP00000428280:R734H;ENSP00000381982:R734H ENSP00000381982:R734H R + 2 0 FER1L6 125104932 1 0.714170 9.810000e-01 0.438750 0.968000 0.652780 9.072000 0.939860 2.751000 0.943900 0.555000 0.697020 CGC TCGA-RB-AA9M-01A-11D-A397-08 FER1L6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381400.1 0 0 0 6 407 0 51 0 0 0 1 0 51 2 0 0 0 0 0 2 1 0.964173 6 403 0 51 2 0 0 0 0 0 2 -2.105455 0 1 120906 9 42 1 1 2 3 2.015428 0 0.100001 2 0.108912 0.340000 0.130000 1.000000 0.290000 0.434948 0.340000 0 0.210000 0.690000 SLC45A4 57210 broad.mit.edu 37 8 142228865 142228865 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr8:142228865C>T ENST00000024061.3 - 4 1028 c.721G>A c.(721-723)Gag>Aag p.E241K SLC45A4_ENST00000517878.1_Missense_Mutation_p.E292K|SLC45A4_ENST00000519067.1_Missense_Mutation_p.E241K|SLC45A4_ENST00000433583.2_Missense_Mutation_p.E234K NM_001080431.1 NP_001073900.1 Q5BKX6 S45A4_HUMAN solute carrier family 45, member 4 31 all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0493) AGGGCCAGCTCGTGCTCCGAC 0.701000 0 SO:0001583 missense ENST00000024061.3 1 1 hg19 CCDS34948.1 . . . . . . . . . . C 17.300000 3.355746 0.612930 . . ENSG00000022567 ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061 T;T;T;T 0.15834 2.44;2.42;2.42;2.39 5.750000 5.750000 0.904690 . 0.057056 0.64402 D 0.000002 T 0.18676 0.0448 L 0.54323 1.7 0.396890 D 0.971018 B;B;B 0.33238 0.084;0.403;0.066 B;B;B 0.22601 0.016;0.04;0.023 T 0.03695 -1.1012 10 0.26408 T 0.33 -22.7247 20.001500 0.974120 0.0:1.0:0.0:0.0 . 292;241;241 E7EV90;Q5BKX6-3;Q5BKX6-2 .;.;. K 241;292;234;241 ENSP00000429059:E241K;ENSP00000428137:E292K;ENSP00000400799:E234K;ENSP00000024061:E241K ENSP00000024061:E241K E - 1 0 SLC45A4 142298047 9.970000e-01 0.396340 1 0.803570 0.545000 0.351470 3.460000 0.530280 2.731000 0.935340 0.555000 0.697020 GAG TCGA-RB-AA9M-01A-11D-A397-08 SLC45A4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378571.3 1 0 0 58 788 0 117 1 3.839344e-01 2 17 0 117 2 0 0 0 0 0 2 1 1.000000 56 779 0 114 2 0 0 0 0 0 2 -3.017764 1 1 121382 2 39 1 1 2 3 2.015428 0 0.100001 2 0.108912 0.990000 0.990000 1.000000 1.000000 0.999717 0.990000 1 0.990000 1.000000 SDCBP 6386 broad.mit.edu 37 8 59484848 59484848 + Missense_Mutation SNP T T C TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr8:59484848T>C ENST00000260130.4 + 4 365 c.215T>C c.(214-216)gTg>gCg p.V72A SDCBP_ENST00000422546.2_Missense_Mutation_p.V72A|SDCBP_ENST00000424270.2_Missense_Mutation_p.V66A|SDCBP_ENST00000413219.2_Missense_Mutation_p.V72A|SDCBP_ENST00000522243.1_3'UTR|SDCBP_ENST00000447267.2_Missense_Mutation_p.V72A|SDCBP_ENST00000520168.1_Missense_Mutation_p.V72A|SDCBP_ENST00000447182.2_Missense_Mutation_p.V72A|SDCBP_ENST00000523483.1_Missense_Mutation_p.V93A NM_001007068.1|NM_001007069.1|NM_005625.3 NP_001007069.1|NP_001007070.1|NP_005616.2 O00560 SDCB1_HUMAN syndecan binding protein (syntenin) 8 all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554) AATGTGGCCGTGGTTTCTGGT 0.363000 0 SO:0001583 missense ENST00000260130.4 1 1 hg19 CCDS6172.1 . . . . . . . . . . T 2.468000 -0.322502 0.053500 . . ENSG00000137575 ENST00000260130;ENST00000422546;ENST00000447182;ENST00000413219;ENST00000424270;ENST00000523483;ENST00000520168;ENST00000447267 T;T;T;T;T;T;T;T 0.34859 2.84;2.78;2.78;2.84;2.82;2.76;2.77;1.34 5.440000 5.440000 0.795420 . 0.878949 0.10248 N 0.697502 T 0.32164 0.0820 N 0.24115 0.695 0.294520 N 0.858412 B;B;B;B 0.22541 0.0;0.071;0.0;0.0 B;B;B;B 0.31946 0.001;0.138;0.006;0.001 T 0.26503 -1.0101 9 . . . 0.0 15.790900 0.783640 0.0:0.0:0.0:1.0 . 