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 STK11 6794 broad.mit.edu 37 19 1207204 1207204 + Splice_Site DEL T T - rs112235354 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 T - T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:1207204delT ENST00000326873.7 + 1 1463 c.e1+2 STK11_ENST00000585748.1_Intron NM_000455.4 NP_000446.1 Q15831 STK11_HUMAN serine/threonine kinase 11 p.0?(20)|p.?(3) 328 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) CGTGAAGAAGTAAGTATGGCT 0.597000 14 D, Mis, N, F, S NSCLC, pancreatic jejunal harmartoma, ovarian, testicular, pancreatic Peutz-Jeghers syndrome TSP Lung(3;<1E-08) yes Rec yes Peutz-Jeghers syndrome 19 19p13.3 6794 serine/threonine kinase 11 gene (LKB1) E, M, O 23 Whole gene deletion(20)|Unknown(3) SO:0001630 splice_region_variant Familial Cancer Database PJS, Hamartous Intestinal Polyposis ENST00000326873.7 0 1 hg19 CCDS45896.1 TCGA-IB-A6UG-01A-32D-A33T-08 STK11-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449839.3 1 0 0 13 71 0 13 1 9.998439e-01 3 90 0 13 2 1 1 167 823 0 569 2 1 0.999654 13 70 0 13 2 0 0 0 0 0 0 -19.999150 1 1 0 0 1 0 3 3 1.828633 1 0.220000 3.280000 0.278713 0.990000 0.900000 1.000000 1.000000 0.994431 0.990000 1 9.900000e-01 1 SEC24D 9871 broad.mit.edu 37 4 119686069 119686069 + Frame_Shift_Del DEL G G - TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr4:119686069delG ENST00000280551.6 - 10 1422 c.1184delC c.(1183-1185)ccafs p.P396fs SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000511481.1_Frame_Shift_Del_p.P27fs|SEC24D_ENST00000379735.5_Frame_Shift_Del_p.P397fs|SEC24D_ENST00000419654.2_5'UTR O94855 SC24D_HUMAN SEC24 family member D 37 ATAGAATGGTGGAACTAATAA 0.323000 0 SO:0001589 frameshift_variant ENST00000280551.6 0 1 hg19 CCDS3710.1 TCGA-IB-A6UG-01A-32D-A33T-08 SEC24D-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000256514.4 1 0 0 31 456 0 76 0 6.517573e-01 0 34 0 76 2 0 0 0 0 1 0.678844 45 451 2 76 29 0 0 0 0 0 0 -2.806919 1 1 0 0 1 1 2 3 1.965441 0 0.220000 3.280000 0.297297 0.640000 0.440000 0.880000 0.630000 0.657001 0.640000 0 5.300000e-01 7.600000e-01 HPS1 3257 broad.mit.edu 37 10 100185374 100185374 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:100185374C>T ENST00000325103.6 - 13 1492 c.1259G>A c.(1258-1260)cGc>cAc p.R420H HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Missense_Mutation_p.R420H NM_000195.3 NP_000186.2 Q92902 HPS1_HUMAN Hermansky-Pudlak syndrome 1 23 Colorectal(252;0.234) GGGCTGGGAGCGCAGGGAGGC 0.637000 Hermansky-Pudlak syndrome OREG0020430 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense Familial Cancer Database HPS, HPS1-8 ENST00000325103.6 1 1 hg19 CCDS7475.1 . . . . . . . . . . C 19.92 3.916483 0.73098 . . ENSG00000107521 ENST00000325103;ENST00000361490;ENST00000407891;ENST00000359632 T;T;T 0.33438 1.41;1.41;1.41 5.38 5.38 0.77491 . 0.000000 0.85682 D 0.000000 T 0.59238 0.2179 M 0.77616 2.38 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.994;1.0;0.999;1.0 T 0.60125 -0.7324 10 0.48119 T 0.1 . 19.1508 0.93487 0.0:1.0:0.0:0.0 . 58;387;420;420 Q658M9;Q92902-2;Q8WXE5;D3DR62 .;.;.;. H 420;420;387;215 ENSP00000326649:R420H;ENSP00000355310:R420H;ENSP00000352652:R215H ENSP00000326649:R420H R - 2 0 HPS1 100175364 1.000000 0.71417 1.000000 0.80357 0.014000 0.08584 5.418000 0.66429 2.524000 0.85096 0.561000 0.74099 CGC TCGA-IB-A6UG-01A-32D-A33T-08 HPS1-009 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049776.1 1 0 1 25 168 0 28 1 9.931675e-01 8 48 0 28 2 0 0 0 0 0 2 1 1.000000 25 167 0 28 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 2 2 4 2.132970 1 0.220000 3.280000 0.360656 0.990000 0.970000 1.000000 1.000000 0.997602 0.990000 1 9.900000e-01 1 PPRC1 23082 broad.mit.edu 37 10 103907023 103907023 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:103907023G>A ENST00000278070.2 + 9 4313 c.4274G>A c.(4273-4275)cGc>cAc p.R1425H PPRC1_ENST00000413464.2_Intron|PPRC1_ENST00000370012.1_Missense_Mutation_p.R392H|PPRC1_ENST00000489648.1_Intron NM_015062.3 NP_055877.3 Q5VV67 PPRC1_HUMAN peroxisome proliferator-activated receptor gamma, coactivator-related 1 56 Colorectal(252;0.122) CGCCGAGGCCGCAACAGCCGT 0.627000 0 SO:0001583 missense ENST00000278070.2 0 1 hg19 CCDS7529.1 . . . . . . . . . . G 9.681 1.149221 0.21288 . . ENSG00000148840 ENST00000278070;ENST00000370012 T;T 0.37915 1.55;1.17 5.04 3.19 0.36642 . 0.407952 0.26903 N 0.021907 T 0.26011 0.0634 L 0.31926 0.97 0.80722 D 1 B;B 0.19817 0.039;0.023 B;B 0.17433 0.018;0.005 T 0.04454 -1.0950 10 0.21014 T 0.42 . 11.9659 0.53035 0.1434:0.0:0.8566:0.0 . 1305;1425 Q5VV67-2;Q5VV67 .;PPRC1_HUMAN H 1425;392 ENSP00000278070:R1425H;ENSP00000359029:R392H ENSP00000278070:R1425H R + 2 0 PPRC1 103897013 1.000000 0.71417 1.000000 0.80357 0.431000 0.31685 2.955000 0.49121 0.805000 0.34159 -0.379000 0.06801 CGC TCGA-IB-A6UG-01A-32D-A33T-08 PPRC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050021.1 0 0 0 6 519 0 104 0 3.037268e-01 0 84 0 104 2 0 0 0 0 0 2 1 0.961890 6 504 0 100 2 0 0 0 0 104 2 -2.256889 0 1 121412 2 37 1 2 2 4 2.132970 1 0.220000 3.280000 0.360656 0.130000 0.040000 0.260000 0.120000 0.146859 0.130000 0 8.000000e-02 2.000000e-01 SFXN4 119559 broad.mit.edu 37 10 120905815 120905815 + Missense_Mutation SNP G G C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:120905815G>C ENST00000355697.2 - 13 888 c.869C>G c.(868-870)tCt>tGt p.S290C SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Missense_Mutation_p.S281C NM_213649.1 NP_998814.1 Q6P4A7 SFXN4_HUMAN sideroflexin 4 11 Lung NSC(174;0.094)|all_lung(145;0.123) GACAGTACAAGACAGTTTCAA 0.433000 0 SO:0001583 missense ENST00000355697.2 1 1 hg19 CCDS7610.1 . . . . . . . . . . G 13.06 2.123757 0.37436 . . ENSG00000183605 ENST00000355697;ENST00000330036;ENST00000392875;ENST00000369131 T;T 0.30182 1.54;1.54 5.07 2.86 0.33363 . 0.835144 0.10718 N 0.642040 T 0.36331 0.0963 L 0.50333 1.59 0.09310 N 1 D 0.65815 0.995 P 0.56788 0.806 T 0.21724 -1.0237 10 0.38643 T 0.18 -13.2476 2.1131 0.03708 0.1085:0.1772:0.4529:0.2614 . 290 Q6P4A7 SFXN4_HUMAN C 290;281;173;174 ENSP00000347924:S290C;ENSP00000333200:S281C ENSP00000333200:S281C S - 2 0 SFXN4 120895805 0.007000 0.16637 0.002000 0.10522 0.045000 0.14185 1.193000 0.32162 1.240000 0.43803 0.650000 0.86243 TCT TCGA-IB-A6UG-01A-32D-A33T-08 SFXN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050642.3 1 0 1 94 452 0 87 1 9.999988e-01 18 77 0 87 2 0 0 0 0 0 2 1 1.000000 92 447 0 86 2 0 0 0 0 87 2 -20.000000 1 1 121412 2 34 1 2 2 4 2.132970 1 0.220000 3.280000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PTPRE 5791 broad.mit.edu 37 10 129871718 129871718 + Missense_Mutation SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:129871718G>T ENST00000254667.3 + 17 1861 c.1582G>T c.(1582-1584)Gtg>Ttg p.V528L PTPRE_ENST00000306042.5_Missense_Mutation_p.V470L|PTPRE_ENST00000419012.2_Missense_Mutation_p.V528L NM_006504.4 NP_006495.1 P23469 PTPRE_HUMAN protein tyrosine phosphatase, receptor type, E 22 all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203) Alendronate(DB00630) GCTGACGGAGGTGCAGGAGAG 0.597000 Colon(52;977 1184 20575 41685) 0 SO:0001583 missense ENST00000254667.3 1 1 hg19 CCDS7657.1 . . . . . . . . . . G 1.142 -0.649108 0.03506 . . ENSG00000132334 ENST00000254667;ENST00000439034;ENST00000419012;ENST00000306042 T;T;T 0.09538 2.97;2.97;2.97 4.75 2.82 0.32997 Protein-tyrosine phosphatase, receptor/non-receptor type (3); 0.089012 0.46758 D 0.000262 T 0.01489 0.0048 N 0.00047 -2.435 0.80722 D 1 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.06405 0.002;0.002;0.001;0.002 T 0.42137 -0.9469 10 0.02654 T 1 . 8.7131 0.34395 0.0777:0.286:0.6363:0.0 . 506;528;470;528 F5H0X4;Q5VWH4;P23469-2;P23469 .;.;.;PTPRE_HUMAN L 528;506;528;470 ENSP00000254667:V528L;ENSP00000402337:V528L;ENSP00000303350:V470L ENSP00000254667:V528L V + 1 0 PTPRE 129761708 1.000000 0.71417 0.989000 0.46669 0.609000 0.37215 2.058000 0.41374 0.557000 0.29117 0.563000 0.77884 GTG TCGA-IB-A6UG-01A-32D-A33T-08 PTPRE-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050990.1 1 0 1 36 157 0 30 1 9.973142e-01 17 26 0 30 2 0 0 0 0 0 2 1 1.000000 36 155 0 30 2 0 0 0 0 30 2 -20.000000 1 1 0 0 1 2 2 4 2.119299 1 0.220000 3.280000 0.358342 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 PWWP2B 170394 broad.mit.edu 37 10 134218205 134218205 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:134218205C>T ENST00000305233.5 + 2 260 c.201C>T c.(199-201)ggC>ggT p.G67G PWWP2B_ENST00000368609.4_Silent_p.G67G NM_138499.3 NP_612508.3 Q6NUJ5 PWP2B_HUMAN PWWP domain containing 2B 9 all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224) ACAGCCATGGCCGGGCTCCCG 0.697000 0 SO:0001819 synonymous_variant ENST00000305233.5 0 1 hg19 CCDS7667.2 TCGA-IB-A6UG-01A-32D-A33T-08 PWWP2B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051075.3 0 0 0 7 854 0 174 0 2.190184e-01 0 94 0 174 2 0 0 0 0 0 2 1 0.980055 6 848 0 171 2 0 0 0 0 174 2 -2.326966 0 1 0 0 1 2 2 4 2.119299 1 0.220000 3.280000 0.358342 0.090000 0.020000 0.200000 0.080000 0.111177 0.090000 0 6.000000e-02 1.400000e-01 ANKRD30A 91074 broad.mit.edu 37 10 37508147 37508147 + Missense_Mutation SNP A A T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:37508147A>T ENST00000602533.1 + 34 3438 c.3339A>T c.(3337-3339)aaA>aaT p.K1113N ANKRD30A_ENST00000374660.1_Missense_Mutation_p.K1232N|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.K1113N Q9BXX3 AN30A_HUMAN ankyrin repeat domain 30A 158 GGCAGCTTAAAGTTCTGATAG 0.353000 0 SO:0001583 missense ENST00000602533.1 1 1 hg19 . . . . . . . . . . a 0 -2.770045 0.00081 . . ENSG00000148513 ENST00000361713;ENST00000374660 T;T 0.11385 2.78;2.78 2.81 -1.34 0.09143 . . . . . T 0.03011 0.0089 N 0.04880 -0.145 0.09310 N 1 B 0.09022 0.002 B 0.06405 0.002 T 0.41288 -0.9517 9 0.02654 T 1 . 0.8546 0.01179 0.1973:0.1254:0.1857:0.4916 . 1169 Q9BXX3 AN30A_HUMAN N 1113;1232 ENSP00000354432:K1113N;ENSP00000363792:K1232N ENSP00000354432:K1113N K + 3 2 ANKRD30A 37548153 0.893000 0.30496 0.000000 0.03702 0.001000 0.01503 1.090000 0.30902 -0.603000 0.05767 -0.457000 0.05445 AAA TCGA-IB-A6UG-01A-32D-A33T-08 ANKRD30A-001 KNOWN NMD_exception|basic|appris_principal protein_coding protein_coding OTTHUMT00000047588.2 1 0 1 130 642 0 136 0 0 0 0 136 2 0 0 0 0 0 2 1 1.000000 130 635 0 135 2 0 0 0 0 136 2 -20.000000 1 0 0 0 1 2 2 4 2.128278 1 0.220000 3.280000 0.359501 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 NEUROG3 50674 broad.mit.edu 37 10 71332359 71332359 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:71332359G>A ENST00000242462.4 - 2 470 c.441C>T c.(439-441)taC>taT p.Y147Y NM_020999.3 NP_066279.2 Q9Y4Z2 NGN3_HUMAN neurogenin 3 13 GCTCCAGCGCGTACAAGCTGT 0.682000 0 SO:0001819 synonymous_variant ENST00000242462.4 0 1 hg19 CCDS31212.1 TCGA-IB-A6UG-01A-32D-A33T-08 NEUROG3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048464.1 0 0 0 5 231 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 0.938201 5 231 0 37 2 0 0 0 0 38 2 -6.272953 1 1 121404 7 34 1 2 2 4 2.128278 1 0.220000 3.280000 0.359501 0.250000 0.090000 0.530000 0.230000 0.277002 0.250000 0 1.600000e-01 3.900000e-01 CYP2C9 1559 broad.mit.edu 37 10 96748637 96748637 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr10:96748637G>A ENST00000260682.6 + 9 1337 c.1325G>A c.(1324-1326)gGc>gAc p.G442D NM_000771.3 NP_000762.2 P11712 CP2C9_HUMAN cytochrome P450, family 2, subfamily C, polypeptide 9 34 Colorectal(252;0.0902) Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198) GCCCTGGCCGGCATGGAGCTG 0.453000 Ovarian(54;1266 1406 16072 35076) 0 SO:0001583 missense ENST00000260682.6 0 1 hg19 CCDS7437.1 . . . . . . . . . . . 9.583 1.123983 0.20959 . . ENSG00000138109 ENST00000260682 T 0.67865 -0.29 3.41 2.47 0.30058 . 0.000000 0.64402 U 0.000002 T 0.41903 0.1179 N 0.04508 -0.205 0.23425 N 0.997706 B;B 0.17465 0.022;0.022 B;B 0.14578 0.011;0.011 T 0.42932 -0.9422 10 0.87932 D 0 . 9.6892 0.40118 0.0:0.0:0.7903:0.2097 . 442;442 Q5VX92;P11712 .;CP2C9_HUMAN D 442 ENSP00000260682:G442D ENSP00000260682:G442D G + 2 0 CYP2C9 96738627 1.000000 0.71417 0.996000 0.52242 0.064000 0.16182 6.266000 0.72540 0.741000 0.32674 0.446000 0.29264 GGC TCGA-IB-A6UG-01A-32D-A33T-08 CYP2C9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049501.1 0 0 0 6 679 0 118 0 0 0 1 0 118 2 0 0 0 0 0 2 1 0.963954 6 672 0 116 2 0 0 0 0 118 2 -2.077616 0 1 0 0 1 2 2 4 2.132970 1 0.220000 3.280000 0.360656 0.100000 0.020000 0.210000 0.090000 0.112749 0.100000 0 6.000000e-02 1.600000e-01 OR10G9 219870 broad.mit.edu 37 11 123893818 123893818 + Silent SNP C C T rs145074505 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:123893818C>T ENST00000375024.1 + 1 99 c.99C>T c.(97-99)taC>taT p.Y33Y NM_001001953.1 NP_001001953.1 Q8NGN4 O10G9_HUMAN olfactory receptor, family 10, subfamily G, member 9 61 Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22) TGGTGGTTTACGTGCTCACTG 0.572000 0 SO:0001819 synonymous_variant ENST00000375024.1 1 1 hg19 CCDS31703.1 TCGA-IB-A6UG-01A-32D-A33T-08 OR10G9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387269.1 1 0 0 216 725 0 145 0 0 0 0 145 2 0 0 0 0 0 2 1 1.000000 208 683 0 177 2 0 0 0 0 145 2 -20.000000 1 1 121412 34 48 1 2 3 5 2.326960 1 0.220000 3.280000 0.410609 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 NELL1 4745 broad.mit.edu 37 11 20968881 20968881 + Splice_Site SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:20968881G>T ENST00000357134.5 + 11 1223 c.e11-1 NELL1_ENST00000298925.5_Splice_Site|NELL1_ENST00000532434.1_Splice_Site|NELL1_ENST00000325319.5_Splice_Site NM_006157.3|NM_201551.1 NP_006148.2|NP_963845.1 Q92832 NELL1_HUMAN NEL-like 1 (chicken) 70 TTGGCTTCCAGGGTGGAGTTT 0.368000 0 SO:0001630 splice_region_variant ENST00000357134.5 1 1 hg19 CCDS7855.1 . . . . . . . . . . G 20.6 4.010372 0.75046 . . ENSG00000165973 ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434 . . . 6.17 6.17 0.99709 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.0599 0.93085 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . NELL1 20925457 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 6.847000 0.75404 2.941000 0.99782 0.655000 0.94253 . TCGA-IB-A6UG-01A-32D-A33T-08 NELL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387588.1 1 0 0 43 466 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 43 458 0 73 2 0 0 0 0 74 2 -2.578431 1 1 0 0 1 2 2 4 2.125679 1 0.220000 3.280000 0.359501 0.930000 0.690000 1.000000 1.000000 0.915721 0.930000 1 8.000000e-01 1 INS-IGF2 723961 broad.mit.edu 37 11 2182109 2182109 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:2182109G>A ENST00000397270.1 - 2 151 c.93C>T c.(91-93)tgC>tgT p.C31C INS_ENST00000512523.1_Silent_p.C31C|INS_ENST00000250971.3_Silent_p.C31C|INS_ENST00000397262.1_Silent_p.C31C|INS_ENST00000381330.4_Silent_p.C31C|INS-IGF2_ENST00000481781.1_5'Flank NM_001042376.2 NP_001035835.1 F8WCM5 INSR2_HUMAN INS-IGF2 readthrough 5 all_epithelial(84;0.00018)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24) Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239) GGTGTGAGCCGCACAGGTGTT 0.652000 0 SO:0001819 synonymous_variant ENST00000397270.1 0 1 hg19 CCDS41598.1 TCGA-IB-A6UG-01A-32D-A33T-08 INS-IGF2-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000388404.1 0 0 0 5 374 0 58 1 9.999979e-01 9 4151 0 58 2 0 0 0 0 0 2 1 0.936626 5 371 0 57 2 0 0 0 0 58 2 -2.721589 1 1 121154 3 34 1 2 2 4 2.125679 1 0.220000 3.280000 0.359501 0.150000 0.050000 0.340000 0.150000 0.173529 0.150000 0 9.000000e-02 2.400000e-01 AHNAK 79026 broad.mit.edu 37 11 62297984 62297984 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:62297984G>A ENST00000378024.4 - 5 4179 c.3905C>T c.(3904-3906)cCg>cTg p.P1302L AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron NM_001620.1 NP_001611.1 Q09666 AHNK_HUMAN AHNAK nucleoprotein 268 Melanoma(852;0.155) CTTTCCTTCCGGGCCCTCAAG 0.552000 0 SO:0001583 missense ENST00000378024.4 1 1 hg19 CCDS31584.1 . . . . . . . . . . g 13.14 2.148809 0.37923 . . ENSG00000124942 ENST00000378024 T 0.03242 4.0 4.66 4.66 0.58398 . 0.000000 0.31612 U 0.007360 T 0.09379 0.0231 M 0.87827 2.91 0.58432 D 0.999999 P 0.50272 0.933 B 0.39152 0.292 T 0.22173 -1.0224 10 0.45353 T 0.12 . 17.5636 0.87913 0.0:0.0:1.0:0.0 . 1302 Q09666 AHNK_HUMAN L 1302 ENSP00000367263:P1302L ENSP00000367263:P1302L P - 2 0 AHNAK 62054560 0.997000 0.39634 0.103000 0.21229 0.003000 0.03518 2.440000 0.44855 2.309000 0.77851 0.645000 0.84053 CCG TCGA-IB-A6UG-01A-32D-A33T-08 AHNAK-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395572.1 0 0 1 215 907 0 193 1 9.999845e-01 26 41 0 193 2 0 0 0 0 0 2 1 1.000000 210 899 0 193 2 0 0 0 0 193 2 -2.554368 1 1 121412 4 40 1 2 2 4 2.130753 1 0.220000 3.280000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 HPX 3263 broad.mit.edu 37 11 6461433 6461433 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:6461433C>T ENST00000265983.3 - 4 398 c.298G>A c.(298-300)Gca>Aca p.A100T HPX_ENST00000525057.1_5'UTR NM_000613.2 NP_000604.1 P02790 HEMO_HUMAN hemopexin 15 Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114) TGACGGAATGCAGCATCCACA 0.517000 0 SO:0001583 missense ENST00000265983.3 0 1 hg19 CCDS7763.1 . . . . . . . . . . C 23.4 4.412896 0.83340 . . ENSG00000110169 ENST00000265983;ENST00000537154 T 0.06528 3.29 4.92 4.92 0.64577 Hemopexin/matrixin, conserved site (1);Hemopexin/matrixin (2); 0.000000 0.85682 D 0.000000 T 0.33904 0.0879 M 0.92122 3.275 0.54753 D 0.999989 D;D 0.89917 1.0;1.0 D;D 0.91635 0.998;0.999 T 0.40496 -0.9560 10 0.87932 D 0 -23.7514 15.653 0.77112 0.0:1.0:0.0:0.0 . 100;100 B7Z8Q4;P02790 .;HEMO_HUMAN T 100 ENSP00000265983:A100T ENSP00000265983:A100T A - 1 0 HPX 6418009 1.000000 0.71417 1.000000 0.80357 0.853000 0.48598 3.482000 0.53186 2.554000 0.86153 0.555000 0.69702 GCA TCGA-IB-A6UG-01A-32D-A33T-08 HPX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257256.1 0 0 0 6 388 1 56 0 0 0 1 1 56 2 0 0 0 0 0 2 0 0.001447 6 385 1 56 22 0 0 0 1 56 2 -2.624164 1 1 0 0 1 2 2 4 2.125679 1 0.220000 3.280000 0.359501 0.180000 0.060000 0.360000 0.160000 0.194824 0.180000 0 1.100000e-01 2.700000e-01 GAL3ST3 89792 broad.mit.edu 37 11 65810433 65810433 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:65810433C>T ENST00000312006.4 - 3 1122 c.841G>A c.(841-843)Gcg>Acg p.A281T GAL3ST3_ENST00000527878.1_Missense_Mutation_p.A281T NM_033036.2 NP_149025.1 Q96A11 G3ST3_HUMAN galactose-3-O-sulfotransferase 3 14 gccagcgccgcggggATGGCG 0.756000 0 SO:0001583 missense ENST00000312006.4 0 1 hg19 CCDS8128.1 . . . . . . . . . . C 4.128 0.022068 0.08006 . . ENSG00000175229 ENST00000312006;ENST00000527878 T;T 0.14640 2.49;2.49 4.49 2.58 0.30949 . 0.711911 0.12996 N 0.422026 T 0.06142 0.0159 N 0.16833 0.445 0.25445 N 0.988058 B 0.34313 0.448 B 0.26517 0.07 T 0.37663 -0.9696 10 0.14656 T 0.56 -8.5029 5.9018 0.18970 0.1877:0.7113:0.0:0.1009 . 281 Q96A11 G3ST3_HUMAN T 281 ENSP00000308591:A281T;ENSP00000434829:A281T ENSP00000308591:A281T A - 1 0 GAL3ST3 65567009 0.004000 0.15560 0.976000 0.42696 0.149000 0.21700 0.363000 0.20301 0.427000 0.26145 -1.512000 0.00943 GCG TCGA-IB-A6UG-01A-32D-A33T-08 GAL3ST3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391052.1 0 0 0 10 36 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.997696 10 35 0 12 2 0 0 0 0 12 2 -19.999990 1 1 0 0 1 2 2 4 2.130753 1 0.220000 3.280000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999621 0.990000 1 9.900000e-01 1 OR2AG2 338755 broad.mit.edu 37 11 6789727 6789727 + Silent SNP C C A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr11:6789727C>A ENST00000338569.2 - 1 559 c.462G>T c.(460-462)ctG>ctT p.L154L NM_001004490.1 NP_001004490.1 A6NM03 O2AG2_HUMAN olfactory receptor, family 2, subfamily AG, member 2 28 Medulloblastoma(188;0.00776)|all_neural(188;0.0652) CTATAGCAATCAGGGATGCCA 0.507000 0 SO:0001819 synonymous_variant ENST00000338569.2 1 1 hg19 CCDS31413.1 TCGA-IB-A6UG-01A-32D-A33T-08 OR2AG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000386775.1 1 0 0 20 329 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 0.999996 20 327 0 58 2 0 0 0 0 58 2 -19.996120 1 1 0 0 1 2 2 4 2.125679 1 0.220000 3.280000 0.359501 0.640000 0.400000 0.960000 0.640000 0.658070 0.640000 0 5.100000e-01 8.000000e-01 NOS1 4842 broad.mit.edu 37 12 117728173 117728173 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:117728173C>T ENST00000338101.4 - 3 915 c.911G>A c.(910-912)cGc>cAc p.R304H NOS1_ENST00000317775.6_Missense_Mutation_p.R304H|NOS1_ENST00000344089.3_Missense_Mutation_p.A323T Q8WY41 NANO1_HUMAN nitric oxide synthase 1 (neuronal) 117 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) CTTGAGGAAGCGTGGACACTT 0.547000 Esophageal Squamous(162;1748 2599 51982 52956) 0 SO:0001583 missense ENST00000338101.4 1 1 hg19 CCDS55890.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 23.8|23.8 4.454934|4.454934 0.84209|0.84209 .|. .|. ENSG00000089250|ENSG00000089250 ENST00000344089|ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101 T|T;T 0.05786|0.01629 3.39|4.77;4.72 5.13|5.13 5.13|5.13 0.70059|0.70059 .|Nitric oxide synthase, oxygenase domain (1); .|0.109676 .|0.64402 .|D .|0.000008 T|T 0.09774|0.09774 0.0240|0.0240 M|M 0.73598|0.73598 2.24|2.24 0.39371|0.39371 D|D 0.96609|0.96609 .|D .|0.89917 .|1.0 .|P .|0.62560 .|0.904 T|T 0.00728|0.00728 -1.1591|-1.1591 7|10 0.87932|0.66056 D|D 0|0.02 -33.7598|-33.7598 18.7669|18.7669 0.91876|0.91876 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|304 .|P29475 .|NOS1_HUMAN T|H 323|304 ENSP00000339862:A323T|ENSP00000320758:R304H;ENSP00000337459:R304H ENSP00000339862:A323T|ENSP00000320758:R304H A|R -|- 1|2 0|0 NOS1|NOS1 116212556|116212556 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.984000|0.984000 0.73092|0.73092 7.382000|7.382000 0.79729|0.79729 2.680000|2.680000 0.91292|0.91292 0.467000|0.467000 0.42956|0.42956 GCT|CGC TCGA-IB-A6UG-01A-32D-A33T-08 NOS1-002 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000268053.1 1 0 1 40 202 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 1.000000 40 197 0 37 2 0 0 0 0 37 2 -19.987410 1 1 0 0 1 1 2 3 1.998772 0 0.220000 3.280000 0.273540 0.990000 0.990000 1.000000 1.000000 0.999952 0.990000 1 9.900000e-01 1 CLIP1 6249 broad.mit.edu 37 12 122825973 122825973 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:122825973G>A ENST00000540338.1 - 10 1819 c.1778C>T c.(1777-1779)aCc>aTc p.T593I CLIP1_ENST00000361654.4_Missense_Mutation_p.T547I|CLIP1_ENST00000545889.1_Missense_Mutation_p.T283I|CLIP1_ENST00000537178.1_Missense_Mutation_p.T547I|CLIP1_ENST00000302528.7_Missense_Mutation_p.T582I|CLIP1_ENST00000358808.2_Missense_Mutation_p.T582I P30622 CLIP1_HUMAN CAP-GLY domain containing linker protein 1 60 all_neural(191;0.0837)|Medulloblastoma(191;0.163) TTCCGTGGCGGTATACAGAGC 0.458000 0 SO:0001583 missense ENST00000540338.1 0 1 hg19 CCDS58285.1 . . . . . . . . . . G 7.866 0.727207 0.15439 . . ENSG00000130779 ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304 T;T;T;T;T;T 0.61627 2.74;0.69;0.69;0.7;0.69;0.09 5.37 0.13 0.14746 . 0.766493 0.13191 N 0.406706 T 0.23965 0.0580 N 0.01352 -0.895 0.09310 N 1 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.04013 0.001;0.001;0.001;0.001 T 0.18116 -1.0347 10 0.44086 T 0.13 3.1754 5.4745 0.16688 0.372:0.1308:0.4972:0.0 . 283;547;582;593 F5H0N7;P30622-2;P30622-1;P30622 .;.;.;CLIP1_HUMAN I 283;582;582;427;547;593;516 ENSP00000438743:T283I;ENSP00000303585:T582I;ENSP00000351665:T582I;ENSP00000445531:T547I;ENSP00000439093:T593I;ENSP00000437786:T516I ENSP00000303585:T582I T - 2 0 CLIP1 121391926 0.848000 0.29623 0.000000 0.03702 0.566000 0.35808 2.612000 0.46343 0.033000 0.15463 0.561000 0.74099 ACC TCGA-IB-A6UG-01A-32D-A33T-08 CLIP1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000401625.1 0 0 0 7 886 0 160 0 1.109853e-01 1 61 0 160 2 0 0 0 0 0 2 1 0.980231 7 881 0 160 2 0 0 0 0 160 2 -2.211683 0 1 0 0 1 1 2 3 1.998772 0 0.220000 3.280000 0.273540 0.090000 0.030000 1.000000 0.080000 0.281781 0.090000 0 5.000000e-02 1 TMEM132D 121256 broad.mit.edu 37 12 130184773 130184773 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:130184773G>A ENST00000422113.2 - 2 876 c.550C>T c.(550-552)Cgg>Tgg p.R184W RP11-174M13.2_ENST00000544036.1_lincRNA NM_133448.2 NP_597705.2 Q14C87 T132D_HUMAN transmembrane protein 132D 152 all_neural(191;0.101)|Medulloblastoma(191;0.163) all_epithelial(31;0.0934)|Breast(359;0.133) CCCTGCAGCCGGCAGCTGCCC 0.692000 0 SO:0001583 missense ENST00000422113.2 1 1 hg19 CCDS9266.1 . . . . . . . . . . G 18.55 3.647589 0.67358 . . ENSG00000151952 ENST00000422113 T 0.13657 2.57 5.22 3.2 0.36748 . 0.585904 0.15144 N 0.278095 T 0.37461 0.1004 M 0.86740 2.835 0.32312 N 0.563638 D 0.76494 0.999 P 0.59288 0.855 T 0.56529 -0.7964 9 . . . -33.4486 13.4612 0.61229 0.0:0.0:0.5014:0.4986 . 184 Q14C87 T132D_HUMAN W 184 ENSP00000408581:R184W . R - 1 2 TMEM132D 128750726 0.099000 0.21834 0.990000 0.47175 0.952000 0.60782 0.262000 0.18460 1.122000 0.41944 0.555000 0.69702 CGG TCGA-IB-A6UG-01A-32D-A33T-08 TMEM132D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399592.1 1 0 0 19 201 0 37 0 0 0 1 0 37 2 0 0 0 0 0 2 1 0.999991 19 196 0 37 2 0 0 0 0 37 2 -20.000000 1 1 121288 2 35 1 1 2 3 1.998772 0 0.220000 3.280000 0.273540 0.910000 0.550000 1.000000 1.000000 0.874464 0.910000 1 7.000000e-01 1 GYS2 2998 broad.mit.edu 37 12 21721886 21721886 + Nonsense_Mutation SNP G G A rs121918419 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:21721886G>A ENST00000261195.2 - 5 990 c.736C>T c.(736-738)Cga>Tga p.R246* NM_021957.3 NP_068776.2 P54840 GYS2_HUMAN glycogen synthase 2 (liver) p.R246*(1) 48 ACGGAAGCTCGCTCCATGCAG 0.423000 Colon(149;9 1820 3690 10544 50424) 1 Substitution - Nonsense(1) GRCh37 CM980965 GYS2 M rs121918419 SO:0001587 stop_gained ENST00000261195.2 0 1 hg19 CCDS8690.1 . . . . . . . . . . G 39 7.668078 0.98422 . . ENSG00000111713 ENST00000261195 . . . 5.16 4.25 0.50352 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -13.9125 15.0535 0.71894 0.0:0.0:0.8571:0.1429 . . . . X 246 . ENSP00000261195:R246X R - 1 2 GYS2 21613153 1.000000 0.71417 0.995000 0.50966 0.995000 0.86356 3.419000 0.52728 1.363000 0.46019 0.655000 0.94253 CGA TCGA-IB-A6UG-01A-32D-A33T-08 GYS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402396.1 0 0 0 6 491 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 0.963835 5 486 0 104 2 0 0 0 0 104 2 -2.666693 1 1 121412 48 49 1 2 2 4 2.075980 0 0.220000 3.280000 0.342881 0.140000 0.050000 1.000000 0.140000 0.251676 0.140000 0 9.000000e-02 2.600000e-01 GYS2 2998 broad.mit.edu 37 12 21733405 21733405 + Silent SNP T T C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:21733405T>C ENST00000261195.2 - 2 428 c.174A>G c.(172-174)gaA>gaG p.E58E NM_021957.3 NP_068776.2 P54840 GYS2_HUMAN glycogen synthase 2 (liver) 48 TCTCTCCCCATTCATCTGCTG 0.378000 Colon(149;9 1820 3690 10544 50424) 0 SO:0001819 synonymous_variant ENST00000261195.2 1 1 hg19 CCDS8690.1 TCGA-IB-A6UG-01A-32D-A33T-08 GYS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402396.1 0 0 0 22 590 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 0.999999 23 587 0 122 2 0 0 0 0 122 2 -3.625987 1 1 121412 1 32 1 2 2 4 2.075980 0 0.220000 3.280000 0.342881 0.400000 0.250000 1.000000 0.400000 0.473870 0.400000 0 3.200000e-01 5.500000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-A6UG-01A-32D-A33T-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 13 117 0 20 1 5.381532e-01 8 9 0 20 2 1 1 75 401 0 273 2 1 0.999626 13 117 0 20 2 1 1 1812 6219 0 20 2 -7.680973 1 1 121404 2 44 1 2 2 4 2.075980 0 0.220000 3.280000 0.342881 0.990000 0.630000 1.000000 1.000000 0.949861 0.990000 1 8.600000e-01 1 CACNA1C 775 broad.mit.edu 37 12 2797686 2797686 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:2797686C>T ENST00000347598.4 + 48 6002 c.6002C>T c.(6001-6003)gCc>gTc p.A2001V CACNA1C_ENST00000399637.1_Missense_Mutation_p.A1972V|CACNA1C_ENST00000399644.1_Missense_Mutation_p.A1953V|CACNA1C_ENST00000399603.1_Missense_Mutation_p.A1953V|CACNA1C-AS1_ENST00000541673.1_RNA|CACNA1C_ENST00000327702.7_Missense_Mutation_p.A1988V|CACNA1C_ENST00000399641.1_Missense_Mutation_p.A1953V|CACNA1C_ENST00000399655.1_Missense_Mutation_p.A1953V|CACNA1C_ENST00000399597.1_Missense_Mutation_p.A1953V|CACNA1C_ENST00000399617.1_Missense_Mutation_p.A1988V|CACNA1C_ENST00000402845.3_Missense_Mutation_p.A1972V|CACNA1C_ENST00000399638.1_Missense_Mutation_p.A1981V|CACNA1C_ENST00000399591.1_Missense_Mutation_p.A1961V|CACNA1C_ENST00000399634.1_Missense_Mutation_p.A2024V|CACNA1C_ENST00000399629.1_Missense_Mutation_p.A1970V|CACNA1C_ENST00000399606.1_Missense_Mutation_p.A1973V|CACNA1C_ENST00000399621.1_Missense_Mutation_p.A1972V|CACNA1C_ENST00000335762.5_Missense_Mutation_p.A1978V|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399649.1_Missense_Mutation_p.A1959V|CACNA1C-AS1_ENST00000544517.1_RNA|CACNA1C_ENST00000344100.3_Missense_Mutation_p.A1994V|CACNA1C_ENST00000399601.1_Missense_Mutation_p.A1953V|CACNA1C_ENST00000399595.1_Missense_Mutation_p.A1961V|CACNA1C_ENST00000406454.3_Missense_Mutation_p.A2024V NM_001129827.1|NM_199460.2 NP_001123299.1|NP_955630.2 Q13936 CAC1C_HUMAN calcium channel, voltage-dependent, L type, alpha 1C subunit 132 OV - Ovarian serous cystadenocarcinoma(31;0.00256) Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) AGGCCTTTTGCCACCCCACCA 0.642000 0 SO:0001583 missense ENST00000347598.4 0 1 hg19 CCDS44788.1 . . . . . . . . . . C 13.56 2.273195 0.40194 . . ENSG00000151067 ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367 T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.58060 0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36 4.86 3.97 0.46021 . 1.113020 0.06702 N 0.771686 T 0.53658 0.1810 M 0.62723 1.935 0.26184 N 0.979682 B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.21520 0.011;0.057;0.01;0.017;0.057;0.026;0.012;0.015;0.007;0.026;0.026;0.01;0.01;0.015;0.006;0.009;0.01;0.008;0.026;0.008;0.012;0.015;0.026;0.01;0.01 B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.26310 0.037;0.068;0.011;0.027;0.068;0.068;0.024;0.068;0.038;0.024;0.036;0.017;0.033;0.068;0.005;0.031;0.033;0.019;0.036;0.032;0.016;0.036;0.036;0.017;0.011 T 0.47129 -0.9141 10 0.44086 T 0.13 . 9.6655 0.39981 0.0:0.7805:0.1415:0.078 . 644;1994;1950;2036;1988;1972;1953;1970;1981;1953;1973;1953;1984;2001;1953;1988;2024;1961;1959;1961;1942;1972;1972;1953;1953 B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12 .;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;. V 1978;1953;1953;1981;1953;1972;1972;1961;1953;2001;1973;1953;1994;1970;1988;1959;1972;1953;2024;1988;2024;1961;1854 ENSP00000336982:A1978V;ENSP00000382563:A1953V;ENSP00000382552:A1953V;ENSP00000382547:A1981V;ENSP00000382506:A1953V;ENSP00000382530:A1972V;ENSP00000382546:A1972V;ENSP00000382500:A1961V;ENSP00000382549:A1953V;ENSP00000266376:A2001V;ENSP00000382515:A1973V;ENSP00000382510:A1953V;ENSP00000341092:A1994V;ENSP00000382537:A1970V;ENSP00000329877:A1988V;ENSP00000382557:A1959V;ENSP00000385724:A1972V;ENSP00000382512:A1953V;ENSP00000382542:A2024V;ENSP00000382526:A1988V;ENSP00000385896:A2024V;ENSP00000382504:A1961V ENSP00000323129:A1854V A + 2 0 CACNA1C 2667947 1.000000 0.71417 0.629000 0.29254 0.517000 0.34286 4.439000 0.59968 1.051000 0.40369 0.462000 0.41574 GCC TCGA-IB-A6UG-01A-32D-A33T-08 CACNA1C-017 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000317035.1 0 0 0 7 674 0 92 0 6.417475e-03 0 10 0 92 2 0 0 0 0 0 2 1 0.978730 7 656 0 87 2 0 0 0 0 92 2 -2.350234 0 1 120832 13 39 1 2 2 4 2.062782 0 0.220000 3.280000 0.339207 0.120000 0.040000 1.000000 0.110000 0.247020 0.120000 0 7.000000e-02 2.300000e-01 FMNL3 91010 broad.mit.edu 37 12 50050953 50050953 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:50050953C>T ENST00000293590.5 - 7 859 c.626G>A c.(625-627)cGc>cAc p.R209H FMNL3_ENST00000352151.5_Missense_Mutation_p.R158H|FMNL3_ENST00000335154.5_Missense_Mutation_p.R209H|FMNL3_ENST00000550488.1_Missense_Mutation_p.R209H Q8IVF7 FMNL3_HUMAN formin-like 3 39 CAGGGCCCTGCGCCCAGGGAG 0.582000 0 SO:0001583 missense ENST00000293590.5 1 1 hg19 . . . . . . . . . . C 35 5.423799 0.96111 0.0 2.39E-4 ENSG00000161791 ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590 D;D;D;D 0.81821 -1.51;-1.5;-1.54;-1.5 5.45 5.45 0.79879 . 0.052637 0.64402 D 0.000001 D 0.89832 0.6829 M 0.77616 2.38 0.49915 D 0.999834 D;D 0.76494 0.999;0.994 D;P 0.80764 0.994;0.754 D 0.89710 0.3911 10 0.52906 T 0.07 . 18.4343 0.90638 0.0:1.0:0.0:0.0 . 158;209 Q8IVF7-2;Q8IVF7-3 .;. H 209;209;158;209 ENSP00000335655:R209H;ENSP00000447479:R209H;ENSP00000344311:R158H;ENSP00000293590:R209H ENSP00000293590:R209H R - 2 0 FMNL3 48337220 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 4.865000 0.62998 2.744000 0.94065 0.561000 0.74099 CGC TCGA-IB-A6UG-01A-32D-A33T-08 FMNL3-201 KNOWN basic protein_coding protein_coding 1 0 1 81 382 0 89 0 6.474576e-01 0 12 0 89 2 0 0 0 0 0 2 1 1.000000 81 382 0 88 2 0 0 0 0 89 2 -3.361336 1 1 120964 10 41 1 1 2 3 1.998772 0 0.220000 3.280000 0.273540 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 NACA 4666 broad.mit.edu 37 12 57108169 57108169 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr12:57108169G>A ENST00000454682.1 - 5 6081 c.5800C>T c.(5800-5802)Cgg>Tgg p.R1934W NACA_ENST00000356769.3_Missense_Mutation_p.R71W|NACA_ENST00000550952.1_Missense_Mutation_p.R781W|NACA_ENST00000552540.1_Missense_Mutation_p.R71W|NACA_ENST00000393891.4_Missense_Mutation_p.R71W|NACA_ENST00000551793.1_5'UTR|NACA_ENST00000546392.1_Missense_Mutation_p.R71W|NACA_ENST00000548563.1_5'UTR NM_001113203.2 NP_001106674.2 E9PAV3 NACAM_HUMAN nascent polypeptide-associated complex alpha subunit 10 TTTTCACTCCGACTCTGTTTT 0.388000 T BCL6 NHL Dom yes 12 12q23-q24.1 4666 nascent-polypeptide-associated complex alpha polypeptide L 0 SO:0001583 missense ENST00000454682.1 1 1 hg19 . . . . . . . . . . G 14.69 2.611275 0.46631 . . ENSG00000196531 ENST00000550920;ENST00000454682;ENST00000550952;ENST00000356769;ENST00000552540;ENST00000393891;ENST00000546392;ENST00000549259;ENST00000552055;ENST00000549855 T;T;T;T;T;T;T;T;T;T 0.67345 0.14;-0.1;-0.26;0.16;0.16;0.16;0.16;0.18;0.0;0.03 4.73 3.82 0.43975 Nascent polypeptide-associated complex NAC (1); 0.000000 0.85682 D 0.000000 D 0.83175 0.5197 H 0.95151 3.63 0.53688 D 0.999979 P;D;B 0.59767 0.946;0.986;0.008 P;P;B 0.57960 0.523;0.83;0.002 D 0.86446 0.1770 10 0.87932 D 0 . 11.0665 0.47979 0.0:0.0:0.663:0.337 . 1934;781;71 E9PAV3;F8VU71;Q13765 .;.;NACA_HUMAN W 69;1934;781;71;71;71;71;71;67;71 ENSP00000448039:R69W;ENSP00000403817:R1934W;ENSP00000448035:R781W;ENSP00000349212:R71W;ENSP00000447821:R71W;ENSP00000377469:R71W;ENSP00000446801:R71W;ENSP00000447133:R71W;ENSP00000450383:R67W;ENSP00000447764:R71W ENSP00000349212:R71W R - 1 2 NACA 55394436 1.000000 0.71417 1.000000 0.80357 0.952000 0.60782 2.742000 0.47434 0.938000 0.37419 0.460000 0.39030 CGG TCGA-IB-A6UG-01A-32D-A33T-08 NACA-201 KNOWN basic protein_coding protein_coding 1 0 0 25 280 0 51 1 1 269 2777 0 51 2 0 0 0 0 0 2 1 1.000000 24 275 0 51 2 0 0 0 0 51 2 -8.276200 1 1 0 0 1 1 2 3 1.998772 0 0.220000 3.280000 0.273540 0.860000 0.550000 1.000000 1.000000 0.849322 0.860000 1 6.800000e-01 1 ZIC5 85416 broad.mit.edu 37 13 100617645 100617645 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a 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 18.14 3.556755 0.65425 . . ENSG00000139800 ENST00000267294 T 0.18016 2.24 6.06 5.14 0.70334 . . . . . T 0.29321 0.0730 L 0.36672 1.1 0.35097 D 0.764889 D 0.89917 1.0 D 0.69654 0.965 T 0.18335 -1.0340 9 0.87932 D 0 . 11.1163 0.48262 0.0:0.0:0.7346:0.2654 . 660 Q96T25 ZIC5_HUMAN W 660 ENSP00000267294:R660W ENSP00000267294:R660W R - 1 2 ZIC5 99415646 0.998000 0.40836 0.997000 0.53966 0.991000 0.79684 2.915000 0.48805 2.871000 0.98454 0.655000 0.94253 CGG TCGA-IB-A6UG-01A-32D-A33T-08 ZIC5-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000045623.3 0 0 0 5 589 0 113 0 1.180399e-04 0 2 0 113 2 0 0 0 0 0 2 1 0.936664 5 585 0 112 2 0 0 0 0 113 2 -2.199264 0 1 121412 10 40 1 0 3 3 1.939135 1 0.220000 3.280000 0.297297 0.090000 0.020000 0.190000 0.090000 0.101150 0.090000 0 5.000000e-02 1.400000e-01 PDS5B 23047 broad.mit.edu 37 13 33258137 33258137 + Nonsense_Mutation SNP A A T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr13:33258137A>T ENST00000315596.10 + 11 1366 c.1180A>T c.(1180-1182)Aga>Tga p.R394* NM_015032.3 NP_055847.1 Q9NTI5 PDS5B_HUMAN PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae) p.R394*(2) 62 Lung SC(185;0.0367) TAATTTTGTGAGAGAGAGAAC 0.274000 2 Substitution - Nonsense(2) SO:0001587 stop_gained ENST00000315596.10 0 1 hg19 CCDS41878.1 . . . . . . . . . . A 36 5.852697 0.97030 . . ENSG00000083642 ENST00000315596;ENST00000421084 . . . 5.11 5.11 0.69529 . 