72;93;66;72 B4DHN5;G5EA09;O00560-3;O00560 .;.;.;SDCB1_HUMAN A 72;72;72;72;66;93;72;72 ENSP00000260130:V72A;ENSP00000391687:V72A;ENSP00000409288:V72A;ENSP00000411771:V72A;ENSP00000395351:V66A;ENSP00000428184:V93A;ENSP00000430730:V72A;ENSP00000397820:V72A . V + 2 0 SDCBP 59647402 1 0.714170 1.400000e-02 0.156080 0.004000 0.042600 6.386000 0.731860 2.183000 0.694580 0.533000 0.621200 GTG TCGA-RB-AA9M-01A-11D-A397-08 SDCBP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000378193.1 1 0 1 36 533 0 82 1 1 60 358 0 82 2 0 0 0 0 0 2 1 1.000000 36 529 0 80 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.015428 0 0.100001 2 0.108912 0.990000 0.920000 1.000000 1.000000 0.995673 0.990000 1 0.990000 1.000000 FCN1 2219 broad.mit.edu 37 9 137803031 137803031 + Silent SNP G G A rs145090957 TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr9:137803031G>A ENST00000371806.3 - 8 772 c.681C>T c.(679-681)gaC>gaT p.D227D NM_002003.3 NP_001994.2 O00602 FCN1_HUMAN ficolin (collagen/fibrinogen domain containing) 1 37 Myeloproliferative disorder(178;0.0333) TCTCTGCCTCGTCAGCCACCT 0.547000 0 SO:0001819 synonymous_variant ENST00000371806.3 1 1 hg19 CCDS6985.1 TCGA-RB-AA9M-01A-11D-A397-08 FCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054963.1 1 0 0 70 1090 0 186 0 2.084371e-02 0 4 0 186 2 0 0 0 0 0 2 1 1.000000 70 1075 0 185 2 0 0 0 0 0 2 -10.293830 1 1 121412 5 46 1 0 1 1 1.902555 0 0.100001 2 0.052632 0.950000 0.810000 1.000000 0.990000 0.944490 0.950000 1 0.890000 0.990000 TMEM215 401498 broad.mit.edu 37 9 32784414 32784414 + Missense_Mutation SNP G G A TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chr9:32784414G>A ENST00000342743.5 + 2 598 c.233G>A c.(232-234)cGc>cAc p.R78H NM_212558.2 NP_997723.2 Q68D42 TM215_HUMAN transmembrane protein 215 12 CTGTGGGTCCGCAAATTGCCC 0.597000 0 SO:0001583 missense ENST00000342743.5 0 1 hg19 CCDS6530.1 . . . . . . . . . . G 8.409000 0.843700 0.169630 . . ENSG00000188133 ENST00000342743 . . . 5.180000 4.280000 0.508680 . 0.113770 0.38326 N 0.001736 T 0.31040 0.0784 N 0.19112 0.55 0.308560 N 0.734062 B 0.25169 0.119 B 0.17433 0.018 T 0.31530 -0.9940 9 0.56958 D 0.05 -16.3167 9.719600 0.402950 0.0963:0.0:0.9037:0.0 . 78 Q68D42 TM215_HUMAN H 78 . ENSP00000345468:R78H R + 2 0 TMEM215 32774414 1 0.714170 1 0.803570 0.111000 0.196430 3.258000 0.515070 1.184000 0.429570 -0.258000 0.108200 CGC TCGA-RB-AA9M-01A-11D-A397-08 TMEM215-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251701.1 0 0 0 6 467 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 0.964495 6 464 0 70 2 0 0 0 0 0 2 -2.066409 0 1 0 0 1 0 1 1 1.902555 0 0.100001 2 0.052632 0.250000 0.100000 0.480000 0.230000 0.269359 0.250000 0 0.160000 0.360000 SAGE1 55511 broad.mit.edu 37 X 134993945 134993945 + Missense_Mutation SNP C C T TCGA-RB-AA9M-01A-11D-A397-08 TCGA-RB-AA9M-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2bbf211a-67f7-4120-8fd4-3b3e56a3f1cc 3ca35289-4e81-450e-9e04-6bd0be0b1642 g.chrX:134993945C>T ENST00000370709.3 + 17 2354 c.2354C>T c.(2353-2355)gCg>gTg p.A785V SAGE1_ENST00000324447.3_Missense_Mutation_p.A785V|SAGE1_ENST00000537770.1_Missense_Mutation_p.A409V|SAGE1_ENST00000535938.1_Missense_Mutation_p.A785V Q9NXZ1 SAGE1_HUMAN sarcoma antigen 1 55 Acute lymphoblastic leukemia(192;0.000127) AATGAATTTGCGGTAGGCACC 0.443000 0 SO:0001583 missense ENST00000370709.3 0 1 hg19 CCDS14652.1 . . . . . . . . . . C 0.078000 -1.188862 0.016070 . . ENSG00000181433 ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709 T;T;T;T 0.30182 1.54;1.54;1.58;1.54 2.670000 -5.340000 0.027050 . 7.345260 0.00851 N 0.001834 T 0.08492 0.0211 N 0.00707 -1.245 0.093100 N 1.000000 B;B 0.12630 0.006;0.003 B;B 0.08055 0.003;0.001 T 0.31251 -0.9950 10 0.07482 T 0.82 . 8.327100 0.321650 0.0:0.1179:0.2009:0.6812 . 409;785 F5H2Z8;Q9NXZ1 .;SAGE1_HUMAN V 785;785;409;785 ENSP00000323191:A785V;ENSP00000445959:A785V;ENSP00000438276:A409V;ENSP00000359743:A785V ENSP00000323191:A785V A + 2 0 SAGE1 134821611 0 0.058580 0 0.037020 0.030000 0.120680 -4.323000 0.002530 -2.402000 0.005770 -1.175000 0.017290 GCG TCGA-RB-AA9M-01A-11D-A397-08 SAGE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058448.1 0 0 0 5 566 0 81 0 0 0 1 0 81 2 0 0 0 0 0 2 1 0.936923 5 563 0 80 2 0 0 0 0 0 2 -2.137665 0 1 0 0 1 0 1 1 0.100001 2 0.100001 0.090000 0.030000 0.190000 0.090000 0.103056 0.090000 0 0.050000 0.140000