0.045487 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.15066 T 0.55 -3.1156 11.2434 0.48982 0.847:0.153:0.0:0.0 . . . . X 394 . ENSP00000313851:R394X R + 1 2 PDS5B 32156137 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.075000 0.50073 2.064000 0.61679 0.482000 0.46254 AGA TCGA-IB-A6UG-01A-32D-A33T-08 PDS5B-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044428.3 0 0 0 5 453 0 96 0 1.793165e-02 0 15 0 96 2 0 0 0 0 0 2 1 0.935675 5 447 0 96 2 0 0 0 0 96 2 -2.167235 0 1 120772 1 23 1 0 3 3 1.939135 1 0.220000 3.280000 0.297297 0.110000 0.030000 0.240000 0.120000 0.130938 0.110000 0 7.000000e-02 1.800000e-01 DIO3 1735 broad.mit.edu 37 14 102028612 102028612 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr14:102028612G>A ENST00000510508.4 + 1 925 c.779G>A c.(778-780)cGt>cAt p.R260H DIO3_ENST00000359323.3_Missense_Mutation_p.R234H|DIO3OS_ENST00000408206.1_lincRNA P55073 IOD3_HUMAN deiodinase, iodothyronine, type III 22 all_neural(303;0.185) TACTTCGAGCGTCTCTATGTC 0.617000 0 SO:0001583 missense ENST00000510508.4 1 1 hg19 CCDS41992.2 . . . . . . . . . . G 28.2 4.902680 0.92035 . . ENSG00000197406;ENSG00000258865 ENST00000359323;ENST00000510508 T;T 0.51325 0.71;0.71 3.86 3.86 0.44501 . 0.000000 0.64402 U 0.000011 T 0.74869 0.3773 M 0.92970 3.365 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.82833 -0.0262 10 0.87932 D 0 . 14.9928 0.71401 0.0:0.0:1.0:0.0 . 234 P55073 IOD3_HUMAN H 234;260 ENSP00000352273:R234H;ENSP00000427336:R260H ENSP00000352273:R260H R + 2 0 DIO3;AL049836.1 101098365 1.000000 0.71417 1.000000 0.80357 0.939000 0.58152 9.515000 0.98015 1.998000 0.58463 0.462000 0.41574 CGT TCGA-IB-A6UG-01A-32D-A33T-08 DIO3-001 KNOWN upstream_ATG|basic|appris_principal|CCDS|seleno protein_coding protein_coding OTTHUMT00000361712.4 0 0 0 42 413 0 89 0 9.039397e-03 0 2 0 89 2 0 0 0 0 0 2 1 1.000000 42 409 0 88 2 0 0 0 0 89 2 -20.000000 1 1 121040 1 27 1 2 2 4 2.102850 1 0.220000 3.280000 0.351297 0.990000 0.740000 1.000000 1.000000 0.955370 0.990000 1 8.700000e-01 1 RPL10L 140801 broad.mit.edu 37 14 47120810 47120810 + Missense_Mutation SNP C C A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr14:47120810C>A ENST00000298283.3 - 1 218 c.130G>T c.(130-132)Gat>Tat p.D44Y NM_080746.2 NP_542784.1 Q96L21 RL10L_HUMAN ribosomal protein L10-like 27 GGGAACTCATCCACTTTTGCC 0.502000 0 SO:0001583 missense ENST00000298283.3 1 1 hg19 CCDS32071.1 . . . . . . . . . . C 19.18 3.777196 0.70107 . . ENSG00000165496 ENST00000298283 T 0.74209 -0.82 4.32 4.32 0.51571 Ribosomal protein L10e/L16 (2); 0.000000 0.85682 D 0.000000 D 0.91123 0.7205 H 0.98629 4.285 0.80722 D 1 D 0.69078 0.997 D 0.72625 0.978 D 0.94002 0.7276 10 0.87932 D 0 -39.9655 15.1202 0.72438 0.0:1.0:0.0:0.0 . 44 Q96L21 RL10L_HUMAN Y 44 ENSP00000298283:D44Y ENSP00000298283:D44Y D - 1 0 RPL10L 46190560 1.000000 0.71417 0.997000 0.53966 0.495000 0.33615 7.003000 0.76310 2.688000 0.91661 0.655000 0.94253 GAT TCGA-IB-A6UG-01A-32D-A33T-08 RPL10L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349819.1 1 0 1 92 477 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 1.000000 89 473 0 104 2 0 0 0 0 104 2 -20.000000 1 1 0 0 1 2 2 4 2.102850 1 0.220000 3.280000 0.351297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 MAX 4149 broad.mit.edu 37 14 65560458 65560458 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr14:65560458G>A ENST00000358664.4 - 3 269 c.139C>T c.(139-141)Cgg>Tgg p.R47W MAX_ENST00000556979.1_Missense_Mutation_p.R47W|RP11-840I19.3_ENST00000553633.1_RNA|RP11-840I19.3_ENST00000555261.1_RNA|MAX_ENST00000358402.4_Missense_Mutation_p.R38W|MAX_ENST00000556443.1_Missense_Mutation_p.R38W|MAX_ENST00000555932.1_Intron|RP11-840I19.3_ENST00000556127.1_RNA|MAX_ENST00000246163.2_Missense_Mutation_p.R47W|MAX_ENST00000557277.1_5'UTR|RP11-840I19.3_ENST00000555898.1_RNA|MAX_ENST00000555419.1_Intron|MAX_ENST00000284165.6_Missense_Mutation_p.R47W|MAX_ENST00000555667.1_Missense_Mutation_p.R38W|MAX_ENST00000557746.1_Missense_Mutation_p.R38W|MAX_ENST00000341653.2_Missense_Mutation_p.R47W NM_002382.4 NP_002373.3 P61244 MAX_HUMAN MYC associated factor X 17 ACTGAGTCCCGCAAACTGTGA 0.483000 0 SO:0001583 missense ENST00000358664.4 0 1 hg19 CCDS9771.1 . . . . . . . . . . G 24.2 4.499453 0.85069 . . ENSG00000125952 ENST00000341653;ENST00000358402;ENST00000284165;ENST00000358664;ENST00000441116;ENST00000556979;ENST00000555667;ENST00000557746;ENST00000556443;ENST00000246163 D;D;D;D;D;D;D;D;D 0.98762 -5.12;-5.12;-5.12;-5.12;-5.12;-5.12;-5.12;-5.12;-5.12 5.93 5.93 0.95920 Helix-loop-helix DNA-binding (5); 0.000000 0.85682 D 0.000000 D 0.99453 0.9806 H 0.97390 3.995 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.998;1.0;0.997;0.998;0.999;0.998;0.999 D 0.98397 1.0566 10 0.87932 D 0 -5.0518 14.004 0.64451 0.0:0.0:0.8485:0.1515 . 47;47;38;38;47;47;47 Q96CY8;Q14803;Q6V3B1;P61244-2;P61244;P61244-3;A6NH73 .;.;.;.;MAX_HUMAN;.;. W 47;38;47;47;54;47;38;38;38;47 ENSP00000342482:R47W;ENSP00000351175:R38W;ENSP00000284165:R47W;ENSP00000351490:R47W;ENSP00000452378:R47W;ENSP00000452286:R38W;ENSP00000452197:R38W;ENSP00000450818:R38W;ENSP00000246163:R47W ENSP00000246163:R47W R - 1 2 MAX 64630211 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.132000 0.71676 2.814000 0.96858 0.563000 0.77884 CGG TCGA-IB-A6UG-01A-32D-A33T-08 MAX-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286386.1 0 0 0 5 357 0 63 0 5.284117e-01 0 114 0 63 2 0 0 0 0 0 2 1 0.936120 5 353 0 63 2 0 0 0 0 63 2 -2.047474 0 1 0 0 1 2 2 4 2.102850 1 0.220000 3.280000 0.351297 0.170000 0.050000 1.000000 0.150000 0.232067 0.170000 0 1.000000e-01 2.800000e-01 TRPM1 4308 broad.mit.edu 37 15 31319127 31319127 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr15:31319127G>A ENST00000256552.6 - 26 3634 c.3487C>T c.(3487-3489)Cgt>Tgt p.R1163C RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000397795.2_Missense_Mutation_p.R1141C|TRPM1_ENST00000542188.1_Missense_Mutation_p.R1180C|RP11-348B17.1_ENST00000561299.1_RNA NM_001252024.1 NP_001238953.1 transient receptor potential cation channel, subfamily M, member 1 99 all_lung(180;1.92e-11) CTCAATCCACGATCCCGTTCC 0.463000 0 SO:0001583 missense ENST00000256552.6 1 1 hg19 CCDS58346.1 . . . . . . . . . . G 18.55 3.648605 0.67358 . . ENSG00000134160 ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793 T;T;T 0.36878 1.23;1.23;1.23 5.79 5.79 0.91817 . 0.110302 0.64402 D 0.000012 T 0.43656 0.1257 L 0.47716 1.5 0.52501 D 0.999952 P;P 0.47962 0.903;0.843 P;P 0.51229 0.663;0.462 T 0.18461 -1.0336 10 0.48119 T 0.1 -12.7835 13.9482 0.64099 0.0:0.0:0.7473:0.2527 . 1135;1141 Q7Z4N2-3;Q7Z4N2 .;TRPM1_HUMAN C 1141;1180;1163;1141 ENSP00000380897:R1141C;ENSP00000437849:R1180C;ENSP00000256552:R1163C ENSP00000256552:R1163C R - 1 0 TRPM1 29106419 0.999000 0.42202 0.962000 0.40283 0.942000 0.58702 2.188000 0.42612 2.736000 0.93811 0.655000 0.94253 CGT TCGA-IB-A6UG-01A-32D-A33T-08 TRPM1-004 PUTATIVE basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000417166.2 1 0 0 42 429 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 41 425 0 68 2 0 0 0 0 70 2 -3.318794 1 1 120844 8 41 1 1 2 3 1.965361 0 0.220000 3.280000 0.297297 0.900000 0.660000 1.000000 1.000000 0.891153 0.900000 1 7.700000e-01 1 RYR3 6263 broad.mit.edu 37 15 33822869 33822869 + Splice_Site SNP T T C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr15:33822869T>C ENST00000389232.4 + 4 424 c.e4+2 RYR3_ENST00000415757.3_Splice_Site NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 311 all_lung(180;7.18e-09) AGCGGAATGGTAAGCAGCTCT 0.498000 0 SO:0001630 splice_region_variant ENST00000389232.4 0 1 hg19 CCDS45210.1 . . . . . . . . . . T 26.1 4.703043 0.88924 . . ENSG00000198838 ENST00000389232;ENST00000415757;ENST00000361728 . . . 5.76 5.76 0.90799 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.0668 0.72002 0.0:0.0:0.0:1.0 . . . . . -1 . . . + . . RYR3 31610161 1.000000 0.71417 1.000000 0.80357 0.953000 0.61014 7.637000 0.83313 2.191000 0.70037 0.533000 0.62120 . TCGA-IB-A6UG-01A-32D-A33T-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 1 0 0 5 128 0 26 0 0 0 0 26 2 0 0 0 0 0 2 1 0.938752 5 128 0 26 2 0 0 0 0 26 2 -7.910571 1 1 0 0 1 1 2 3 1.965361 0 0.220000 3.280000 0.297297 0.410000 0.150000 0.800000 0.370000 0.440040 0.410000 0 2.600000e-01 6.000000e-01 ISLR2 57611 broad.mit.edu 37 15 74426584 74426584 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr15:74426584G>A ENST00000361742.3 + 4 2258 c.1489G>A c.(1489-1491)Gag>Aag p.E497K ISLR2_ENST00000453268.2_Missense_Mutation_p.E497K|ISLR2_ENST00000565540.1_Missense_Mutation_p.E497K|ISLR2_ENST00000435464.1_Missense_Mutation_p.E497K|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000419208.1_Missense_Mutation_p.E497K|ISLR2_ENST00000565159.1_Missense_Mutation_p.E497K|ISLR2_ENST00000445793.1_Missense_Mutation_p.E497K NM_001130136.1|NM_020851.2 NP_001123608.1|NP_065902.1 Q6UXK2 ISLR2_HUMAN immunoglobulin superfamily containing leucine-rich repeat 2 36 GGCGGAGCGCGAGGCGCGGGT 0.731000 0 SO:0001583 missense ENST00000361742.3 0 1 hg19 CCDS10259.1 . . . . . . . . . . G 21.0 4.082884 0.76642 . . ENSG00000167178 ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000419208 T;T;T;T;T 0.59083 0.29;0.29;0.29;0.29;0.29 4.83 4.83 0.62350 . 0.000000 0.85682 D 0.000000 T 0.41351 0.1155 L 0.27053 0.805 0.58432 D 0.999995 P 0.48407 0.91 B 0.32805 0.153 T 0.51787 -0.8661 10 0.56958 D 0.05 . 16.6691 0.85261 0.0:0.0:1.0:0.0 . 497 Q6UXK2 ISLR2_HUMAN K 497 ENSP00000403244:E497K;ENSP00000355402:E497K;ENSP00000411443:E497K;ENSP00000411834:E497K;ENSP00000408872:E497K ENSP00000355402:E497K E + 1 0 ISLR2 72213637 1.000000 0.71417 1.000000 0.80357 0.940000 0.58332 6.347000 0.73004 2.223000 0.72356 0.313000 0.20887 GAG TCGA-IB-A6UG-01A-32D-A33T-08 ISLR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269046.1 1 0 0 16 33 0 11 0 0 0 0 11 2 0 0 0 0 0 2 1 0.999980 16 33 0 11 2 0 0 0 0 11 2 -20.000000 1 1 0 0 1 1 2 3 1.952518 0 0.220000 3.280000 0.297297 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 LMAN1L 79748 broad.mit.edu 37 15 75115914 75115914 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr15:75115914G>A ENST00000309664.5 + 12 1353 c.1214G>A c.(1213-1215)cGc>cAc p.R405H LMAN1L_ENST00000379709.3_Missense_Mutation_p.R393H|RP11-414J4.2_ENST00000564823.1_RNA|CPLX3_ENST00000395018.4_5'Flank NM_021819.2 NP_068591.2 Q9HAT1 LMA1L_HUMAN lectin, mannose-binding, 1 like 19 GCAGCTGTCCGCATGGCTGCA 0.557000 0 SO:0001583 missense ENST00000309664.5 0 1 hg19 CCDS10270.1 . . . . . . . . . . G 7.607 0.673992 0.14841 . . ENSG00000140506 ENST00000309664;ENST00000379709 T;T 0.39406 1.11;1.08 5.18 -5.19 0.02832 . 1.400440 0.04515 N 0.383606 T 0.25158 0.0611 N 0.22421 0.69 0.25604 N 0.986564 B;B 0.14012 0.009;0.005 B;B 0.09377 0.004;0.002 T 0.18493 -1.0335 10 0.33940 T 0.23 . 6.2762 0.20981 0.2272:0.0:0.5161:0.2567 . 393;405 Q9HAT1-3;Q9HAT1 .;LMA1L_HUMAN H 405;393 ENSP00000310431:R405H;ENSP00000369031:R393H ENSP00000310431:R405H R + 2 0 LMAN1L 72902967 0.000000 0.05858 0.052000 0.19188 0.262000 0.26303 -0.908000 0.04063 -0.806000 0.04398 0.561000 0.74099 CGC TCGA-IB-A6UG-01A-32D-A33T-08 LMAN1L-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286397.4 0 0 0 5 374 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.935285 5 368 0 61 2 0 0 0 0 61 2 -3.068703 1 1 121412 14 42 1 1 2 3 1.952518 0 0.220000 3.280000 0.297297 0.140000 0.040000 0.290000 0.130000 0.157920 0.140000 0 8.000000e-02 2.200000e-01 ACAN 176 broad.mit.edu 37 15 89388927 89388927 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr15:89388927G>A ENST00000561243.1 + 6 1243 c.1243G>A c.(1243-1245)Gag>Aag p.E415K ACAN_ENST00000559004.1_Missense_Mutation_p.E415K|ACAN_ENST00000558207.1_Missense_Mutation_p.E415K|ACAN_ENST00000352105.7_Missense_Mutation_p.E415K|ACAN_ENST00000439576.2_Missense_Mutation_p.E415K P16112 PGCA_HUMAN aggrecan 93 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) CCTGGAACCCGAGGAGCCCTT 0.612000 0 SO:0001583 missense ENST00000561243.1 1 1 hg19 CCDS53970.1 . . . . . . . . . . G 12.68 2.010026 0.35415 . . ENSG00000157766 ENST00000439576;ENST00000352105;ENST00000268134 T;T 0.02236 4.62;4.38 5.52 3.57 0.40892 . . . . . T 0.02494 0.0076 M 0.68952 2.095 0.09310 N 0.999998 P;P;P 0.43352 0.804;0.804;0.477 B;B;B 0.33392 0.124;0.163;0.032 T 0.38672 -0.9650 9 0.14252 T 0.57 -5.9214 6.9498 0.24538 0.0925:0.1781:0.7295:0.0 . 415;415;415 E7ENV9;E7EX88;Q6PID9 .;.;. K 415 ENSP00000387356:E415K;ENSP00000341615:E415K ENSP00000268134:E415K E + 1 0 ACAN 87189931 0.576000 0.26700 0.684000 0.30055 0.329000 0.28539 1.208000 0.32345 1.410000 0.46936 0.591000 0.81541 GAG TCGA-IB-A6UG-01A-32D-A33T-08 ACAN-006 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416267.2 1 0 0 21 198 0 42 0 0 0 1 0 42 2 0 0 0 0 0 2 1 0.999998 21 196 0 40 2 0 0 0 0 42 2 -3.017773 1 1 121126 2 36 1 1 2 3 1.952518 0 0.220000 3.280000 0.297297 0.970000 0.630000 1.000000 1.000000 0.916758 0.970000 1 7.800000e-01 1 ZC3H7A 29066 broad.mit.edu 37 16 11859420 11859420 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr16:11859420G>A ENST00000396516.2 - 13 1841 c.1644C>T c.(1642-1644)ggC>ggT p.G548G ZC3H7A_ENST00000355758.4_Silent_p.G548G Q8IWR0 Z3H7A_HUMAN zinc finger CCCH-type containing 7A 25 TTCCATTGCCGCCAAAGAAAG 0.453000 0 SO:0001819 synonymous_variant ENST00000396516.2 0 1 hg19 CCDS10550.1 TCGA-IB-A6UG-01A-32D-A33T-08 ZC3H7A-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437066.1 0 0 0 5 503 1 71 0 1.979483e-03 0 61 1 71 5 0 0 0 0 0 2 0 0.000601 5 499 1 71 22 0 0 0 1 71 2 -2.258984 0 1 121412 1 34 1 1 2 3 1.970767 0 0.220000 3.280000 0.297297 0.100000 0.030000 0.220000 0.090000 0.118155 0.100000 0 6.000000e-02 1.600000e-01 IRX6 79190 broad.mit.edu 37 16 55361532 55361532 + Nonsense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr16:55361532C>T ENST00000290552.7 + 4 1780 c.448C>T c.(448-450)Cga>Tga p.R150* IRX6_ENST00000558315.1_3'UTR|RP11-26L20.3_ENST00000558730.2_RNA NM_024335.2 NP_077311.2 P78412 IRX6_HUMAN iroquois homeobox 6 33 CGCCGGTCGCCGAAAGAACGC 0.577000 0 SO:0001587 stop_gained ENST00000290552.7 0 1 hg19 CCDS32449.1 . . . . . . . . . . C 47 13.157336 0.99723 . . ENSG00000159387 ENST00000290552 . . . 6.08 -6.48 0.01896 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -23.7892 21.412 0.99953 0.7449:0.2551:0.0:0.0 . . . . X 150 . ENSP00000290552:R150X R + 1 2 IRX6 53919033 0.747000 0.28283 0.913000 0.36048 0.165000 0.22458 1.262000 0.32992 -1.091000 0.03065 -0.989000 0.02550 CGA TCGA-IB-A6UG-01A-32D-A33T-08 IRX6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417445.4 1 0 0 12 166 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 0.999163 12 164 0 30 2 0 0 0 0 31 2 -15.938870 1 1 121412 2 31 1 1 2 3 1.953366 0 0.220000 3.280000 0.297297 0.690000 0.380000 1.000000 1.000000 0.710069 0.690000 0 5.200000e-01 9.000000e-01 SETD6 79918 broad.mit.edu 37 16 58550831 58550831 + Splice_Site SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr16:58550831C>T ENST00000219315.4 + 5 841 c.791C>T c.(790-792)gCg>gTg p.A264V SETD6_ENST00000394266.4_Splice_Site_p.A195V|SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000310682.2_Splice_Site_p.A240V Q8TBK2 SETD6_HUMAN SET domain containing 6 7 GAATACTCTGCGGTGAGTGGA 0.463000 0 SO:0001630 splice_region_variant ENST00000219315.4 0 1 hg19 CCDS54013.1 . . . . . . . . . . C 17.07 3.295317 0.60086 . . ENSG00000103037 ENST00000310682;ENST00000394266;ENST00000219315 T;T;T 0.14022 2.54;2.54;2.54 5.42 4.46 0.54185 SET domain (2); 0.231004 0.44097 D 0.000482 T 0.11965 0.0291 L 0.48642 1.525 0.36533 D 0.870835 P;P;P 0.42039 0.563;0.769;0.558 B;B;B 0.32724 0.039;0.151;0.023 T 0.17137 -1.0379 10 0.35671 T 0.21 -2.8694 14.3423 0.66636 0.1576:0.8424:0.0:0.0 . 240;264;240 E9PC53;Q8TBK2;Q8TBK2-2 .;SETD6_HUMAN;. V 240;195;264 ENSP00000310082:A240V;ENSP00000377809:A195V;ENSP00000219315:A264V ENSP00000219315:A264V A + 2 0 SETD6 57108332 0.966000 0.33281 0.999000 0.59377 0.365000 0.29674 2.801000 0.47908 1.237000 0.43756 0.491000 0.48974 GCG TCGA-IB-A6UG-01A-32D-A33T-08 SETD6-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000317274.2 0 0 0 5 642 0 148 0 7.028587e-02 0 45 0 148 2 0 0 0 0 0 2 1 0.937246 5 640 0 147 2 0 0 0 0 148 2 -2.103654 0 1 0 0 1 1 2 3 1.953366 0 0.220000 3.280000 0.297297 0.080000 0.020000 0.170000 0.090000 0.092888 0.080000 0 4.000000e-02 1.300000e-01 GLG1 2734 broad.mit.edu 37 16 74527016 74527016 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr16:74527016C>T ENST00000422840.2 - 7 1072 c.1073G>A c.(1072-1074)cGc>cAc p.R358H GLG1_ENST00000205061.5_Missense_Mutation_p.R358H|GLG1_ENST00000447066.2_Missense_Mutation_p.R347H NM_001145667.1 NP_001139139.1 Q92896 GSLG1_HUMAN golgi glycoprotein 1 57 CAGCTTTTGGCGGGTTGTAAG 0.443000 0 SO:0001583 missense ENST00000422840.2 0 1 hg19 CCDS45527.1 . . . . . . . . . . C 35 5.459970 0.96240 . . ENSG00000090863 ENST00000205061;ENST00000447066;ENST00000422840 . . . 5.52 5.52 0.82312 . 0.000000 0.85682 D 0.000000 D 0.82706 0.5095 M 0.76170 2.325 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.999;1.0 D 0.83731 0.0198 9 0.72032 D 0.01 -3.7566 19.793 0.96468 0.0:1.0:0.0:0.0 . 358;358;347 Q92896;Q92896-2;B7Z8Y4 GSLG1_HUMAN;.;. H 358;347;358 . ENSP00000205061:R358H R - 2 0 GLG1 73084517 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 7.564000 0.82326 2.744000 0.94065 0.655000 0.94253 CGC TCGA-IB-A6UG-01A-32D-A33T-08 GLG1-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000435750.1 0 0 0 6 482 0 85 0 2.739205e-01 0 72 0 85 2 0 0 0 0 0 2 1 0.963582 6 475 0 85 2 0 0 0 0 85 2 -1.829765 0 1 0 0 1 1 2 3 1.964395 0 0.220000 3.280000 0.297297 0.130000 0.040000 0.260000 0.120000 0.143460 0.130000 0 8.000000e-02 1.900000e-01 CDH15 1013 broad.mit.edu 37 16 89251637 89251637 + Missense_Mutation SNP G G C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr16:89251637G>C ENST00000289746.2 + 5 624 c.559G>C c.(559-561)Gca>Cca p.A187P NM_004933.2 NP_004924.1 P55291 CAD15_HUMAN cadherin 15, type 1, M-cadherin (myotubule) 18 GACGGACAACGCAGCGCTGCG 0.662000 0 SO:0001583 missense ENST00000289746.2 1 1 hg19 CCDS10976.1 . . . . . . . . . . G 21.1 4.090995 0.76756 . . ENSG00000129910 ENST00000289746 T 0.54675 0.56 4.76 4.76 0.60689 Cadherin (4);Cadherin-like (1); 0.000000 0.52532 D 0.000065 T 0.80722 0.4677 H 0.95294 3.65 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.86687 0.1920 10 0.59425 D 0.04 . 16.5411 0.84385 0.0:0.0:1.0:0.0 . 187 P55291 CAD15_HUMAN P 187 ENSP00000289746:A187P ENSP00000289746:A187P A + 1 0 CDH15 87779138 1.000000 0.71417 0.840000 0.33206 0.279000 0.26890 9.248000 0.95456 2.187000 0.69744 0.462000 0.41574 GCA TCGA-IB-A6UG-01A-32D-A33T-08 CDH15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269920.1 1 0 1 16 74 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 0.999962 16 74 0 15 2 0 0 0 0 15 2 -20.000000 1 1 0 0 1 1 2 3 1.964395 0 0.220000 3.280000 0.297297 0.990000 0.990000 1.000000 1.000000 0.999126 0.990000 1 9.900000e-01 1 TTC19 54902 broad.mit.edu 37 17 15903527 15903527 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr17:15903527G>A ENST00000261647.5 + 2 749 c.280G>A c.(280-282)Gca>Aca p.A94T TTC19_ENST00000486880.2_Missense_Mutation_p.A215T|ZSWIM7_ENST00000472495.1_5'Flank|ZSWIM7_ENST00000399277.1_5'Flank|ZSWIM7_ENST00000399280.2_5'Flank|ZSWIM7_ENST00000486655.1_5'Flank|TTC19_ENST00000497842.2_3'UTR NM_001271420.1|NM_017775.3 NP_001258349.1|NP_060245.3 Q6DKK2 TTC19_HUMAN tetratricopeptide repeat domain 19 5 CGAGGCCGAGGCAGAGATCAT 0.731000 0 SO:0001583 missense ENST00000261647.5 0 1 hg19 CCDS11174.2 . . . . . . . . . . G 11.61 1.688773 0.29962 . . ENSG00000011295 ENST00000261647;ENST00000555605;ENST00000395886 D 0.83419 -1.72 5.06 4.02 0.46733 . 0.498025 0.19407 N 0.115021 T 0.74313 0.3700 L 0.28115 0.83 0.26820 N 0.968808 . . . . . . T 0.62210 -0.6902 8 0.14656 T 0.56 -9.3213 12.296 0.54847 0.0:0.1872:0.8128:0.0 . . . . T 94;215;94 ENSP00000261647:A94T ENSP00000261647:A215T A + 1 0 TTC19 15844252 1.000000 0.71417 0.999000 0.59377 0.372000 0.29890 2.821000 0.48065 2.355000 0.79922 0.549000 0.68633 GCA TCGA-IB-A6UG-01A-32D-A33T-08 TTC19-001 NOVEL upstream_ATG|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000131725.6 1 0 0 18 107 0 15 1 9.771074e-01 9 31 0 15 2 0 0 0 0 0 2 1 0.999986 17 105 0 15 2 0 0 0 0 15 2 -20.000000 1 1 0 0 1 0 2 2 1.799994 1 0.220000 3.280000 0.220000 0.990000 0.810000 1.000000 1.000000 0.987035 0.990000 1 9.900000e-01 1 FBXW10 10517 broad.mit.edu 37 17 18671872 18671872 + Missense_Mutation SNP T T C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr17:18671872T>C ENST00000395665.4 + 10 1951 c.1730T>C c.(1729-1731)gTg>gCg p.V577A FBXW10_ENST00000308799.4_Missense_Mutation_p.V606A|FBXW10_ENST00000301938.4_Missense_Mutation_p.V577A|FBXW10_ENST00000395667.1_Missense_Mutation_p.V577A Q5XX13 FBW10_HUMAN F-box and WD repeat domain containing 10 42 GAGGGAGCCGTGAAATGCCTG 0.527000 0 SO:0001583 missense ENST00000395665.4 0 1 hg19 CCDS11199.3 . . . . . . . . . . T 12.96 2.095926 0.36952 . . ENSG00000171931 ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665 T;T;T;T 0.73789 -0.78;-0.78;-0.78;-0.78 2.97 2.97 0.34412 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.081272 0.49305 U 0.000154 D 0.86439 0.5933 M 0.90542 3.125 0.42816 D 0.993975 D;D;D;D 0.89917 0.999;0.998;0.997;1.0 D;D;D;D 0.83275 0.991;0.99;0.992;0.996 D 0.87673 0.2542 10 0.87932 D 0 . 9.3557 0.38164 0.0:0.0:0.0:1.0 . 577;606;577;577 Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4 .;.;FBW10_HUMAN;. A 577;606;577;577 ENSP00000379026:V577A;ENSP00000310382:V606A;ENSP00000306937:V577A;ENSP00000379025:V577A ENSP00000306937:V577A V + 2 0 FBXW10 18612597 1.000000 0.71417 0.971000 0.41717 0.150000 0.21749 6.656000 0.74396 1.356000 0.45884 0.163000 0.16589 GTG TCGA-IB-A6UG-01A-32D-A33T-08 FBXW10-003 KNOWN NAGNAG_splice_site|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000313531.2 0 0 0 5 292 0 40 0 0 0 1 0 40 2 0 0 0 0 0 2 1 0.935813 5 288 0 40 2 0 0 0 0 40 2 -3.274253 1 1 0 0 1 1 2 3 1.986990 0 0.220000 3.280000 0.297297 0.180000 0.060000 0.370000 0.180000 0.200883 0.180000 0 1.100000e-01 2.800000e-01 KCNJ12 3768 broad.mit.edu 37 17 21319100 21319100 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr17:21319100G>A ENST00000583088.1 + 3 1341 c.446G>A c.(445-447)cGc>cAc p.R149H KCNJ12_ENST00000331718.5_Missense_Mutation_p.R149H NM_021012.4 NP_066292.2 Q14500 KCJ12_HUMAN potassium inwardly-rectifying channel, subfamily J, member 12 70 Dofetilide(DB00204)|Yohimbine(DB01392) TACGGGCTGCGCTGTGTGACG 0.642000 Prostate(3;0.18) 0 SO:0001583 missense ENST00000583088.1 1 1 hg19 CCDS11219.1 . . . . . . . . . . G 29.4 4.998856 0.93227 . . ENSG00000184185 ENST00000331718 D 0.97016 -4.21 5.32 5.32 0.75619 Potassium channel, inwardly rectifying, Kir, conserved region 2 (2); 0.000000 0.85682 D 0.000000 D 0.98735 0.9575 H 0.94808 3.585 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.99663 1.0994 10 0.87932 D 0 . 18.9979 0.92821 0.0:0.0:1.0:0.0 . 149 Q14500 IRK12_HUMAN H 149 ENSP00000328150:R149H ENSP00000328150:R149H R + 2 0 KCNJ12 21259693 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.690000 0.98676 2.496000 0.84212 0.655000 0.94253 CGC TCGA-IB-A6UG-01A-32D-A33T-08 KCNJ12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255060.2 0 0 0 16 321 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 0.999930 16 316 0 54 2 0 0 0 0 56 2 -17.287860 1 1 121410 43 40 1 1 2 3 1.999556 0 0.220000 3.280000 0.297297 0.480000 0.280000 0.740000 0.480000 0.502480 0.480000 0 3.700000e-01 6.200000e-01 GIT1 28964 broad.mit.edu 37 17 27908966 27908966 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr17:27908966C>T ENST00000225394.3 - 5 850 c.602G>A c.(601-603)cGc>cAc p.R201H GIT1_ENST00000394869.3_Missense_Mutation_p.R201H|GIT1_ENST00000579937.1_Missense_Mutation_p.R201H|GIT1_ENST00000581348.1_Missense_Mutation_p.R201H|RP11-68I3.2_ENST00000581474.1_RNA NM_014030.3 NP_054749.2 Q9Y2X7 GIT1_HUMAN G protein-coupled receptor kinase interacting ArfGAP 1 9 AATGGGTGTGCGGCCATTAAC 0.627000 Colon(81;41 1719 20078 35068) 0 SO:0001583 missense ENST00000225394.3 0 1 hg19 CCDS11250.1 . . . . . . . . . . C 20.9 4.063141 0.76187 . . ENSG00000108262 ENST00000225394;ENST00000394869 T;T 0.66460 -0.21;-0.21 5.11 5.11 0.69529 Ankyrin repeat-containing domain (4); 0.000000 0.85682 D 0.000000 T 0.63355 0.2504 L 0.45470 1.425 0.51012 D 0.999901 P;P;P;P 0.39250 0.665;0.482;0.538;0.538 B;B;B;B 0.37650 0.255;0.094;0.153;0.108 T 0.67381 -0.5685 10 0.56958 D 0.05 . 18.7075 0.91644 0.0:1.0:0.0:0.0 . 205;201;201;201 Q59FC3;Q9Y2X7-3;B4DGU9;Q9Y2X7 .;.;.;GIT1_HUMAN H 201 ENSP00000225394:R201H;ENSP00000378338:R201H ENSP00000225394:R201H R - 2 0 GIT1 24933092 0.094000 0.21725 1.000000 0.80357 0.999000 0.98932 0.947000 0.29082 2.826000 0.97356 0.655000 0.94253 CGC TCGA-IB-A6UG-01A-32D-A33T-08 GIT1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000256073.1 0 0 0 5 327 0 63 0 2.537132e-01 0 54 0 63 2 0 0 0 0 0 2 1 0.935993 5 323 0 63 2 0 0 0 0 63 2 -2.931837 1 1 121356 4 35 1 1 2 3 1.999556 0 0.220000 3.280000 0.297297 0.160000 0.050000 0.330000 0.150000 0.179983 0.160000 0 1.000000e-01 2.500000e-01 CACNA1G 8913 broad.mit.edu 37 17 48649968 48649968 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr17:48649968G>A ENST00000359106.5 + 6 800 c.800G>A c.(799-801)aGc>aAc p.S267N CACNA1G_ENST00000515411.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000354983.4_Missense_Mutation_p.S267N|CACNA1G_ENST00000507896.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000513689.2_Missense_Mutation_p.S267N|CACNA1G_ENST00000352832.5_Missense_Mutation_p.S267N|CACNA1G_ENST00000515765.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000514717.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000429973.2_Missense_Mutation_p.S267N|CACNA1G_ENST00000507336.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000505165.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000510115.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000514079.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000512389.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000514181.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000507609.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000360761.4_Missense_Mutation_p.S267N|CACNA1G_ENST00000515165.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000416767.4_Missense_Mutation_p.S267N|CACNA1G_ENST00000510366.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000502264.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000507510.2_Missense_Mutation_p.S267N|CACNA1G_ENST00000358244.5_Missense_Mutation_p.S267N|CACNA1G_ENST00000503485.1_Missense_Mutation_p.S267N|CACNA1G_ENST00000442258.2_Missense_Mutation_p.S267N|CACNA1G_ENST00000513964.1_Missense_Mutation_p.S267N NM_018896.4 NP_061496.2 O43497 CAC1G_HUMAN calcium channel, voltage-dependent, T type, alpha 1G subunit 47 Breast(11;6.7e-17) BRCA - Breast invasive adenocarcinoma(22;7.52e-09) Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909) GAGGATGAGAGCCCCTTCATC 0.667000 0 SO:0001583 missense ENST00000359106.5 0 1 hg19 CCDS45730.1 . . . . . . . . . . g 5.134 0.210390 0.09757 . . ENSG00000006283 ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.96522 -3.9;-3.9;-4.04;-3.84;-3.9;-3.91;-3.92;-4.01;-3.98;-3.99;-4.0;-3.87;-3.87;-3.94;-3.89;-3.85;-3.92;-3.89;-3.87;-3.92;-3.91;-3.87;-3.93;-3.87;-3.94;-3.94 5.36 4.37 0.52481 Ion transport (1); 0.547135 0.21976 N 0.066369 D 0.85991 0.5826 N 0.03608 -0.345 0.24066 N 0.995992 B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.06786 0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.001;0.0;0.0;0.0;0.0;0.0 B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.15052 0.008;0.003;0.003;0.003;0.007;0.002;0.012;0.007;0.012;0.006;0.005;0.002;0.001;0.005;0.012;0.002;0.006;0.001;0.003;0.003;0.003;0.003;0.003;0.001;0.001;0.003 T 0.73662 -0.3912 10 0.02654 T 1 . 7.0875 0.25266 0.3255:0.0:0.6745:0.0 . 267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267;267 Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11 .;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;. N 267 ENSP00000353990:S267N;ENSP00000339302:S267N;ENSP00000392390:S267N;ENSP00000347078:S267N;ENSP00000409759:S267N;ENSP00000425522:S267N;ENSP00000426261:S267N;ENSP00000425451:S267N;ENSP00000422407:S267N;ENSP00000426814:S267N;ENSP00000427238:S267N;ENSP00000423112:S267N;ENSP00000420918:S267N;ENSP00000426172:S267N;ENSP00000423045:S267N;ENSP00000427173:S267N;ENSP00000426098:S267N;ENSP00000425698:S267N;ENSP00000426232:S267N;ENSP00000423317:S267N;ENSP00000350979:S267N;ENSP00000352011:S267N;ENSP00000414388:S267N;ENSP00000423155:S267N;ENSP00000422268:S267N;ENSP00000421518:S267N ENSP00000339302:S267N S + 2 0 CACNA1G 46004967 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 2.681000 0.46926 1.156000 0.42514 0.505000 0.49811 AGC TCGA-IB-A6UG-01A-32D-A33T-08 CACNA1G-013 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000367895.1 1 0 0 4 52 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 0.888573 4 51 0 16 2 0 0 0 0 16 2 -8.875416 1 1 0 0 1 1 2 3 2.005240 0 0.220000 3.280000 0.297297 0.770000 0.270000 1.000000 1.000000 0.755070 0.770000 0 4.800000e-01 1 TP53 7157 broad.mit.edu 37 17 7577539 7577539 + Missense_Mutation SNP G G A rs121912651 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr17:7577539G>A ENST00000269305.4 - 7 931 c.742C>T c.(742-744)Cgg>Tgg p.R248W TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W 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.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ATGGGCCTCCGGTTCATGCCG 0.577000 R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE) 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 617 Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2) GRCh37 CM010465|CM900211 TP53 M rs121912651 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 18.84 3.710019 0.68730 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.62 2.56 0.30785 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99843 0.9928 M 0.92507 3.315 0.58432 A 0.999997 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0 D 0.97208 0.9869 9 0.87932 D 0 -9.5643 7.568 0.27890 0.0893:0.0:0.7471:0.1636 . 248;248;155;248;248;248 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. W 248;248;248;248;248;248;237;155;116;155 ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W ENSP00000269305:R248W R - 1 2 TP53 7518264 1.000000 0.71417 1.000000 0.80357 0.910000 0.53928 1.447000 0.35101 0.644000 0.30656 0.462000 0.41574 CGG TCGA-IB-A6UG-01A-32D-A33T-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 37 256 0 70 1 9.999188e-01 50 51 0 70 2 1 1 164 699 0 631 2 1 1.000000 37 253 0 69 2 0 0 0 0 70 2 -2.598876 1 1 121412 1 37 1 0 2 2 1.799994 1 0.220000 3.280000 0.220000 0.990000 0.830000 1.000000 1.000000 0.984300 0.990000 1 9.700000e-01 1 DSC1 1823 broad.mit.edu 37 18 28723623 28723623 + Silent SNP A A T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr18:28723623A>T ENST00000257198.5 - 8 1332 c.1071T>A c.(1069-1071)acT>acA p.T357T DSC1_ENST00000257197.3_Silent_p.T357T|RP11-408H20.2_ENST00000581836.1_RNA NM_024421.2 NP_077739.1 Q08554 DSC1_HUMAN desmocollin 1 53 OV - Ovarian serous cystadenocarcinoma(10;0.00778) TACTCACAGAAGTTTCTGTGA 0.358000 0 SO:0001819 synonymous_variant ENST00000257198.5 1 1 hg19 CCDS11894.1 TCGA-IB-A6UG-01A-32D-A33T-08 DSC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254946.1 1 0 0 18 167 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.999984 17 165 0 46 2 0 0 0 0 46 2 -20.000000 1 1 0 0 1 1 2 3 1.777217 0 0.220000 3.280000 0.228487 0.920000 0.560000 1.000000 1.000000 0.881198 0.920000 1 7.200000e-01 1 NOL4 8715 broad.mit.edu 37 18 31685089 31685089 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr18:31685089C>T ENST00000261592.5 - 3 747 c.450G>A c.(448-450)gcG>gcA p.A150A NOL4_ENST00000269185.4_Silent_p.A36A|NOL4_ENST00000589544.1_Silent_p.A150A|NOL4_ENST00000538587.1_Silent_p.A76A|NOL4_ENST00000535475.1_5'UTR NM_001198546.1|NM_003787.4 NP_001185475.1|NP_003778.2 O94818 NOL4_HUMAN nucleolar protein 4 51 ATCGTGTCACCGCTTCTCTTG 0.393000 0 SO:0001819 synonymous_variant ENST00000261592.5 1 1 hg19 CCDS11907.2 TCGA-IB-A6UG-01A-32D-A33T-08 NOL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255386.1 1 0 0 19 314 0 77 0 0 0 1 0 77 2 0 0 0 0 0 2 1 0.999991 19 311 0 76 2 0 0 0 0 77 2 -2.188533 0 1 121410 3 35 1 1 2 3 1.777217 0 0.220000 3.280000 0.228487 0.540000 0.330000 1.000000 0.520000 0.580098 0.540000 0 4.200000e-01 7.100000e-01 ZNF24 7572 broad.mit.edu 37 18 32920384 32920384 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr18:32920384G>A ENST00000261332.6 - 2 410 c.231C>T c.(229-231)tgC>tgT p.C77C ZNF24_ENST00000399061.3_Silent_p.C77C|ZNF24_ENST00000589881.1_Silent_p.C77C NM_006965.2 NP_008896.2 P17028 ZNF24_HUMAN zinc finger protein 24 15 GCCACAGACGGCAAAGTTCTC 0.537000 Colon(42;769 913 8916 19469 46270) 0 SO:0001819 synonymous_variant ENST00000261332.6 0 1 hg19 CCDS11912.1 TCGA-IB-A6UG-01A-32D-A33T-08 ZNF24-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255769.1 0 0 0 6 654 0 145 0 3.353563e-02 0 26 0 145 2 0 0 0 0 0 2 1 0.963745 6 646 0 143 2 0 0 0 0 145 2 -2.349021 0 1 0 0 1 1 2 3 1.777217 0 0.220000 3.280000 0.228487 0.090000 0.030000 1.000000 0.080000 0.169772 0.090000 0 5.000000e-02 1.500000e-01 SBNO2 22904 broad.mit.edu 37 19 1119153 1119153 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:1119153C>T ENST00000361757.3 - 14 1621 c.1384G>A c.(1384-1386)Gcc>Acc p.A462T SBNO2_ENST00000438103.2_Missense_Mutation_p.A405T|SBNO2_ENST00000587024.1_Missense_Mutation_p.A462T NM_014963.2 NP_055778.2 Q9Y2G9 SBNO2_HUMAN strawberry notch homolog 2 (Drosophila) 14 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137) ATCTCCATGGCGCCAACGCCC 0.667000 0 SO:0001583 missense ENST00000361757.3 0 1 hg19 CCDS45894.1 . . . . . . . . . . C 23.0 4.368391 0.82463 0.0 1.17E-4 ENSG00000064932 ENST00000361757;ENST00000438103;ENST00000250872 . . . 4.19 4.19 0.49359 . 0.000000 0.85682 D 0.000000 D 0.85414 0.5691 M 0.92169 3.28 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.83275 0.99;0.996;0.993 D 0.89565 0.3809 9 0.87932 D 0 -24.553 15.6769 0.77336 0.0:1.0:0.0:0.0 . 462;462;405 B4DV91;Q9Y2G9;Q9Y2G9-3 .;SBNO2_HUMAN;. T 462;405;486 . ENSP00000250872:A486T A - 1 0 SBNO2 1070153 1.000000 0.71417 0.986000 0.45419 0.416000 0.31233 7.514000 0.81750 2.160000 0.67779 0.462000 0.41574 GCC TCGA-IB-A6UG-01A-32D-A33T-08 SBNO2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000458065.2 1 0 1 9 51 0 14 1 9.999649e-01 94 44 0 14 2 0 0 0 0 0 2 1 0.995435 9 51 0 14 2 0 0 0 0 14 2 -16.892900 1 1 120690 1 26 1 0 3 3 1.828633 1 0.220000 3.280000 0.278713 0.990000 0.790000 1.000000 1.000000 0.986764 0.990000 1 9.900000e-01 1 TSHZ3 57616 broad.mit.edu 37 19 31769759 31769759 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:31769759C>T ENST00000240587.4 - 2 1267 c.940G>A c.(940-942)Gcc>Acc p.A314T NM_020856.2 NP_065907.2 Q63HK5 TSH3_HUMAN teashirt zinc finger homeobox 3 p.A314T(1)|p.A131T(1) 123 Esophageal squamous(110;0.226) ATGATTTTGGCGGCGACAGGA 0.537000 2 Substitution - Missense(2) SO:0001583 missense ENST00000240587.4 0 1 hg19 CCDS12421.2 . . . . . . . . . . C 0.019 -1.449292 0.01080 . . ENSG00000121297 ENST00000240587 T 0.11821 2.74 5.46 3.34 0.38264 . 0.108055 0.64402 N 0.000007 T 0.07324 0.0185 N 0.16790 0.44 0.80722 D 1 B 0.09022 0.002 B 0.06405 0.002 T 0.14587 -1.0467 10 0.07325 T 0.83 -21.948 11.5359 0.50636 0.0:0.8554:0.0:0.1446 . 314 Q63HK5 TSH3_HUMAN T 314 ENSP00000240587:A314T ENSP00000240587:A314T A - 1 0 TSHZ3 36461599 1.000000 0.71417 0.875000 0.34327 0.217000 0.24651 5.772000 0.68889 1.294000 0.44707 -0.150000 0.13652 GCC TCGA-IB-A6UG-01A-32D-A33T-08 TSHZ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316743.2 0 0 0 7 584 0 108 0 5.351609e-03 0 8 0 108 2 0 0 0 0 0 2 1 0.978181 7 564 0 104 2 0 0 0 0 108 2 -1.817239 0 1 121412 2 39 1 2 2 4 2.187476 1 0.220000 3.280000 0.360656 0.130000 0.050000 0.260000 0.120000 0.149211 0.130000 0 9.000000e-02 2.000000e-01 PIAS4 51588 broad.mit.edu 37 19 4033577 4033577 + Splice_Site SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:4033577G>A ENST00000262971.2 + 9 1256 c.1141G>A c.(1141-1143)Ggg>Agg p.G381R NM_015897.2 NP_056981.2 Q8N2W9 PIAS4_HUMAN protein inhibitor of activated STAT, 4 p.G381R(1) 17 CATCATCGACGGGTGAGCCCG 0.672000 1 Substitution - Missense(1) SO:0001630 splice_region_variant ENST00000262971.2 0 0 hg19 CCDS12118.1 . . . . . . . . . . G 18.95 3.732488 0.69189 . . ENSG00000105229 ENST00000262971 T 0.15487 2.42 3.95 3.95 0.45737 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, MIZ-type (1); 0.000000 0.85682 U 0.000000 T 0.44871 0.1314 M 0.83774 2.66 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 T 0.54721 -0.8251 10 0.87932 D 0 -26.8132 14.9977 0.71446 0.0:0.0:1.0:0.0 . 381 Q8N2W9 PIAS4_HUMAN R 381 ENSP00000262971:G381R ENSP00000262971:G381R G + 1 0 PIAS4 3984577 1.000000 0.71417 0.801000 0.32222 0.314000 0.28054 9.755000 0.98912 1.762000 0.52044 0.491000 0.48974 GGG TCGA-IB-A6UG-01A-32D-A33T-08 PIAS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457496.1 1 0 1 10 65 0 10 1 8.892844e-01 5 23 0 10 2 0 0 0 0 0 2 1 0.997169 9 64 0 10 2 0 0 0 0 10 2 -17.647890 1 1 0 0 1 0 2 2 1.806944 1 0.220000 3.280000 0.220000 0.990000 0.640000 1.000000 1.000000 0.956851 0.990000 1 8.900000e-01 1 GRIK5 2901 broad.mit.edu 37 19 42546729 42546729 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:42546729C>T ENST00000262895.3 - 11 1447 c.1448G>A c.(1447-1449)gGc>gAc p.G483D GRIK5_ENST00000301218.4_Missense_Mutation_p.G483D|GRIK5_ENST00000593562.1_Missense_Mutation_p.G483D NM_002088.4 NP_002079.3 Q16478 GRIK5_HUMAN glutamate receptor, ionotropic, kainate 5 35 Prostate(69;0.059) GCCAACCATGCCCGTCCAGGA 0.697000 0 SO:0001583 missense ENST00000262895.3 0 1 hg19 CCDS12595.1 . . . . . . . . . . C 36 5.610721 0.96637 . . ENSG00000105737 ENST00000262895;ENST00000301218 D;D 0.95949 -3.86;-3.86 6.17 6.17 0.99709 Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1); 0.000000 0.85682 D 0.000000 D 0.98760 0.9583 H 0.97390 3.995 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.99107 1.0845 10 0.87932 D 0 . 19.6509 0.95805 0.0:1.0:0.0:0.0 . 483 Q16478 GRIK5_HUMAN D 483 ENSP00000262895:G483D;ENSP00000301218:G483D ENSP00000262895:G483D G - 2 0 GRIK5 47238569 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.699000 0.84547 2.941000 0.99782 0.655000 0.94253 GGC TCGA-IB-A6UG-01A-32D-A33T-08 GRIK5-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463453.1 0 0 0 6 597 0 102 0 2.195097e-03 0 6 0 102 2 0 0 0 0 0 2 1 0.963070 7 586 0 96 2 0 0 0 0 102 2 -2.186031 0 1 0 0 1 2 2 4 2.187476 1 0.220000 3.280000 0.360656 0.110000 0.040000 0.230000 0.120000 0.127997 0.110000 0 7.000000e-02 1.800000e-01 CIC 23152 broad.mit.edu 37 19 42795450 42795450 + Missense_Mutation SNP C C G TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:42795450C>G ENST00000575354.2 + 10 2570 c.2530C>G c.(2530-2532)Cca>Gca p.P844A CIC_ENST00000160740.3_Missense_Mutation_p.P844A|CIC_ENST00000572681.2_Missense_Mutation_p.P1753A NM_015125.3 NP_055940.3 Q96RK0 CIC_HUMAN capicua transcriptional repressor 82 Prostate(69;0.00682) TGCCCCAGCACCAGCCCCTGG 0.672000 Mis, F, S oligodendroglioma Rec yes 19 19q13.2 23152 capicua homolog O 0 SO:0001583 missense ENST00000575354.2 1 1 hg19 CCDS12601.1 . . . . . . . . . . C 12.46 1.943409 0.34283 . . ENSG00000079432 ENST00000160740 . . . 5.16 1.44 0.22558 . . . . . T 0.23210 0.0561 N 0.08118 0 0.26798 N 0.96927 B 0.02656 0.0 B 0.04013 0.001 T 0.23583 -1.0184 8 0.87932 D 0 -1.575 9.4699 0.38835 0.1253:0.4976:0.3771:0.0 . 844 Q96RK0 CIC_HUMAN A 844 . ENSP00000160740:P844A P + 1 0 CIC 47487290 0.986000 0.35501 1.000000 0.80357 0.990000 0.78478 0.581000 0.23819 0.537000 0.28751 0.561000 0.74099 CCA TCGA-IB-A6UG-01A-32D-A33T-08 CIC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000438532.2 0 0 0 8 243 0 47 1 6.852046e-01 3 68 0 47 2 0 0 0 0 0 2 1 0.989172 8 240 0 45 2 0 0 0 0 47 2 -10.017220 1 1 0 0 1 2 2 4 2.187476 1 0.220000 3.280000 0.360656 0.370000 0.170000 0.650000 0.360000 0.391759 0.370000 0 2.500000e-01 5.100000e-01 ZNF473 25888 broad.mit.edu 37 19 50548807 50548807 + Silent SNP C C T rs148474136 byFrequency TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:50548807C>T ENST00000595661.1 + 6 1602 c.1107C>T c.(1105-1107)caC>caT p.H369H ZNF473_ENST00000391821.2_Silent_p.H369H|ZNF473_ENST00000270617.3_Silent_p.H369H|CTD-2126E3.3_ENST00000599410.1_RNA|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000601364.1_Intron|ZNF473_ENST00000445728.3_Silent_p.H357H Q8WTR7 ZN473_HUMAN zinc finger protein 473 37 all_neural(266;0.0459)|Ovarian(192;0.0728) AGAAAACTCACGCTGCAAAAA 0.498000 0 SO:0001819 synonymous_variant ENST00000595661.1 1 1 hg19 CCDS33077.1 TCGA-IB-A6UG-01A-32D-A33T-08 ZNF473-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464833.1 0 0 0 16 429 0 66 0 3.611762e-02 0 8 0 66 2 0 0 0 0 0 2 1 0.999934 17 427 0 66 2 0 0 0 0 66 2 -15.080770 1 1 121412 11 41 1 3 3 6 2.271201 1 0.220000 3.280000 0.399631 0.470000 0.260000 1.000000 0.420000 0.563535 0.470000 0 3.500000e-01 1 KLK15 55554 broad.mit.edu 37 19 51330167 51330167 + Missense_Mutation SNP C C G TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:51330167C>G ENST00000598239.1 - 3 478 c.448G>C c.(448-450)Gag>Cag p.E150Q KLK15_ENST00000596931.1_Missense_Mutation_p.E149Q|KLK15_ENST00000416184.1_Intron|KLK15_ENST00000326856.4_Missense_Mutation_p.E149Q|KLK15_ENST00000301421.2_Missense_Mutation_p.E150Q NM_017509.2 NP_059979.2 Q9H2R5 KLK15_HUMAN kallikrein-related peptidase 15 24 all_neural(266;0.057) GTCCCAGGCTCGTTGTGGGAC 0.687000 Pancreas(140;10 2513 7143 9246) 0 SO:0001583 missense ENST00000598239.1 1 1 hg19 CCDS12805.1 . . . . . . . . . . c 9.453 1.091027 0.20471 . . ENSG00000174562 ENST00000326856;ENST00000301421;ENST00000544946 D 0.88741 -2.42 4.5 -5.03 0.02973 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 1.995620 0.02210 N 0.063038 T 0.81317 0.4797 N 0.14661 0.345 0.09310 N 1 B;B;B 0.25719 0.132;0.003;0.002 B;B;B 0.34652 0.187;0.013;0.004 T 0.69060 -0.5245 10 0.15952 T 0.53 . 12.5901 0.56437 0.0:0.1856:0.0:0.8144 . 150;149;150 Q6UBM2;Q6ISI0;Q9H2R5 .;.;KLK15_HUMAN Q 150 ENSP00000301421:E150Q ENSP00000301421:E150Q E - 1 0 KLK15 56021979 0.000000 0.05858 0.000000 0.03702 0.042000 0.13812 -0.363000 0.07593 -0.801000 0.04427 0.555000 0.69702 GAG TCGA-IB-A6UG-01A-32D-A33T-08 KLK15-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465160.1 1 0 1 67 257 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 65 251 0 51 2 0 0 0 0 51 2 -20.000000 1 1 0 0 1 3 3 6 2.271201 1 0.220000 3.280000 0.399631 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SIGLEC5 8778 broad.mit.edu 37 19 52132769 52132769 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:52132769G>A ENST00000534261.2 - 4 941 c.542C>T c.(541-543)aCg>aTg p.T181M SIGLEC5_ENST00000429354.3_Missense_Mutation_p.T181M|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.T181M|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.T181M|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.T181M O15389 SIGL5_HUMAN sialic acid binding Ig-like lectin 5 27 all_neural(266;0.0726) GGCATTCCCCGTCCAGGAGAA 0.657000 0 SO:0001583 missense ENST00000534261.2 0 1 hg19 CCDS33088.1 . . . . . . . . . . g 2.485 -0.318873 0.05386 . . ENSG00000105501 ENST00000222107;ENST00000429354 T;T 0.22743 1.94;1.94 3.83 -7.65 0.01281 Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1); 3.012550 0.01183 N 0.007122 T 0.11067 0.0270 N 0.16266 0.395 0.09310 N 1 P 0.40660 0.726 B 0.39068 0.289 T 0.14364 -1.0475 10 0.15066 T 0.55 . 7.7193 0.28723 0.6524:0.0:0.1321:0.2155 . 181 O15389 SIGL5_HUMAN M 181 ENSP00000222107:T181M;ENSP00000415200:T181M ENSP00000222107:T181M T - 2 0 SIGLEC5 56824581 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -4.692000 0.00198 -2.466000 0.00533 -0.948000 0.02665 ACG TCGA-IB-A6UG-01A-32D-A33T-08 SIGLEC5-001 PUTATIVE basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466897.2 0 0 0 25 65 0 19 0 0 0 1 0 19 2 0 0 0 0 0 2 1 0.999993 14 44 0 28 2 0 0 0 0 19 2 -19.863340 1 1 119122 1 29 1 0.220000 3.280000 0 0 ZNF480 147657 broad.mit.edu 37 19 52817449 52817449 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:52817449C>T ENST00000595962.1 + 3 182 c.116C>T c.(115-117)gCg>gTg p.A39V ZNF480_ENST00000334564.7_Missense_Mutation_p.A39V|ZNF480_ENST00000490272.1_Intron|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000335090.6_Intron NM_144684.2 NP_653285.2 Q8WV37 ZN480_HUMAN zinc finger protein 480 12 TTCTCTCAGGCGGAGTGGAAA 0.473000 0 SO:0001583 missense ENST00000595962.1 1 1 hg19 CCDS12850.2 . . . . . . . . . . C 5.169 0.216831 0.09810 2.27E-4 0.0 ENSG00000198464 ENST00000354515;ENST00000468240;ENST00000334564 T;T 0.01725 4.67;4.67 2.04 0.945 0.19543 Krueppel-associated box (4); . . . . T 0.01695 0.0054 L 0.46157 1.445 0.22933 N 0.998546 P;B 0.40476 0.718;0.161 B;B 0.30782 0.038;0.12 T 0.47484 -0.9114 9 0.66056 D 0.02 . 6.0962 0.20021 0.7277:0.2723:0.0:0.0 . 39;39 F8WEZ9;Q8WV37 .;ZN480_HUMAN V 61;39;39 ENSP00000417424:A39V;ENSP00000334164:A39V ENSP00000334164:A39V A + 2 0 ZNF480 57509261 0.981000 0.34729 0.315000 0.25238 0.071000 0.16799 0.684000 0.25364 0.048000 0.15891 -0.602000 0.04101 GCG TCGA-IB-A6UG-01A-32D-A33T-08 ZNF480-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000349001.3 1 0 1 77 642 0 128 0 8.982995e-01 0 35 0 128 2 0 0 0 0 0 2 1 1.000000 76 638 0 125 2 0 0 0 0 128 2 -3.318794 1 1 0 0 1 3 3 6 2.270755 1 0.220000 3.280000 0.399631 0.990000 0.990000 1.000000 1.000000 0.999413 0.990000 1 9.900000e-01 1 ZNF549 256051 broad.mit.edu 37 19 58049499 58049499 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:58049499G>A ENST00000376233.3 + 4 1308 c.1127G>A c.(1126-1128)cGc>cAc p.R376H ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000594943.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.R363H NM_001199295.1 NP_001186224 Q6P9A3 ZN549_HUMAN zinc finger protein 549 21 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221) TCCTATGACCGCATTCGACAC 0.433000 0 SO:0001583 missense ENST00000376233.3 0 1 hg19 CCDS56106.1 . . . . . . . . . . G 14.17 2.456252 0.43634 . . ENSG00000121406 ENST00000240719;ENST00000376233 T;T 0.15139 2.45;2.45 2.64 -5.28 0.02755 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.16471 0.0396 M 0.73598 2.24 0.09310 N 1 B;B 0.18863 0.0;0.031 B;B 0.12156 0.0;0.007 T 0.39623 -0.9605 9 0.87932 D 0 . 4.6998 0.12822 0.3606:0.0:0.142:0.4974 . 376;363 Q6P9A3;Q6P9A3-2 ZN549_HUMAN;. H 363;376 ENSP00000240719:R363H;ENSP00000365407:R376H ENSP00000240719:R363H R + 2 0 ZNF549 62741311 0.001000 0.12720 0.000000 0.03702 0.575000 0.36095 0.804000 0.27098 -1.086000 0.03084 -0.350000 0.07774 CGC TCGA-IB-A6UG-01A-32D-A33T-08 ZNF549-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000466780.1 0 0 0 5 319 0 58 0 3.751610e-03 0 5 0 58 2 0 0 0 0 0 2 1 0.935430 5 314 0 58 2 0 0 0 0 58 2 -2.794334 1 1 121412 3 37 1 3 3 6 2.271543 1 0.220000 3.280000 0.399631 0.230000 0.070000 1.000000 0.190000 0.380765 0.230000 0 1.300000e-01 1 ZNF418 147686 broad.mit.edu 37 19 58437576 58437576 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr19:58437576C>T ENST00000396147.1 - 4 2264 c.1973G>A c.(1972-1974)cGa>cAa p.R658Q ZNF418_ENST00000425570.3_Missense_Mutation_p.R679Q|ZNF418_ENST00000595830.1_Missense_Mutation_p.R658Q|ZNF418_ENST00000599852.1_Missense_Mutation_p.R573Q|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank NM_133460.1 NP_597717.1 Q8TF45 ZN418_HUMAN zinc finger protein 418 31 Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156) AGAAGAGCTTCGATGAAATGA 0.413000 0 SO:0001583 missense ENST00000396147.1 1 1 hg19 CCDS42642.1 . . . . . . . . . . . 3.656 -0.070523 0.07228 0.0 1.16E-4 ENSG00000196724 ENST00000396147;ENST00000425570;ENST00000545403 T;T 0.07567 3.18;3.18 2.41 -1.42 0.08913 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.02267 0.0070 N 0.02334 -0.595 0.09310 N 1 B 0.24132 0.098 B 0.10450 0.005 T 0.44283 -0.9338 9 0.02654 T 1 . 6.7371 0.23415 0.0:0.4089:0.0:0.5911 . 658 Q8TF45 ZN418_HUMAN Q 658;679;624 ENSP00000379451:R658Q;ENSP00000407039:R679Q ENSP00000379451:R658Q R - 2 0 ZNF418 63129388 0.000000 0.05858 0.000000 0.03702 0.831000 0.47069 -3.966000 0.00324 -0.253000 0.09514 0.313000 0.20887 CGA TCGA-IB-A6UG-01A-32D-A33T-08 ZNF418-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466693.1 0 0 0 13 505 0 79 0 2.953536e-02 0 10 0 79 2 0 0 0 0 0 2 1 0.999499 13 499 0 79 2 0 0 0 0 79 2 -2.649041 1 1 121408 1 40 1 3 3 6 2.271543 1 0.220000 3.280000 0.399631 0.330000 0.160000 1.000000 0.290000 0.460330 0.330000 0 2.300000e-01 1 CHRNB2 1141 broad.mit.edu 37 1 154543680 154543680 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:154543680C>T ENST00000368476.3 + 5 645 c.381C>T c.(379-381)taC>taT p.Y127Y NM_000748.2 NP_000739.1 P17787 ACHB2_HUMAN cholinergic receptor, nicotinic, beta 2 (neuronal) 28 all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088) LUSC - Lung squamous cell carcinoma(543;0.185) Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184) ACGGCATGTACGAGGTGTCCT 0.552000 0 SO:0001819 synonymous_variant ENST00000368476.3 1 1 hg19 CCDS1070.1 TCGA-IB-A6UG-01A-32D-A33T-08 CHRNB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090697.1 1 0 1 274 486 0 110 0 0 0 1 0 110 2 0 0 0 0 0 2 1 1.000000 273 479 0 108 2 0 0 0 0 110 2 -20.000000 1 1 0 0 1 0 5 5 2.256617 1 0.220000 3.280000 0.400138 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 NME7 29922 broad.mit.edu 37 1 169256604 169256604 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:169256604C>T ENST00000367811.3 - 7 947 c.691G>A c.(691-693)Gca>Aca p.A231T NME7_ENST00000469474.1_5'UTR|NME7_ENST00000472647.1_Missense_Mutation_p.A195T NM_013330.3 NP_037462.1 Q9Y5B8 NDK7_HUMAN NME/NM23 family member 7 p.A231T(1) 16 all_hematologic(923;0.208) GCAGTGTTTGCCGGCCCACAA 0.358000 1 Substitution - Missense(1) SO:0001583 missense ENST00000367811.3 0 1 hg19 CCDS1277.1 . . . . . . . . . . C 12.52 1.961854 0.34659 . . ENSG00000143156 ENST00000472647;ENST00000367811 T;T 0.55413 0.52;0.52 4.57 3.65 0.41850 . 0.526155 0.22030 N 0.065617 T 0.15565 0.0375 L 0.27053 0.805 0.29275 N 0.870411 B;B 0.06786 0.001;0.001 B;B 0.09377 0.004;0.001 T 0.09378 -1.0677 9 0.14252 T 0.57 -11.2605 7.7247 0.28753 0.0:0.8061:0.0:0.1939 . 235;231 Q59GR0;Q9Y5B8 .;NDK7_HUMAN T 195;231 ENSP00000433341:A195T;ENSP00000356785:A231T ENSP00000356785:A231T A - 1 0 NME7 167523228 0.999000 0.42202 0.998000 0.56505 0.981000 0.71138 1.468000 0.35332 0.914000 0.36822 0.637000 0.83480 GCA TCGA-IB-A6UG-01A-32D-A33T-08 NME7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083688.1 0 0 0 7 1121 0 199 0 5.615228e-02 0 52 0 199 2 0 0 0 0 0 2 1 0.979703 7 1107 0 199 2 0 0 0 0 199 2 -1.667255 0 1 121410 2 33 1 0 5 5 2.256617 1 0.220000 3.280000 0.400138 0.080000 0.010000 1.000000 0.090000 0.148931 0.080000 0 4.000000e-02 1.300000e-01 TNR 7143 broad.mit.edu 37 1 175292513 175292513 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:175292513G>A ENST00000367674.2 - 23 4765 c.4057C>T c.(4057-4059)Cgg>Tgg p.R1353W TNR_ENST00000263525.2_Missense_Mutation_p.R1353W|RP3-518E13.2_ENST00000569593.1_RNA Q92752 TENR_HUMAN tenascin R 177 Renal(580;0.146) AAGGACTGCCGTTTTCTCCCT 0.478000 0 SO:0001583 missense ENST00000367674.2 1 1 hg19 CCDS1318.1 . . . . . . . . . . G 15.41 2.823924 0.50739 . . ENSG00000116147 ENST00000367674;ENST00000263525;ENST00000367673 T;T 0.29142 1.58;1.58 5.37 5.37 0.77165 . 0.000000 0.85682 D 0.000000 T 0.45776 0.1359 L 0.47716 1.5 0.53005 D 0.99996 D 0.89917 1.0 D 0.63283 0.913 T 0.40213 -0.9575 10 0.87932 D 0 . 13.652 0.62316 0.0:0.0:0.8451:0.1549 . 1353 Q92752 TENR_HUMAN W 1353;1353;1263 ENSP00000356646:R1353W;ENSP00000263525:R1353W ENSP00000263525:R1353W R - 1 2 TNR 173559136 1.000000 0.71417 1.000000 0.80357 0.104000 0.19210 3.266000 0.51569 2.513000 0.84729 0.561000 0.74099 CGG TCGA-IB-A6UG-01A-32D-A33T-08 TNR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084414.4 1 0 0 50 559 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 1.000000 49 547 0 94 2 0 0 0 0 95 2 -12.802390 1 1 0 0 1 0 5 5 2.256617 1 0.220000 3.280000 0.400138 0.980000 0.730000 1.000000 1.000000 0.942902 0.980000 1 8.500000e-01 1 TMEM52 339456 broad.mit.edu 37 1 1849752 1849752 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:1849752G>A ENST00000310991.3 - 4 296 c.289C>T c.(289-291)Ccc>Tcc p.P97S TMEM52_ENST00000378602.3_Missense_Mutation_p.P82S NM_178545.3 NP_848640.1 Q8NDY8 TMM52_HUMAN transmembrane protein 52 3 all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217) ACGTCGCAGGGCTGCCGTGCT 0.632000 0 SO:0001583 missense ENST00000310991.3 1 1 hg19 CCDS35.1 . . . . . . . . . . . 13.04 2.117061 0.37339 . . ENSG00000178821 ENST00000378602;ENST00000310991 T;T 0.56776 0.44;0.44 3.92 2.99 0.34606 . 0.000000 0.52532 D 0.000072 T 0.57710 0.2072 M 0.68317 2.08 0.29515 N 0.853898 B;P 0.50819 0.06;0.939 B;P 0.50934 0.046;0.654 T 0.59542 -0.7435 10 0.72032 D 0.01 -26.7541 9.9162 0.41436 0.1049:0.0:0.8951:0.0 . 97;82 Q8NDY8;Q8NDY8-2 TMM52_HUMAN;. S 82;97 ENSP00000367865:P82S;ENSP00000311122:P97S ENSP00000311122:P97S P - 1 0 TMEM52 1839612 0.947000 0.32204 0.526000 0.27913 0.180000 0.23129 1.620000 0.36976 0.763000 0.33175 0.511000 0.50034 CCC TCGA-IB-A6UG-01A-32D-A33T-08 TMEM52-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000002781.1 1 0 0 25 253 0 69 0 9.997177e-01 0 132 0 69 2 0 0 0 0 0 2 1 1.000000 25 247 0 67 2 0 0 0 0 69 2 -2.540643 1 1 121308 1 36 1 2 2 4 1.841880 1 0.220000 3.280000 0.260664 0.910000 0.590000 1.000000 1.000000 0.882618 0.910000 1 7.300000e-01 1 LAX1 54900 broad.mit.edu 37 1 203739994 203739994 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:203739994C>T ENST00000442561.2 + 2 518 c.128C>T c.(127-129)gCg>gTg p.A43V LAX1_ENST00000367217.5_Missense_Mutation_p.A27V|LAX1_ENST00000367215.1_3'UTR NM_017773.3 NP_060243.2 Q8IWV1 LAX1_HUMAN lymphocyte transmembrane adaptor 1 p.A43V(1) 24 all_cancers(21;0.0915) BRCA - Breast invasive adenocarcinoma(75;0.109) TCCGGGTTTGCGGGACTCCTC 0.483000 1 Substitution - Missense(1) SO:0001583 missense ENST00000442561.2 0 1 hg19 CCDS1441.2 . . . . . . . . . . C 5.080 0.200425 0.09652 . . ENSG00000122188 ENST00000442561;ENST00000367217 . . . 5.38 1.43 0.22495 . 0.327636 0.26007 N 0.026914 T 0.20210 0.0486 L 0.32530 0.975 0.09310 N 1 B;B 0.33379 0.41;0.201 B;B 0.28139 0.086;0.055 T 0.18147 -1.0346 9 0.17832 T 0.49 -3.1747 7.1389 0.25543 0.0:0.6291:0.0:0.3709 . 27;43 B7Z744;Q8IWV1 .;LAX1_HUMAN V 43;27 . ENSP00000356186:A27V A + 2 0 LAX1 202006617 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 0.145000 0.16157 0.013000 0.14918 -0.254000 0.11334 GCG TCGA-IB-A6UG-01A-32D-A33T-08 LAX1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000087468.3 0 0 0 6 607 0 81 0 8.697730e-04 0 4 0 81 2 0 0 0 0 0 2 1 0.964575 6 604 0 81 2 0 0 0 0 81 2 -1.689357 0 1 121412 1 39 1 0 5 5 2.254602 1 0.220000 3.280000 0.403168 0.120000 0.030000 1.000000 0.100000 0.183170 0.120000 0 7.000000e-02 2.000000e-01 NBPF3 84224 broad.mit.edu 37 1 21801427 21801427 + Silent SNP A A G TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:21801427A>G ENST00000318249.5 + 8 1325 c.975A>G c.(973-975)aaA>aaG p.K325K NBPF3_ENST00000342104.5_Silent_p.K325K|NBPF3_ENST00000318220.6_Silent_p.K269K|NBPF3_ENST00000454000.2_Silent_p.K255K NM_032264.3 NP_115640.1 Q9H094 NBPF3_HUMAN neuroblastoma breakpoint family, member 3 20 all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255) AGGAAGAAAAAGGGCCAGTGT 0.398000 0 SO:0001819 synonymous_variant ENST00000318249.5 0 1 hg19 CCDS216.1 TCGA-IB-A6UG-01A-32D-A33T-08 NBPF3-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 0 0 0 5 604 0 137 0 2.985218e-03 0 8 0 137 2 0 0 0 0 0 2 1 0.936410 5 599 0 137 2 0 0 0 0 137 2 -2.239016 0 1 0 0 1 1 2 3 1.821982 0 0.220000 3.280000 0.237611 0.090000 0.020000 1.000000 0.070000 0.234101 0.090000 0 5.000000e-02 2.300000e-01 SUSD4 55061 broad.mit.edu 37 1 223465929 223465929 + Silent SNP G G A rs148470082 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:223465929G>A ENST00000343846.3 - 2 846 c.213C>T c.(211-213)agC>agT p.S71S SUSD4_ENST00000484758.2_Intron|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000366878.4_Silent_p.S71S|SUSD4_ENST00000494793.2_Silent_p.S71S|SUSD4_ENST00000454695.2_5'UTR|SUSD4_ENST00000344029.6_Silent_p.S71S Q5VX71 SUSD4_HUMAN sushi domain containing 4 17 AAACCCCTCCGCTGGGGGTCC 0.498000 0 SO:0001819 synonymous_variant ENST00000343846.3 1 1 hg19 CCDS41471.1 TCGA-IB-A6UG-01A-32D-A33T-08 SUSD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092592.2 1 0 0 43 466 0 88 1 6.996838e-01 2 26 0 88 2 0 0 0 0 0 2 1 1.000000 41 463 0 86 2 0 0 0 0 88 2 -11.933480 1 1 121412 34 46 1 0 5 5 2.273711 1 0.220000 3.280000 0.403168 0.990000 0.740000 1.000000 1.000000 0.953533 0.990000 1 8.700000e-01 1 EPHA8 2046 broad.mit.edu 37 1 22903359 22903359 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:22903359G>A ENST00000166244.3 + 3 881 c.809G>A c.(808-810)cGg>cAg p.R270Q EPHA8_ENST00000538803.1_Missense_Mutation_p.R270Q|EPHA8_ENST00000374644.4_Missense_Mutation_p.R270Q NM_020526.3 NP_065387.1 P29322 EPHA8_HUMAN EPH receptor A8 61 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) GAGGAGCGGCGGGATGCCTGT 0.677000 0 SO:0001583 missense ENST00000166244.3 0 1 hg19 CCDS225.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 11.89 1.773458 0.31411 . . ENSG00000070886 ENST00000166244;ENST00000374644;ENST00000538803 T;D;D 0.97256 1.61;-4.31;-4.31 4.09 0.842 0.18927 . 0.145914 0.44097 N 0.000490 D 0.92120 0.7502 L 0.41236 1.265 0.37767 D 0.926539 B;B 0.22851 0.003;0.076 B;B 0.15870 0.004;0.014 D 0.85467 0.1170 10 0.45353 T 0.12 . 3.7537 0.08576 0.3071:0.0:0.5103:0.1826 . 270;270 P29322;P29322-2 EPHA8_HUMAN;. Q 270 ENSP00000166244:R270Q;ENSP00000363775:R270Q;ENSP00000440274:R270Q ENSP00000166244:R270Q R + 2 0 EPHA8 22775946 0.735000 0.28153 0.998000 0.56505 0.990000 0.78478 1.043000 0.30316 0.358000 0.24211 0.442000 0.29010 CGG TCGA-IB-A6UG-01A-32D-A33T-08 EPHA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008085.1 0 0 0 8 141 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 0.987816 8 134 0 22 2 0 0 0 0 24 2 -2.896200 1 1 121064 1 26 1 1 2 3 1.821982 0 0.220000 3.280000 0.237611 0.560000 0.250000 1.000000 0.480000 0.613626 0.560000 0 3.800000e-01 1 GJA4 2701 broad.mit.edu 37 1 35260163 35260163 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:35260163C>T ENST00000342280.4 + 2 437 c.349C>T c.(349-351)Ccg>Tcg p.P117S NM_002060.2 NP_002051.2 P35212 CXA4_HUMAN gap junction protein, alpha 4, 37kDa 14 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234) GCGGGCACTGCCGGCCAAGGA 0.667000 0 SO:0001583 missense ENST00000342280.4 0 1 hg19 CCDS30669.1 . . . . . . . . . . C 2.482 -0.319516 0.05386 . . ENSG00000187513 ENST00000342280;ENST00000450137;ENST00000543143 D;D 0.97232 -4.27;-4.3 5.11 4.2 0.49525 . 0.976137 0.08425 N 0.947757 D 0.93128 0.7812 L 0.29908 0.895 0.19300 N 0.999979 B;B 0.02656 0.0;0.0 B;B 0.06405 0.002;0.001 T 0.83316 -0.0020 10 0.13470 T 0.59 . 9.298 0.37827 0.0:0.7788:0.1446:0.0766 . 117;117 Q5JW71;P35212 .;CXA4_HUMAN S 117 ENSP00000343676:P117S;ENSP00000409186:P117S ENSP00000343676:P117S P + 1 0 GJA4 35032750 0.958000 0.32768 0.903000 0.35520 0.138000 0.21146 1.218000 0.32467 1.146000 0.42352 0.563000 0.77884 CCG TCGA-IB-A6UG-01A-32D-A33T-08 GJA4-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000011556.1 0 0 0 4 214 0 45 0 1.025126e-01 0 23 0 45 2 0 0 0 0 0 2 1 0.891170 4 214 0 44 2 0 0 0 0 45 2 -3.884781 1 1 0 0 1 1 2 3 1.821982 0 0.220000 3.280000 0.237611 0.210000 0.060000 1.000000 0.160000 0.333027 0.210000 0 1.200000e-01 5.500000e-01 PTPRF 5792 broad.mit.edu 37 1 44069169 44069169 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:44069169G>A ENST00000359947.4 + 15 2763 c.2423G>A c.(2422-2424)cGc>cAc p.R808H PTPRF_ENST00000438120.1_Missense_Mutation_p.R799H|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000372414.3_Missense_Mutation_p.R808H|PTPRF_ENST00000372413.3_Missense_Mutation_p.R799H|PTPRF_ENST00000422171.2_Missense_Mutation_p.R156H NM_002840.3 NP_002831.2 P10586 PTPRF_HUMAN protein tyrosine phosphatase, receptor type, F 72 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) GATGGTGCCCGCAGCAAGCCC 0.632000 0 SO:0001583 missense ENST00000359947.4 0 1 hg19 CCDS489.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 19.81|19.81 3.895738|3.895738 0.72639|0.72639 .|. .|. ENSG00000142949|ENSG00000142949 ENST00000429895|ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407 .|T;T;T;T;T;T .|0.54279 .|2.28;0.58;2.28;0.58;0.58;0.59 4.79|4.79 4.79|4.79 0.61399|0.61399 .|Fibronectin, type III (3);Immunoglobulin-like fold (1); .|0.000000 .|0.31660 .|N .|0.007279 T|T 0.73682|0.73682 0.3618|0.3618 M|M 0.80422|0.80422 2.495|2.495 0.80722|0.80722 D|D 1|1 .|D;D;P;D;D .|0.89917 .|1.0;1.0;0.88;1.0;1.0 .|D;D;B;D;D .|0.97110 .|0.999;0.986;0.288;0.995;1.0 T|T 0.73007|0.73007 -0.4118|-0.4118 5|10 .|0.30854 .|T .|0.27 .|. 18.2203|18.2203 0.89899|0.89899 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|455;156;567;799;808 .|Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586 .|.;.;.;.;PTPRF_HUMAN T|H 456|808;799;808;799;156;62 .|ENSP00000353030:R808H;ENSP00000398822:R799H;ENSP00000361491:R808H;ENSP00000361490:R799H;ENSP00000387885:R156H;ENSP00000361484:R62H .|ENSP00000353030:R808H A|R +|+ 1|2 0|0 PTPRF|PTPRF 43841756|43841756 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.972000|0.972000 0.66771|0.66771 7.456000|7.456000 0.80751|0.80751 2.387000|2.387000 0.81309|0.81309 0.655000|0.655000 0.94253|0.94253 GCA|CGC TCGA-IB-A6UG-01A-32D-A33T-08 PTPRF-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000019710.1 0 0 0 7 451 0 94 0 5.910966e-01 0 120 0 94 2 0 0 0 0 0 2 1 0.979681 7 444 0 93 2 0 0 0 0 94 2 -2.533984 1 1 121412 1 36 1 1 2 3 1.821982 0 0.220000 3.280000 0.237611 0.160000 0.060000 1.000000 0.140000 0.292874 0.160000 0 1.000000e-01 3.600000e-01 DEPDC1 55635 broad.mit.edu 37 1 68947194 68947194 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr1:68947194G>A ENST00000456315.2 - 9 1978 c.1864C>T c.(1864-1866)Cgt>Tgt p.R622C DEPDC1_ENST00000370966.5_Missense_Mutation_p.R338C|RP4-694A7.2_ENST00000425820.1_RNA NM_001114120.1 NP_001107592.1 Q5TB30 DEP1A_HUMAN DEP domain containing 1 13 GAAATCATACGCATTAAAAGT 0.398000 0 SO:0001583 missense ENST00000456315.2 1 1 hg19 CCDS44159.1 . . . . . . . . . . G 14.77 2.635313 0.47049 . . ENSG00000024526 ENST00000456315;ENST00000370966 D;D 0.86627 -2.15;-2.15 5.72 4.78 0.61160 Rho GTPase-activating protein domain (1);Rho GTPase activation protein (1); 0.000000 0.85682 D 0.000000 D 0.92770 0.7701 M 0.83483 2.645 0.44539 D 0.997495 P;D 0.89917 0.793;1.0 B;D 0.87578 0.181;0.998 D 0.93210 0.6599 10 0.72032 D 0.01 -2.5002 15.1757 0.72910 0.0:0.0:0.7481:0.2519 . 622;338 Q5TB30;Q5TB30-2 DEP1A_HUMAN;. C 622;338 ENSP00000412292:R622C;ENSP00000360005:R338C ENSP00000360005:R338C R - 1 0 DEPDC1 68719782 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 3.266000 0.51569 2.691000 0.91804 0.655000 0.94253 CGT TCGA-IB-A6UG-01A-32D-A33T-08 DEPDC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000025514.2 1 0 0 10 124 0 30 1 1.991898e-02 3 0 0 30 2 0 0 0 0 0 2 1 0.997013 10 122 0 30 2 0 0 0 0 30 2 -5.355585 1 1 121310 3 35 1 1 2 3 1.821982 0 0.220000 3.280000 0.237611 0.760000 0.380000 1.000000 1.000000 0.764171 0.760000 0 5.400000e-01 1 RIN2 54453 broad.mit.edu 37 20 19970910 19970910 + Missense_Mutation SNP C C A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr20:19970910C>A ENST00000255006.6 + 9 2319 c.2170C>A c.(2170-2172)Ctg>Atg p.L724M RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Missense_Mutation_p.L242M NM_001242581.1|NM_018993.3 NP_001229510.1|NP_061866.1 Q8WYP3 RIN2_HUMAN Ras and Rab interactor 2 27 CATGCTGCTGCTGCGGGTCTG 0.557000 0 SO:0001583 missense ENST00000255006.6 1 1 hg19 CCDS56182.1 . . . . . . . . . . C 19.53 3.845521 0.71603 . . ENSG00000132669 ENST00000255006;ENST00000440354 T;T 0.36699 1.24;1.24 5.83 2.72 0.32119 Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2); 0.000000 0.85682 D 0.000000 T 0.62490 0.2432 M 0.88704 2.975 0.58432 D 0.99999 D;D 0.89917 1.0;1.0 D;D 0.97110 0.999;1.0 T 0.64554 -0.6380 9 . . . -20.4278 10.7252 0.46064 0.0:0.7838:0.0:0.2162 . 242;675 E7EPJ1;Q8WYP3 .;RIN2_HUMAN M 724;242 ENSP00000255006:L724M;ENSP00000391239:L242M . L + 1 2 RIN2 19918910 1.000000 0.71417 0.997000 0.53966 0.985000 0.73830 1.382000 0.34374 0.313000 0.23062 -0.194000 0.12790 CTG TCGA-IB-A6UG-01A-32D-A33T-08 RIN2-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078212.1 1 0 1 15 124 0 26 1 9.772297e-01 8 47 0 26 2 0 0 0 0 0 2 1 0.999891 15 122 0 26 2 0 0 0 0 26 2 -19.998580 1 1 0 0 1 1 2 3 1.957393 0 0.220000 3.280000 0.294501 0.990000 0.650000 1.000000 1.000000 0.949536 0.990000 1 8.600000e-01 1 INSM1 3642 broad.mit.edu 37 20 20349690 20349690 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr20:20349690C>T ENST00000310227.1 + 1 926 c.779C>T c.(778-780)gCg>gTg p.A260V NM_002196.2 NP_002187.1 Q01101 INSM1_HUMAN insulinoma-associated 1 6 gcggggggcgcggcgcggccg 0.716000 0 SO:0001583 missense ENST00000310227.1 0 1 hg19 CCDS13143.1 . . . . . . . . . . C 4.993 0.184394 0.09495 . . ENSG00000173404 ENST00000310227 T 0.00711 5.8 3.53 2.46 0.29980 . 0.183785 0.33553 U 0.004798 T 0.00496 0.0016 N 0.12182 0.205 0.24619 N 0.993683 B 0.33103 0.397 B 0.20184 0.028 T 0.53906 -0.8372 10 0.41790 T 0.15 . 6.9677 0.24632 0.0:0.5981:0.2959:0.1059 . 260 Q01101 INSM1_HUMAN V 260 ENSP00000312631:A260V ENSP00000312631:A260V A + 2 0 INSM1 20297690 0.003000 0.15002 0.122000 0.21767 0.349000 0.29174 1.908000 0.39907 1.699000 0.51192 0.306000 0.20318 GCG TCGA-IB-A6UG-01A-32D-A33T-08 INSM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078223.1 1 0 0 13 70 0 11 0 0 0 0 11 2 0 0 0 0 0 2 1 0.999655 13 69 0 10 2 0 0 0 0 11 2 -19.999610 1 1 114260 1 20 1 1 2 3 1.957393 0 0.220000 3.280000 0.294501 0.990000 0.920000 1.000000 1.000000 0.994963 0.990000 1 9.900000e-01 1 DSCAM 1826 broad.mit.edu 37 21 41648061 41648061 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr21:41648061G>A ENST00000400454.1 - 11 2796 c.2319C>T c.(2317-2319)ggC>ggT p.G773G NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) TGACGTCTGCGCCCACATCGT 0.483000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001819 synonymous_variant ENST00000400454.1 1 1 hg19 CCDS42929.1 TCGA-IB-A6UG-01A-32D-A33T-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 1 0 1 61 283 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 1.000000 60 281 0 79 2 0 0 0 0 79 2 -3.040396 1 1 121034 1 35 1 0 2 2 1.779519 1 0.220000 3.280000 0.220000 0.990000 0.990000 1.000000 1.000000 0.999996 0.990000 1 9.900000e-01 1 COL6A1 1291 broad.mit.edu 37 21 47423408 47423408 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr21:47423408C>T ENST00000361866.3 + 35 2682 c.2568C>T c.(2566-2568)gcC>gcT p.A856A COL6A1_ENST00000498614.1_3'UTR NM_001848.2 NP_001839.2 P12109 CO6A1_HUMAN collagen, type VI, alpha 1 33 all_hematologic(128;0.24) AGCGCCTGGCCGAGCGCTTCC 0.706000 0 SO:0001819 synonymous_variant ENST00000361866.3 1 1 hg19 CCDS13727.1 TCGA-IB-A6UG-01A-32D-A33T-08 COL6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206877.1 1 0 1 29 150 0 49 1 1 7 246 0 49 2 0 0 0 0 0 2 1 1.000000 29 146 0 49 2 0 0 0 0 49 2 -20.000000 1 1 120706 14 42 1 0 2 2 1.779519 1 0.220000 3.280000 0.220000 0.990000 0.990000 1.000000 1.000000 0.998783 0.990000 1 9.900000e-01 1 POTEH 23784 broad.mit.edu 37 22 16279226 16279226 + Missense_Mutation SNP C C A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr22:16279226C>A ENST00000343518.6 - 4 1048 c.997G>T c.(997-999)Gca>Tca p.A333S POTEH-AS1_ENST00000422014.1_RNA|RNU6-816P_ENST00000390914.1_RNA NM_001136213.1 NP_001129685.1 Q6S545 POTEH_HUMAN POTE ankyrin domain family, member H 37 TTTAAATTTGCTTTTTTCTTG 0.323000 0 SO:0001583 missense ENST00000343518.6 0 1 hg19 CCDS46658.1 . . . . . . . . . . . 12.84 2.059525 0.36373 . . ENSG00000198062 ENST00000359587;ENST00000343518 T 0.61392 0.11 1.38 0.308 0.15815 Ankyrin repeat-containing domain (4); 0.217456 0.22410 U 0.060437 T 0.70116 0.3187 M 0.82823 2.61 0.09310 N 1 D;D 0.76494 0.976;0.999 D;D 0.87578 0.91;0.998 T 0.58306 -0.7659 10 0.72032 D 0.01 . 3.5736 0.07926 0.0:0.7344:0.0:0.2656 . 333;296 Q6S545;A6NKF6 POTEH_HUMAN;. S 296;333 ENSP00000340610:A333S ENSP00000340610:A333S A - 1 0 POTEH 14659226 0.302000 0.24454 0.001000 0.08648 0.061000 0.15899 1.944000 0.40263 0.148000 0.19059 0.175000 0.17021 GCA TCGA-IB-A6UG-01A-32D-A33T-08 POTEH-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000276918.4 0 0 0 34 2461 0 408 0 0 0 0 408 2 0 0 0 0 0 2 1 0.999968 19 1079 0 424 2 0 0 0 0 408 2 -3.221884 1 1 0 0 1 0.220000 3.280000 0 0 RTDR1 0 broad.mit.edu 37 22 23406095 23406095 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr22:23406095G>A ENST00000216036.4 - 5 834 c.638C>T c.(637-639)gCg>gTg p.A213V NM_014433.2 NP_055248.1 Q9UHP6 RTDR1_HUMAN 18 all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181) ATTAAGGAGCGCACGGGCGGC 0.632000 0 SO:0001583 missense ENST00000216036.4 0 1 hg19 CCDS13803.1 . . . . . . . . . . G 5.511 0.279316 0.10458 . . ENSG00000100218 ENST00000216036 T 0.54279 0.58 4.71 1.43 0.22495 Armadillo-like helical (1);Armadillo-type fold (1); 1.325690 0.04962 N 0.462276 T 0.46521 0.1397 L 0.56769 1.78 0.09310 N 0.999997 B 0.29115 0.233 B 0.20384 0.029 T 0.22765 -1.0207 10 0.28530 T 0.3 -5.5588 6.8903 0.24226 0.3029:0.0:0.6971:0.0 . 213 Q9UHP6 RTDR1_HUMAN V 213 ENSP00000216036:A213V ENSP00000216036:A213V A - 2 0 RTDR1 21736095 0.002000 0.14202 0.000000 0.03702 0.002000 0.02628 1.081000 0.30791 0.169000 0.19679 0.555000 0.69702 GCG TCGA-IB-A6UG-01A-32D-A33T-08 RTDR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319049.1 0 0 0 4 247 0 49 0 1.374886e-03 0 3 0 49 2 0 0 0 0 0 2 1 0.887291 4 243 0 48 2 0 0 0 0 49 2 -5.063110 1 1 121412 1 32 1 1 2 3 2.005848 0 0.220000 3.280000 0.297297 0.170000 0.050000 0.380000 0.150000 0.197542 0.170000 0 1.000000e-01 2.800000e-01 GNAZ 2781 broad.mit.edu 37 22 23438122 23438122 + Silent SNP G G A rs143475223 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr22:23438122G>A ENST00000248996.4 + 2 906 c.240G>A c.(238-240)tcG>tcA p.S80S RTDR1_ENST00000216036.4_Intron NM_002073.2 NP_002064.1 P19086 GNAZ_HUMAN guanine nucleotide binding protein (G protein), alpha z polypeptide 19 all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181) CCATCGACTCGCTGACCCGCA 0.622000 0 SO:0001819 synonymous_variant ENST00000248996.4 1 1 hg19 CCDS13804.1 TCGA-IB-A6UG-01A-32D-A33T-08 GNAZ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319073.1 1 0 0 57 1147 0 265 0 0 0 1 0 265 2 0 0 0 0 0 2 1 1.000000 57 1142 0 262 2 0 0 0 0 265 2 -5.607851 1 1 121412 7 46 1 1 2 3 2.005848 0 0.220000 3.280000 0.297297 0.470000 0.360000 0.600000 0.480000 0.484349 0.470000 0 4.100000e-01 5.400000e-01 MYH9 4627 broad.mit.edu 37 22 36712651 36712651 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr22:36712651G>A ENST00000216181.5 - 12 1521 c.1291C>T c.(1291-1293)Ctg>Ttg p.L431L RN7SL349P_ENST00000582364.1_RNA NM_002473.4 NP_002464.1 P35579 MYH9_HUMAN myosin, heavy chain 9, non-muscle 86 TTGATGCGCAGCACCAGCCAG 0.607000 T ALK ALCL Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome Hereditary Macrothrombocytopenia, MYH9-associated Dom yes 22 22q13.1 4627 myosin, heavy polypeptide 9, non-muscle yes L 0 SO:0001819 synonymous_variant Familial Cancer Database MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA ENST00000216181.5 0 1 hg19 CCDS13927.1 TCGA-IB-A6UG-01A-32D-A33T-08 MYH9-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000259110.3 0 0 0 5 481 0 85 0 9.167354e-01 0 432 0 85 2 0 0 0 0 0 2 1 0.936133 5 476 0 83 2 0 0 0 0 85 2 -2.528261 1 1 0 0 1 1 2 3 2.005848 0 0.220000 3.280000 0.297297 0.110000 0.030000 0.230000 0.100000 0.123459 0.110000 0 6.000000e-02 1.700000e-01 MCHR1 2847 broad.mit.edu 37 22 41077637 41077637 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr22:41077637G>A ENST00000249016.4 + 2 1670 c.974G>A c.(973-975)cGc>cAc p.R325H MCHR1_ENST00000498400.1_3'UTR|MCHR1_ENST00000381433.2_Missense_Mutation_p.R199H NM_005297.3 NP_005288.3 Q99705 MCHR1_HUMAN melanin-concentrating hormone receptor 1 20 AGGGTGACCCGCACAGCCATC 0.617000 0 SO:0001583 missense ENST00000249016.4 0 1 hg19 CCDS14004.1 . . . . . . . . . . G 26.5 4.747866 0.89663 . . ENSG00000128285 ENST00000249016;ENST00000381433 T;T 0.40225 1.04;1.04 5.24 5.24 0.73138 GPCR, rhodopsin-like superfamily (1); 0.000000 0.85682 D 0.000000 T 0.68805 0.3041 M 0.85630 2.765 0.51233 D 0.999918 D 0.89917 1.0 D 0.91635 0.999 T 0.73344 -0.4012 10 0.62326 D 0.03 . 16.6948 0.85332 0.0:0.0:1.0:0.0 . 325 Q99705 MCHR1_HUMAN H 325;199 ENSP00000249016:R325H;ENSP00000370841:R199H ENSP00000249016:R325H R + 2 0 MCHR1 39407583 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 6.679000 0.74513 2.607000 0.88179 0.655000 0.94253 CGC TCGA-IB-A6UG-01A-32D-A33T-08 MCHR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317142.1 0 0 0 6 396 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 0.964433 6 393 0 71 2 0 0 0 0 73 2 -2.924391 1 1 121412 4 36 1 0.220000 3.280000 0 0 MERTK 10461 broad.mit.edu 37 2 112785977 112785977 + Missense_Mutation SNP A A G TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:112785977A>G ENST00000295408.4 + 19 2793 c.2536A>G c.(2536-2538)Acc>Gcc p.T846A MERTK_ENST00000421804.2_Missense_Mutation_p.T846A|MERTK_ENST00000409780.1_Missense_Mutation_p.T670A Q12866 MERTK_HUMAN MER proto-oncogene, tyrosine kinase 46 AGACCGCCCCACCTTTTCAGT 0.443000 0 SO:0001583 missense ENST00000295408.4 1 1 hg19 CCDS2094.1 . . . . . . . . . . A 11.42 1.634279 0.29068 . . ENSG00000153208 ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780;ENST00000449344 T;T;T;T 0.66638 -0.22;-0.22;-0.22;-0.22 5.75 1.76 0.24704 Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.494897 0.14911 U 0.291237 T 0.60932 0.2307 M 0.64676 1.99 0.18873 N 0.999985 B 0.20988 0.05 B 0.25614 0.062 T 0.55617 -0.8113 10 0.62326 D 0.03 -7.7489 6.9481 0.24530 0.4709:0.126:0.0:0.4031 . 846 Q12866 MERTK_HUMAN A 846;846;505;670;170 ENSP00000295408:T846A;ENSP00000389152:T846A;ENSP00000387277:T670A;ENSP00000412660:T170A ENSP00000295408:T846A T + 1 0 MERTK 112502448 0.001000 0.12720 0.045000 0.18777 0.584000 0.36387 0.722000 0.25925 0.040000 0.15660 0.533000 0.62120 ACC TCGA-IB-A6UG-01A-32D-A33T-08 MERTK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254046.2 1 0 0 33 354 0 89 0 4.149036e-02 0 4 0 89 2 0 0 0 0 0 2 1 1.000000 32 350 0 88 2 0 0 0 0 89 2 -20.000000 1 1 0 0 1 1 2 3 1.949331 0 0.220000 3.280000 0.297297 0.860000 0.600000 1.000000 1.000000 0.859452 0.860000 1 7.200000e-01 1 SCN3A 6328 broad.mit.edu 37 2 166018859 166018859 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:166018859C>T ENST00000360093.3 - 9 1481 c.990G>A c.(988-990)ggG>ggA p.G330G SCN3A_ENST00000283254.7_Silent_p.G330G|SCN3A_ENST00000409101.3_Silent_p.G330G NM_001081677.1 NP_001075146.1 Q9NY46 SCN3A_HUMAN sodium channel, voltage-gated, type III, alpha subunit 120 Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909) GGTCTTTTTGCCCATCCAAAA 0.294000 0 SO:0001819 synonymous_variant ENST00000360093.3 0 1 hg19 TCGA-IB-A6UG-01A-32D-A33T-08 SCN3A-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 0 6 811 0 144 0 0 0 0 144 2 0 0 0 0 0 2 1 0.963405 6 799 0 142 2 0 0 0 0 144 2 -1.698013 0 1 0 0 1 1 2 3 1.949331 0 0.220000 3.280000 0.297297 0.070000 0.020000 0.160000 0.070000 0.086016 0.070000 0 4.000000e-02 1.200000e-01 SCN2A 6326 broad.mit.edu 37 2 166245632 166245632 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:166245632C>T ENST00000375437.2 + 27 5606 c.5316C>T c.(5314-5316)atC>atT p.I1772I SCN2A_ENST00000357398.3_Silent_p.I1772I|SCN2A_ENST00000375427.2_Silent_p.I1772I|SCN2A_ENST00000283256.6_Silent_p.I1772I NM_001040142.1 NP_001035232.1 Q99250 SCN2A_HUMAN sodium channel, voltage-gated, type II, alpha subunit 118 Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909) ACATGTACATCGCGGTCATCC 0.443000 0 SO:0001819 synonymous_variant ENST00000375437.2 0 1 hg19 CCDS33314.1 TCGA-IB-A6UG-01A-32D-A33T-08 SCN2A-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000102659.2 1 0 1 114 442 0 126 0 0 0 0 126 2 0 0 0 0 0 2 1 1.000000 104 397 0 151 2 0 0 0 0 126 2 -20.000000 1 1 0 0 1 1 2 3 1.949331 0 0.220000 3.280000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 HECW2 57520 broad.mit.edu 37 2 197135945 197135945 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:197135945G>A ENST00000260983.3 - 17 3489 c.3307C>T c.(3307-3309)Cct>Tct p.P1103S HECW2_ENST00000409111.1_Missense_Mutation_p.P747S NM_020760.1 NP_065811.1 Q9P2P5 HECW2_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 113 GTAAGATCAGGTTGACGCTCC 0.328000 0 SO:0001583 missense ENST00000260983.3 1 1 hg19 CCDS33354.1 . . . . . . . . . . G 21.7 4.186065 0.78789 . . ENSG00000138411 ENST00000409111;ENST00000260983 D;D 0.84660 -1.88;-1.88 5.72 5.72 0.89469 . 0.000000 0.85682 D 0.000000 D 0.85911 0.5807 L 0.51422 1.61 0.80722 D 1 D 0.57899 0.981 P 0.49140 0.601 T 0.82764 -0.0296 10 0.22706 T 0.39 . 19.8791 0.96888 0.0:0.0:1.0:0.0 . 1103 Q9P2P5 HECW2_HUMAN S 747;1103 ENSP00000386775:P747S;ENSP00000260983:P1103S ENSP00000260983:P1103S P - 1 0 HECW2 196844190 1.000000 0.71417 1.000000 0.80357 0.967000 0.64934 9.821000 0.99360 2.706000 0.92434 0.467000 0.42956 CCT TCGA-IB-A6UG-01A-32D-A33T-08 HECW2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335199.3 1 0 0 20 186 0 27 0 0 0 1 0 27 2 0 0 0 0 0 2 1 0.999996 20 186 0 27 2 0 0 0 0 27 2 -9.159397 1 1 0 0 1 1 2 3 1.966308 0 0.220000 3.280000 0.297297 0.980000 0.630000 1.000000 1.000000 0.920897 0.980000 1 7.900000e-01 1 CCDC108 255101 broad.mit.edu 37 2 219870881 219870881 + Missense_Mutation SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:219870881G>T ENST00000341552.5 - 31 4867 c.4784C>A c.(4783-4785)cCa>cAa p.P1595Q CCDC108_ENST00000441968.1_Missense_Mutation_p.P1595Q|AC097468.4_ENST00000441450.1_RNA|CCDC108_ENST00000453220.1_Missense_Mutation_p.P1595Q NM_194302.2 NP_919278.2 Q6ZU64 CC108_HUMAN coiled-coil domain containing 108 80 Renal(207;0.0915) CTCCTCCTTTGGGGTCTGCAG 0.622000 0 SO:0001583 missense ENST00000341552.5 1 1 hg19 CCDS2430.2 . . . . . . . . . . G 6.343 0.431430 0.12045 . . ENSG00000181378 ENST00000341552;ENST00000441968;ENST00000453220 T;T;T 0.04917 3.53;3.53;3.53 5.56 3.73 0.42828 . 1.183400 0.06364 N 0.712220 T 0.08223 0.0205 L 0.48642 1.525 0.09310 N 1 B 0.19935 0.04 B 0.17979 0.02 T 0.42310 -0.9459 10 0.30854 T 0.27 0.573 8.21 0.31478 0.0809:0.3029:0.6162:0.0 . 1595 Q6ZU64 CC108_HUMAN Q 1595 ENSP00000340776:P1595Q;ENSP00000413377:P1595Q;ENSP00000409117:P1595Q ENSP00000340776:P1595Q P - 2 0 CCDC108 219579125 0.055000 0.20627 0.001000 0.08648 0.215000 0.24574 2.473000 0.45145 0.681000 0.31386 0.655000 0.94253 CCA TCGA-IB-A6UG-01A-32D-A33T-08 CCDC108-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256598.4 1 0 0 55 505 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 1.000000 55 498 0 103 2 0 0 0 0 104 2 -2.806910 1 1 0 0 1 1 2 3 1.966308 0 0.220000 3.280000 0.297297 0.980000 0.750000 1.000000 1.000000 0.949885 0.980000 1 8.600000e-01 1 TMEM198 130612 broad.mit.edu 37 2 220414551 220414551 + Missense_Mutation SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:220414551G>T ENST00000344458.2 + 6 1643 c.1058G>T c.(1057-1059)tGc>tTc p.C353F RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA|TMEM198_ENST00000373883.3_Missense_Mutation_p.C353F Q66K66 TM198_HUMAN transmembrane protein 198 16 Renal(207;0.0376) CTGACAGCCTGCTCAGGCCCC 0.627000 0 SO:0001583 missense ENST00000344458.2 1 1 hg19 CCDS33385.1 . . . . . . . . . . G 13.93 2.385363 0.42308 . . ENSG00000188760 ENST00000344458;ENST00000373883 . . . 5.1 5.1 0.69264 . 0.567610 0.18237 N 0.147345 T 0.41442 0.1159 N 0.08118 0 0.42499 D 0.992924 B 0.29909 0.261 B 0.28139 0.086 T 0.41288 -0.9517 9 0.46703 T 0.11 -22.6022 18.6999 0.91617 0.0:0.0:1.0:0.0 . 353 Q66K66 TM198_HUMAN F 353 . ENSP00000343507:C353F C + 2 0 TMEM198 220122795 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 3.327000 0.52045 2.824000 0.97209 0.655000 0.94253 TGC TCGA-IB-A6UG-01A-32D-A33T-08 TMEM198-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131063.1 1 0 0 42 476 0 102 0 4.697136e-01 1 18 0 102 2 0 0 0 0 0 2 1 1.000000 42 474 0 100 2 0 0 0 0 102 2 -20.000000 1 0 0 0 1 1 2 3 1.966308 0 0.220000 3.280000 0.297297 0.810000 0.600000 1.000000 1.000000 0.825001 0.810000 0 7.000000e-01 9.500000e-01 SPHKAP 80309 broad.mit.edu 37 2 228996774 228996774 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:228996774G>A ENST00000392056.3 - 2 106 c.60C>T c.(58-60)gaC>gaT p.D20D SPHKAP_ENST00000344657.5_Silent_p.D20D NM_001142644.1 NP_001136116.1 Q2M3C7 SPKAP_HUMAN SPHK1 interactor, AKAP domain containing 185 Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23) GTTCCAAAACGTCATACATCC 0.463000 0 SO:0001819 synonymous_variant ENST00000392056.3 1 1 hg19 CCDS46537.1 TCGA-IB-A6UG-01A-32D-A33T-08 SPHKAP-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000331750.1 1 0 1 55 364 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 55 360 0 73 2 0 0 0 0 73 2 -19.999120 1 1 0 0 1 1 2 3 1.966308 0 0.220000 3.280000 0.297297 0.990000 0.990000 1.000000 1.000000 0.999214 0.990000 1 9.900000e-01 1 KIF1A 547 broad.mit.edu 37 2 241679772 241679772 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:241679772C>T ENST00000320389.7 - 34 3614 c.3456G>A c.(3454-3456)ccG>ccA p.P1152P KIF1A_ENST00000498729.2_Silent_p.P1253P NM_004321.6 NP_004312.2 Q12756 KIF1A_HUMAN kinesin family member 1A 66 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) CCACCACGGCCGGGATGTAAC 0.652000 0 SO:0001819 synonymous_variant ENST00000320389.7 1 1 hg19 CCDS46561.1 . . . . . . . . . . C 8.323 0.824643 0.16678 . . ENSG00000130294 ENST00000431776 . . . 4.3 -8.6 0.00889 . . . . . T 0.32466 0.0830 . . . 0.80722 D 1 . . . . . . T 0.38628 -0.9652 4 . . . . 0.4882 0.00559 0.3187:0.2189:0.1339:0.3285 . . . . Q 76 . . R - 2 0 KIF1A 241328445 0.000000 0.05858 0.332000 0.25469 0.904000 0.53231 -1.756000 0.01813 -2.439000 0.00551 -1.728000 0.00702 CGG TCGA-IB-A6UG-01A-32D-A33T-08 KIF1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324536.3 1 0 1 73 216 0 55 0 8.747266e-01 0 13 0 55 2 0 0 0 0 0 2 1 1.000000 71 213 0 54 2 0 0 0 0 55 2 -5.023670 1 1 121014 5 36 1 1 2 3 1.966308 0 0.220000 3.280000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 POMC 5443 broad.mit.edu 37 2 25384428 25384428 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr2:25384428G>A ENST00000405623.1 - 3 781 c.326C>T c.(325-327)gCg>gTg p.A109V POMC_ENST00000264708.3_Missense_Mutation_p.A109V|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000395826.2_Missense_Mutation_p.A109V|POMC_ENST00000380794.1_Missense_Mutation_p.A109V P01189 COLI_HUMAN proopiomelanocortin 12 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Loperamide(DB00836) GTCTTCGCCCGCTGAGACGTC 0.721000 Colon(110;1515 1566 8452 10082 43216) 0 SO:0001583 missense ENST00000405623.1 0 1 hg19 CCDS1717.1 . . . . . . . . . . G 6.712 0.500039 0.12762 . . ENSG00000115138 ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220 T;T;T;T;T 0.79554 -1.27;-1.27;-1.27;-1.27;-1.28 4.67 -2.23 0.06930 . 0.794205 0.10616 N 0.653875 T 0.50633 0.1627 N 0.03050 -0.425 0.09310 N 1 B 0.13145 0.007 B 0.04013 0.001 T 0.37361 -0.9709 10 0.39692 T 0.17 -10.6454 1.6553 0.02780 0.3084:0.2269:0.3493:0.1154 . 109 P01189 COLI_HUMAN V 109 ENSP00000370171:A109V;ENSP00000384092:A109V;ENSP00000264708:A109V;ENSP00000379170:A109V;ENSP00000387993:A109V ENSP00000264708:A109V A - 2 0 POMC 25237932 0.000000 0.05858 0.000000 0.03702 0.024000 0.10985 0.224000 0.17738 -0.089000 0.12484 0.462000 0.41574 GCG TCGA-IB-A6UG-01A-32D-A33T-08 POMC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211573.3 1 0 0 9 51 0 10 0 1.298963e-01 0 4 0 10 2 0 0 0 0 0 2 1 0.994642 9 49 0 10 2 0 0 0 0 10 2 -19.953260 1 1 0 0 1 1 2 3 1.949331 0 0.220000 3.280000 0.297297 0.990000 0.780000 1.000000 1.000000 0.986281 0.990000 1 9.900000e-01 1 KIAA1407 57577 broad.mit.edu 37 3 113755633 113755633 + Splice_Site SNP T T A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr3:113755633T>A ENST00000295878.3 - 5 562 c.416A>T c.(415-417)gAt>gTt p.D139V KIAA1407_ENST00000545063.1_5'UTR NM_020817.1 NP_065868.1 Q8NCU4 K1407_HUMAN KIAA1407 40 GCCACATAAATCTGGGGGAAA 0.294000 0 SO:0001630 splice_region_variant ENST00000295878.3 0 1 hg19 CCDS2977.1 . . . . . . . . . . T 20.2 3.949426 0.73787 . . ENSG00000163617 ENST00000295878;ENST00000491000;ENST00000483766 T;T 0.52983 1.26;0.64 5.28 5.28 0.74379 . 0.056870 0.64402 D 0.000002 T 0.62660 0.2446 L 0.55481 1.735 0.80722 D 1 D;D;D 0.67145 0.996;0.996;0.989 P;D;P 0.66497 0.9;0.944;0.892 T 0.64521 -0.6388 10 0.56958 D 0.05 . 15.3725 0.74577 0.0:0.0:0.0:1.0 . 126;15;139 C9JA89;B4DIZ9;Q8NCU4 .;.;K1407_HUMAN V 139;126;103 ENSP00000295878:D139V;ENSP00000418099:D126V ENSP00000295878:D139V D - 2 0 KIAA1407 115238323 1.000000 0.71417 0.990000 0.47175 0.968000 0.65278 5.908000 0.69916 2.207000 0.71202 0.528000 0.53228 GAT TCGA-IB-A6UG-01A-32D-A33T-08 KIAA1407-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354724.2 0 0 0 44 194 0 38 0 6.813097e-01 0 12 0 38 2 0 0 0 0 0 2 1 1.000000 44 193 0 38 2 0 0 0 0 38 2 -20.000000 1 1 0 0 1 2 2 4 2.111415 1 0.220000 3.280000 0.354839 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TRANK1 9881 broad.mit.edu 37 3 36896676 36896676 + Missense_Mutation SNP T T C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr3:36896676T>C ENST00000429976.2 - 12 4652 c.4405A>G c.(4405-4407)Agg>Ggg p.R1469G TRANK1_ENST00000428977.2_Missense_Mutation_p.R919G|TRANK1_ENST00000301807.6_Missense_Mutation_p.R919G NM_014831.2 NP_055646.2 O15050 TRNK1_HUMAN tetratricopeptide repeat and ankyrin repeat containing 1 73 GAGTGGGACCTGTAATTCTGG 0.527000 0 SO:0001583 missense ENST00000429976.2 0 1 hg19 CCDS46789.2 . . . . . . . . . . T 18.87 3.714865 0.68844 . . ENSG00000168016 ENST00000428977;ENST00000429976;ENST00000301807 D;D;D 0.98090 -4.71;-4.71;-4.71 5.54 2.99 0.34606 . 0.000000 0.64402 D 0.000006 D 0.98248 0.9420 M 0.72894 2.215 0.42207 D 0.99179 D 0.89917 1.0 D 0.83275 0.996 D 0.98977 1.0803 10 0.87932 D 0 . 13.4212 0.60998 0.0:0.0:0.304:0.696 . 1469 O15050 TRNK1_HUMAN G 919;1469;919 ENSP00000416826:R919G;ENSP00000416168:R1469G;ENSP00000301807:R919G ENSP00000301807:R919G R - 1 2 TRANK1 36871680 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 0.445000 0.21677 1.021000 0.39600 0.459000 0.35465 AGG TCGA-IB-A6UG-01A-32D-A33T-08 TRANK1-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 4 200 0 33 0 1.320877e-02 0 7 0 33 2 0 0 0 0 0 2 1 0.888885 4 198 0 33 2 0 0 0 0 33 2 -3.272842 1 1 0 0 1 2 2 4 2.111415 1 0.220000 3.280000 0.354839 0.240000 0.070000 1.000000 0.200000 0.292329 0.240000 0 1.400000e-01 4.000000e-01 PDZRN3 23024 broad.mit.edu 37 3 73433515 73433515 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr3:73433515G>A ENST00000263666.4 - 10 2316 c.2202C>T c.(2200-2202)gaC>gaT p.D734D PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Silent_p.D456D|PDZRN3_ENST00000466780.1_Silent_p.D391D|PDZRN3_ENST00000479530.1_Silent_p.D451D|PDZRN3_ENST00000462146.2_Silent_p.D391D NM_015009.1 NP_055824.1 Q9UPQ7 PZRN3_HUMAN PDZ domain containing ring finger 3 69 Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236) GTCTGCGCACGTCGATGCTGG 0.612000 0 SO:0001819 synonymous_variant ENST00000263666.4 1 1 hg19 CCDS33789.1 TCGA-IB-A6UG-01A-32D-A33T-08 PDZRN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352460.1 1 0 1 49 203 0 58 0 6.100392e-01 0 10 0 58 2 0 0 0 0 0 2 1 1.000000 49 201 0 58 2 0 0 0 0 58 2 -20.000000 1 1 0 0 1 2 2 4 2.111415 1 0.220000 3.280000 0.354839 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PDZRN3 23024 broad.mit.edu 37 3 73434878 73434878 + Missense_Mutation SNP T T C TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr3:73434878T>C ENST00000263666.4 - 9 1691 c.1577A>G c.(1576-1578)gAc>gGc p.D526G PDZRN3_ENST00000466348.1_5'UTR|PDZRN3_ENST00000535920.1_Missense_Mutation_p.D248G|PDZRN3_ENST00000466780.1_Missense_Mutation_p.D183G|PDZRN3_ENST00000479530.1_Missense_Mutation_p.D243G|PDZRN3_ENST00000462146.2_Missense_Mutation_p.D183G NM_015009.1 NP_055824.1 Q9UPQ7 PZRN3_HUMAN PDZ domain containing ring finger 3 69 Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236) CTCCAGCATGTCCATGTGCAG 0.567000 0 SO:0001583 missense ENST00000263666.4 1 1 hg19 CCDS33789.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 18.35|18.35 3.603678|3.603678 0.66445|0.66445 .|. .|. ENSG00000121440|ENSG00000121440 ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000416926;ENST00000492909|ENST00000494559 T;T;T;T;T;T|. 0.10477|. 2.87;3.59;3.48;3.48;3.59;3.58|. 5.58|5.58 5.58|5.58 0.84498|0.84498 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.70029|0.70029 0.3177|0.3177 L|L 0.56769|0.56769 1.78|1.78 0.80722|0.80722 D|D 1|1 B;D;B;D|. 0.89917|. 0.004;1.0;0.005;0.999|. B;D;B;D|. 0.87578|. 0.02;0.998;0.013;0.995|. T|T 0.68625|0.68625 -0.5359|-0.5359 10|5 0.32370|. T|. 0.25|. .|. 15.4073|15.4073 0.74890|0.74890 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. 248;243;243;526|. F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7|. .;.;.;PZRN3_HUMAN|. G|A 526;248;183;183;243;526;224|123 ENSP00000263666:D526G;ENSP00000442026:D248G;ENSP00000418168:D183G;ENSP00000418484:D183G;ENSP00000418624:D243G;ENSP00000419250:D224G|. ENSP00000263666:D526G|. D|T -|- 2|1 0|0 PDZRN3|PDZRN3 73517568|73517568 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.996000|0.996000 0.88848|0.88848 7.852000|7.852000 0.86927|0.86927 2.117000|2.117000 0.64856|0.64856 0.533000|0.533000 0.62120|0.62120 GAC|ACA TCGA-IB-A6UG-01A-32D-A33T-08 PDZRN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352460.1 1 0 0 34 436 0 79 0 1.154710e-01 0 8 0 79 2 0 0 0 0 0 2 1 1.000000 33 435 0 79 2 0 0 0 0 79 2 -9.208489 1 1 0 0 1 2 2 4 2.111415 1 0.220000 3.280000 0.354839 0.800000 0.560000 1.000000 1.000000 0.813223 0.800000 0 6.700000e-01 9.600000e-01 TRPC3 7222 broad.mit.edu 37 4 122846207 122846207 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr4:122846207C>T ENST00000379645.3 - 3 1215 c.1142G>A c.(1141-1143)cGt>cAt p.R381H TRPC3_ENST00000264811.5_Missense_Mutation_p.R308H|TRPC3_ENST00000513531.1_Missense_Mutation_p.R308H NM_001130698.1 NP_001124170.1 Q13507 TRPC3_HUMAN transient receptor potential cation channel, subfamily C, member 3 p.R308P(1) 51 AAGTTTGACACGACTTAATGA 0.423000 1 Substitution - Missense(1) SO:0001583 missense ENST00000379645.3 1 1 hg19 CCDS47130.1 . . . . . . . . . . C 36 5.670425 0.96754 . . ENSG00000138741 ENST00000264811;ENST00000379645;ENST00000513531 T;T;T 0.74315 -0.83;-0.83;-0.83 5.92 5.92 0.95590 . 0.075570 0.56097 D 0.000024 D 0.89643 0.6774 M 0.91768 3.24 0.80722 D 1 D;D;D 0.89917 0.986;1.0;0.996 P;D;P 0.70716 0.684;0.97;0.781 D 0.90928 0.4788 10 0.87932 D 0 -16.1466 20.3081 0.98638 0.0:1.0:0.0:0.0 . 296;308;381 Q13507;E9PCJ9;Q5G1L5 TRPC3_HUMAN;.;. H 308;381;308 ENSP00000264811:R308H;ENSP00000368966:R381H;ENSP00000426899:R308H ENSP00000264811:R308H R - 2 0 TRPC3 123065657 1.000000 0.71417 0.999000 0.59377 0.994000 0.84299 7.755000 0.85180 2.795000 0.96236 0.655000 0.94253 CGT TCGA-IB-A6UG-01A-32D-A33T-08 TRPC3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000364252.1 1 0 1 96 475 0 93 0 0 0 0 93 2 0 0 1 0 0 0 2 1 1.000000 95 470 0 93 2 0 0 0 0 93 2 -20.000000 1 1 121412 1 37 1 1 2 3 1.965441 0 0.220000 3.280000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SLC12A7 10723 broad.mit.edu 37 5 1083957 1083957 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:1083957G>A ENST00000264930.5 - 8 1075 c.1032C>T c.(1030-1032)aaC>aaT p.N344N NM_006598.2 NP_006589.2 Q9Y666 S12A7_HUMAN solute carrier family 12 (potassium/chloride transporter), member 7 32 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09) Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165) Potassium Chloride(DB00761) GCTGGGAGCCGTTGCAGAAGA 0.647000 0 SO:0001819 synonymous_variant ENST00000264930.5 0 1 hg19 CCDS34129.1 TCGA-IB-A6UG-01A-32D-A33T-08 SLC12A7-001 KNOWN non_canonical_TEC|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366446.2 0 0 0 5 466 0 86 0 2.077010e-01 0 66 0 86 2 0 0 0 0 0 2 1 0.935364 5 459 0 84 2 0 0 0 0 86 2 -3.295407 1 1 121174 34 43 1 2 4 6 2.534355 1 0.220000 3.280000 0.458333 0.150000 0.030000 0.310000 0.130000 0.165380 0.150000 0 9.000000e-02 2.300000e-01 SLC6A18 348932 broad.mit.edu 37 5 1246093 1246093 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:1246093G>A ENST00000324642.3 + 12 1910 c.1787G>A c.(1786-1788)cGg>cAg p.R596Q NM_182632.2 NP_872438.2 Q96N87 S6A18_HUMAN solute carrier family 6 (neutral amino acid transporter), member 18 34 all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10) Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185) CGGCGGAGGCGGACGTGGAGG 0.731000 0 SO:0001583 missense ENST00000324642.3 0 1 hg19 CCDS3860.1 . . . . . . . . . . G 7.231 0.599235 0.13939 . . ENSG00000164363 ENST00000324642 T 0.74002 -0.8 4.41 0.824 0.18818 . 6.616820 0.01082 N 0.005003 T 0.53077 0.1774 N 0.08118 0 0.09310 N 0.999999 B 0.21147 0.052 B 0.06405 0.002 T 0.41592 -0.9500 10 0.12766 T 0.61 . 6.3418 0.21327 0.4495:0.0:0.5505:0.0 . 596 Q96N87 S6A18_HUMAN Q 596 ENSP00000323549:R596Q ENSP00000323549:R596Q R + 2 0 SLC6A18 1299093 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -1.408000 0.02485 -0.179000 0.10654 0.305000 0.20034 CGG TCGA-IB-A6UG-01A-32D-A33T-08 SLC6A18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206728.3 1 0 0 9 144 0 17 0 0 0 0 17 2 0 0 0 0 0 2 1 0.993779 9 139 0 17 2 0 0 0 0 17 2 -13.054980 1 1 0 0 1 2 4 6 2.534355 1 0.220000 3.280000 0.458333 0.800000 0.400000 1.000000 1.000000 0.792628 0.800000 0 5.700000e-01 1 DNAH5 1767 broad.mit.edu 37 5 13776708 13776708 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:13776708G>A ENST00000265104.4 - 55 9317 c.9213C>T c.(9211-9213)caC>caT p.H3071H NM_001369.2 NP_001360.1 Q8TE73 DYH5_HUMAN dynein, axonemal, heavy chain 5 378 Lung NSC(4;0.00476) TGAAGTAGTCGTGCAGGTTCT 0.468000 Kartagener syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000265104.4 0 1 hg19 CCDS3882.1 TCGA-IB-A6UG-01A-32D-A33T-08 DNAH5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207057.2 0 0 0 8 569 0 85 0 2.680007e-04 0 2 0 85 2 0 0 0 0 0 2 1 0.988908 8 562 0 85 2 0 0 0 0 85 2 -2.924833 1 1 121410 2 38 1 2 4 6 2.534355 1 0.220000 3.280000 0.458333 0.190000 0.070000 0.350000 0.180000 0.203107 0.190000 0 1.200000e-01 2.700000e-01 PCDHA10 56139 broad.mit.edu 37 5 140236911 140236911 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:140236911G>A ENST00000307360.5 + 1 1278 c.1278G>A c.(1276-1278)gcG>gcA p.A426A PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Silent_p.A426A|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron NM_018901.2 NP_061724.1 Q9Y5I2 PCDAA_HUMAN protocadherin alpha 10 79 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGGTGACCGCGCGGGACGGGG 0.647000 0 SO:0001819 synonymous_variant ENST00000307360.5 1 1 hg19 CCDS54921.1 TCGA-IB-A6UG-01A-32D-A33T-08 PCDHA10-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372895.2 1 0 1 203 684 0 236 0 0 0 1 0 236 2 0 0 0 0 0 2 1 1.000000 202 682 0 235 2 0 0 0 0 236 2 -20.000000 1 1 0 0 1 0 2 2 1.763896 1 0.220000 3.280000 0.220000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 GRIA1 2890 broad.mit.edu 37 5 153174277 153174277 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:153174277C>T ENST00000285900.5 + 14 2710 c.2367C>T c.(2365-2367)agC>agT p.S789S GRIA1_ENST00000518142.1_Silent_p.S709S|GRIA1_ENST00000340592.5_Intron|GRIA1_ENST00000448073.4_Intron|GRIA1_ENST00000521843.2_Silent_p.S720S|GRIA1_ENST00000518783.1_Silent_p.S799S NM_000827.3|NM_001258019.1 NP_000818.2|NP_001244948.1 P42261 GRIA1_HUMAN glutamate receptor, ionotropic, AMPA 1 81 Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21) Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236) AGTGCGGCAGCGGGGGAGGTG 0.463000 0 SO:0001819 synonymous_variant ENST00000285900.5 1 1 hg19 CCDS4322.1 TCGA-IB-A6UG-01A-32D-A33T-08 GRIA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252456.3 1 0 1 40 180 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1.000000 40 178 0 46 2 0 0 0 0 46 2 -3.886840 1 1 121412 1 28 1 0 2 2 1.763896 1 0.220000 3.280000 0.220000 0.990000 0.990000 1.000000 1.000000 0.999960 0.990000 1 9.900000e-01 1 KIF4B 285643 broad.mit.edu 37 5 154393886 154393886 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:154393886G>A ENST00000435029.4 + 1 627 c.467G>A c.(466-468)cGt>cAt p.R156H NM_001099293.1 NP_001092763.1 Q2VIQ3 KIF4B_HUMAN kinesin family member 4B p.R156L(2) 58 Renal(175;0.00488) Medulloblastoma(196;0.0523) KIRC - Kidney renal clear cell carcinoma(527;0.00112) TGCCCATCTCGTGAGAAAGCT 0.358000 2 Substitution - Missense(2) SO:0001583 missense ENST00000435029.4 1 1 hg19 CCDS47324.1 . . . . . . . . . . g 9.001 0.980005 0.18812 . . ENSG00000226650 ENST00000435029 T 0.72835 -0.69 1.73 0.834 0.18880 Kinesin, motor domain (4); . . . . T 0.57169 0.2035 L 0.39514 1.22 0.36431 D 0.864927 B 0.14012 0.009 B 0.18561 0.022 T 0.55256 -0.8169 9 0.54805 T 0.06 . 6.1483 0.20298 0.1824:0.0:0.8176:0.0 . 156 Q2VIQ3 KIF4B_HUMAN H 156 ENSP00000387875:R156H ENSP00000387875:R156H R + 2 0 KIF4B 154374079 0.001000 0.12720 0.940000 0.37924 0.851000 0.48451 -1.547000 0.02186 0.307000 0.22880 0.655000 0.94253 CGT TCGA-IB-A6UG-01A-32D-A33T-08 KIF4B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377478.1 1 0 1 135 509 1 113 0 0 0 1 113 2 0 0 0 0 0 2 1 1.000000 132 507 1 113 19 0 0 0 1 113 2 -20.000000 1 1 121412 3 38 1 0 2 2 1.763896 1 0.220000 3.280000 0.220000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 FBXL7 23194 broad.mit.edu 37 5 15928366 15928366 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:15928366C>T ENST00000504595.1 + 3 976 c.495C>T c.(493-495)aaC>aaT p.N165N FBXL7_ENST00000329673.7_Silent_p.N153N|FBXL7_ENST00000510662.1_Silent_p.N118N NM_001278317.1|NM_012304.3 NP_001265246.1|NP_036436.1 Q9UJT9 FBXL7_HUMAN F-box and leucine-rich repeat protein 7 60 AGACCATCAACGTGGACCGCG 0.667000 0 SO:0001819 synonymous_variant ENST00000504595.1 0 1 hg19 CCDS54833.1 TCGA-IB-A6UG-01A-32D-A33T-08 FBXL7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366117.1 1 0 0 7 130 0 18 0 3.204897e-02 0 5 0 18 2 0 0 0 0 0 2 1 0.979953 7 127 0 17 2 0 0 0 0 18 2 -10.625520 1 1 0 0 1 2 4 6 2.534355 1 0.220000 3.280000 0.458333 0.710000 0.320000 1.000000 1.000000 0.719186 0.710000 0 4.800000e-01 9.900000e-01 FLT4 2324 broad.mit.edu 37 5 180051060 180051060 + Splice_Site SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:180051060G>A ENST00000261937.6 - 11 1501 c.1423C>T c.(1423-1425)Cgg>Tgg p.R475W FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Splice_Site_p.R475W|FLT4_ENST00000393347.3_Splice_Site_p.R475W 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) TGCCGCCGCCGGCTGCCAGGA 0.647000 Colon(97;1075 1466 27033 27547 35871) 0 SO:0001630 splice_region_variant ENST00000261937.6 1 0 hg19 CCDS4457.1 . . . . . . . . . . G 13.41 2.228890 0.39399 . . ENSG00000037280 ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868 T;T;T 0.77489 -1.1;-1.09;-1.09 4.79 2.85 0.33270 Immunoglobulin subtype (1);Immunoglobulin-like (1);Tyrosine-protein kinase, vascular endothelial growth factor receptor 3 (VEGFR3), N-terminal (1); . . . . T 0.68650 0.3024 N 0.08118 0 0.43462 D 0.995669 D;D;D;D 0.71674 0.998;0.998;0.996;0.998 P;P;P;P 0.58970 0.849;0.809;0.72;0.72 T 0.66344 -0.5947 9 0.37606 T 0.19 . 7.737 0.28821 0.084:0.0:0.7557:0.1603 . 475;285;475;475 P35916-3;E9PFB0;E9PD35;P35916 .;.;.;VGFR3_HUMAN W 475;475;475;285 ENSP00000261937:R475W;ENSP00000377016:R475W;ENSP00000426057:R475W ENSP00000261937:R475W R - 1 2 FLT4 179983666 0.775000 0.28604 0.985000 0.45067 0.017000 0.09413 0.047000 0.14056 1.163000 0.42636 -0.258000 0.10820 CGG TCGA-IB-A6UG-01A-32D-A33T-08 FLT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253527.4 1 0 1 28 187 0 47 0 1.874583e-01 0 6 0 47 2 0 0 0 0 0 2 1 1.000000 28 184 0 45 2 0 0 0 0 47 2 -20.000000 1 1 121272 3 33 1 0 2 2 1.763896 1 0.220000 3.280000 0.220000 0.990000 0.810000 1.000000 1.000000 0.983675 0.990000 1 9.800000e-01 1 ADAMTS12 81792 broad.mit.edu 37 5 33576636 33576636 + Missense_Mutation SNP C C A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:33576636C>A ENST00000504830.1 - 19 3830 c.3495G>T c.(3493-3495)caG>caT p.Q1165H ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Q1080H|ADAMTS12_ENST00000504582.1_5'Flank NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 216 TGTCCTCAGGCTGTTCTCTTT 0.473000 HNSCC(64;0.19) 0 SO:0001583 missense ENST00000504830.1 1 1 hg19 CCDS34140.1 . . . . . . . . . . C 5.753 0.323334 0.10900 . . ENSG00000151388 ENST00000504830;ENST00000352040 T;T 0.60171 0.22;0.21 5.28 -0.364 0.12553 . 1.070710 0.07089 N 0.838451 T 0.50497 0.1619 L 0.32530 0.975 0.09310 N 1 P;P 0.46220 0.874;0.8 P;B 0.48141 0.568;0.365 T 0.43540 -0.9385 10 0.15499 T 0.54 . 9.923 0.41474 0.0:0.5766:0.0:0.4234 . 1080;1165 P58397-3;P58397 .;ATS12_HUMAN H 1165;1080 ENSP00000422554:Q1165H;ENSP00000344847:Q1080H ENSP00000344847:Q1080H Q - 3 2 ADAMTS12 33612393 0.000000 0.05858 0.000000 0.03702 0.070000 0.16714 0.263000 0.18478 0.012000 0.14892 0.655000 0.94253 CAG TCGA-IB-A6UG-01A-32D-A33T-08 ADAMTS12-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367164.2 1 0 1 86 429 0 105 0 4.594746e-01 0 9 0 105 2 0 0 0 0 0 2 1 1.000000 86 425 0 104 2 0 0 0 0 105 2 -20.000000 1 1 0 0 1 2 2 4 2.143143 1 0.220000 3.280000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ADAMTS16 170690 broad.mit.edu 37 5 5191804 5191804 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr5:5191804C>T ENST00000274181.7 + 8 1352 c.1214C>T c.(1213-1215)gCa>gTa p.A405V ADAMTS16_ENST00000511368.1_Missense_Mutation_p.A405V NM_139056.2 NP_620687.2 Q8TE57 ATS16_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 16 107 ACAGGATTTGCACCCATAAGT 0.388000 0 SO:0001583 missense ENST00000274181.7 0 1 hg19 CCDS43299.1 . . . . . . . . . . C 27.9 4.870816 0.91587 . . ENSG00000145536 ENST00000274181;ENST00000511368;ENST00000536857 D;D 0.95656 -3.77;-3.77 4.74 4.74 0.60224 Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2); 0.000000 0.85682 D 0.000000 D 0.98629 0.9541 H 0.97783 4.075 0.80722 D 1 D;D;D 0.89917 0.992;1.0;0.995 D;D;D 0.75020 0.939;0.985;0.976 D 0.99818 1.1045 10 0.87932 D 0 . 16.5194 0.84309 0.0:1.0:0.0:0.0 . 405;405;405 Q8TE57;Q8TE57-2;Q2XQZ0 ATS16_HUMAN;.;. V 405 ENSP00000274181:A405V;ENSP00000421631:A405V ENSP00000274181:A405V A + 2 0 ADAMTS16 5244804 1.000000 0.71417 0.952000 0.39060 0.889000 0.51656 7.324000 0.79115 2.186000 0.69663 0.655000 0.94253 GCA TCGA-IB-A6UG-01A-32D-A33T-08 ADAMTS16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365657.1 0 0 0 6 613 0 86 0 4.307491e-04 0 3 0 86 2 0 0 0 0 0 2 1 0.964577 7 609 0 86 2 0 0 0 0 86 2 -2.178036 0 1 0 0 1 2 4 6 2.534355 1 0.220000 3.280000 0.458333 0.130000 0.030000 0.270000 0.120000 0.147143 0.130000 0 8.000000e-02 2.000000e-01 ZNF184 7738 broad.mit.edu 37 6 27419354 27419354 + Nonsense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr6:27419354G>A ENST00000211936.6 - 6 2268 c.1984C>T c.(1984-1986)Cga>Tga p.R662* ZNF184_ENST00000377419.1_Nonsense_Mutation_p.R662* NM_007149.2 NP_009080.2 Q99676 ZN184_HUMAN zinc finger protein 184 48 GTGTGAATTCGTTGATGCTGA 0.423000 0 SO:0001587 stop_gained ENST00000211936.6 0 0 hg19 CCDS4624.1 . . . . . . . . . . G 38 6.740066 0.97805 0.0 1.16E-4 ENSG00000096654 ENST00000211936;ENST00000377419;ENST00000341087 . . . 4.85 2.87 0.33458 . 0.385319 0.19188 N 0.120492 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 10.467 0.44614 0.0:0.0:0.4853:0.5147 . . . . X 662;662;578 . ENSP00000211936:R662X R - 1 2 ZNF184 27527333 0.006000 0.16342 0.276000 0.24689 0.998000 0.95712 1.414000 0.34736 1.336000 0.45506 0.591000 0.81541 CGA TCGA-IB-A6UG-01A-32D-A33T-08 ZNF184-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040146.1 1 0 1 40 347 0 77 1 3.253306e-01 3 8 0 77 2 0 0 0 0 0 2 1 1.000000 40 344 0 77 2 0 0 0 0 77 2 -3.142702 1 1 121412 1 18 1 0 2 2 1.759974 1 0.220000 3.280000 0.220000 0.930000 0.680000 1.000000 1.000000 0.914488 0.930000 1 8.000000e-01 1 DAXX 1616 broad.mit.edu 37 6 33289539 33289539 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr6:33289539C>T ENST00000374542.5 - 2 368 c.164G>A c.(163-165)gGc>gAc p.G55D DAXX_ENST00000414083.2_Intron|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Missense_Mutation_p.G55D NM_001141969.1|NM_001141970.1|NM_001350.4 NP_001135441.1|NP_001135442.1|NP_001341.1 Q9UER7 DAXX_HUMAN death-domain associated protein 55 GCATTTCTTGCCGCCCGAACT 0.602000 Mis, F, N Pancreatic neuroendocrine tumors. Paediatric GBM Rec yes 6 6p21.3 1616 death-domain associated protein E 0 SO:0001583 missense ENST00000374542.5 0 1 hg19 CCDS4776.1 . . . . . . . . . . C 11.34 1.608951 0.28623 . . ENSG00000204209 ENST00000266000;ENST00000374542;ENST00000446403;ENST00000453407 . . . 4.89 4.02 0.46733 . 0.660504 0.16364 N 0.217655 T 0.29355 0.0731 L 0.36672 1.1 0.80722 D 1 P;P 0.46784 0.884;0.884 P;P 0.44860 0.462;0.462 T 0.03503 -1.1030 9 0.25106 T 0.35 -0.4917 10.4358 0.44435 0.1947:0.8053:0.0:0.0 . 67;55 B4E1C1;Q9UER7 .;DAXX_HUMAN D 55 . ENSP00000266000:G55D G - 2 0 DAXX 33397517 0.869000 0.29996 0.983000 0.44433 0.735000 0.41995 1.033000 0.30191 1.281000 0.44480 0.549000 0.68633 GGC TCGA-IB-A6UG-01A-32D-A33T-08 DAXX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076403.1 0 0 0 7 1316 1 290 0 2.296276e-02 0 37 1 290 2 0 0 0 0 0 2 0 0.029433 7 1302 1 287 17 0 0 0 1 290 2 -2.138773 0 1 0 0 1 0 2 2 1.773331 1 0.220000 3.280000 0.220000 0.040000 0.010000 0.100000 0.050000 0.054794 0.040000 0 2.000000e-02 7.000000e-02 KIF6 221458 broad.mit.edu 37 6 39513398 39513398 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr6:39513398C>T ENST00000287152.7 - 11 1342 c.1248G>A c.(1246-1248)gcG>gcA p.A416A KIF6_ENST00000538893.1_Silent_p.A416A|KIF6_ENST00000373216.3_Silent_p.A416A|KIF6_ENST00000373215.3_Silent_p.A416A|KIF6_ENST00000373213.4_Silent_p.A255A NM_145027.4 NP_659464.3 Q6ZMV9 KIF6_HUMAN kinesin family member 6 52 TACGCATATCCGCGCCAACCT 0.363000 0 SO:0001819 synonymous_variant ENST00000287152.7 1 1 hg19 CCDS4844.1 . . . . . . . . . . C 1.650 -0.514326 0.04200 . . ENSG00000164627 ENST00000458470 . . . 5.56 -10.3 0.00346 . . . . . T 0.26231 0.0640 . . . 0.47584 D 0.999465 . . . . . . T 0.48990 -0.8985 4 . . . . 6.4908 0.22115 0.2761:0.1099:0.5103:0.1038 . . . . Q 308 . . R - 2 0 KIF6 39621376 0.004000 0.15560 0.015000 0.15790 0.301000 0.27625 -1.882000 0.01624 -1.844000 0.01178 -2.773000 0.00119 CGG TCGA-IB-A6UG-01A-32D-A33T-08 KIF6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000040455.2 1 0 1 55 367 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1.000000 54 360 0 66 2 0 0 0 0 66 2 -2.540688 1 1 121410 3 36 1 2 2 4 2.168044 1 0.220000 3.280000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999874 0.990000 1 9.900000e-01 1 SUPT3H 8464 broad.mit.edu 37 6 44929553 44929553 + Missense_Mutation SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr6:44929553G>T ENST00000371459.1 - 7 682 c.517C>A c.(517-519)Caa>Aaa p.Q173K SUPT3H_ENST00000306867.5_Missense_Mutation_p.Q173K|SUPT3H_ENST00000371461.2_Missense_Mutation_p.Q184K|SUPT3H_ENST00000371460.1_Missense_Mutation_p.Q184K NM_001261823.1|NM_003599.3 NP_001248752.1|NP_003590.1 O75486 SUPT3_HUMAN suppressor of Ty 3 homolog (S. cerevisiae) 12 ATTCGAGTTTGTCTTTCTGCT 0.274000 0 SO:0001583 missense ENST00000371459.1 1 0 hg19 CCDS34465.1 . . . . . . . . . . G 13.80 2.344276 0.41498 . . ENSG00000196284 ENST00000371460;ENST00000371459;ENST00000306867;ENST00000371461 T;T;T;T 0.42900 0.96;0.98;0.98;0.96 5.69 5.69 0.88448 . 0.269901 0.43260 D 0.000594 T 0.48642 0.1511 L 0.45581 1.43 0.53005 D 0.999967 B;D 0.54964 0.169;0.969 B;D 0.64877 0.075;0.93 T 0.15407 -1.0438 10 0.26408 T 0.33 . 19.8205 0.96591 0.0:0.0:1.0:0.0 . 184;255 O75486-3;O75486 .;SUPT3_HUMAN K 184;173;173;184 ENSP00000360515:Q184K;ENSP00000360514:Q173K;ENSP00000306718:Q173K;ENSP00000360516:Q184K ENSP00000306718:Q173K Q - 1 0 SUPT3H 45037531 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 6.017000 0.70805 2.670000 0.90874 0.585000 0.79938 CAA TCGA-IB-A6UG-01A-32D-A33T-08 SUPT3H-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000106911.2 1 0 0 17 341 0 58 0 4.402228e-01 0 30 0 58 2 0 0 0 0 0 2 0 0.999945 0 336 0 58 2 0 0 0 0 58 2 -18.070020 1 0 0 0 1 1 3 4 2.112062 0 0.220000 3.280000 0.360656 0.530000 0.320000 0.800000 0.520000 0.551738 0.530000 0 4.100000e-01 6.700000e-01 GABRR2 2570 broad.mit.edu 37 6 89974189 89974189 + Missense_Mutation SNP G G A rs149245573 by1000genomes TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr6:89974189G>A ENST00000402938.3 - 8 1161 c.1028C>T c.(1027-1029)gCg>gTg p.A343V GABRR2_ENST00000602399.1_Missense_Mutation_p.A368V NM_002043.3 NP_002034.3 P28476 GBRR2_HUMAN gamma-aminobutyric acid (GABA) A receptor, rho 2 p.A343V(3) 21 all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238) Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897) GTTGACAGCCGCATACTCCAG 0.597000 3 Substitution - Missense(3) SO:0001583 missense ENST00000402938.3 0 1 hg19 CCDS5020.3 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 36 5.780845 0.96929 . . ENSG00000111886 ENST00000402938 . . . 5.93 5.93 0.95920 Neurotransmitter-gated ion-channel transmembrane domain (2); 0.000000 0.85682 D 0.000000 T 0.82015 0.4945 M 0.82323 2.585 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.81116 -0.1079 8 . . . . 20.3437 0.98782 0.0:0.0:1.0:0.0 . 368 P28476 GBRR2_HUMAN V 368 . . A - 2 0 GABRR2 90030908 1.000000 0.71417 0.997000 0.53966 0.965000 0.64279 9.869000 0.99810 2.815000 0.96918 0.561000 0.74099 GCG TCGA-IB-A6UG-01A-32D-A33T-08 GABRR2-001 KNOWN upstream_ATG|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000041482.3 0 0 0 4 223 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.890111 4 222 0 46 2 0 0 0 0 46 2 -3.062005 1 1 121412 1 29 1 0 2 2 1.766904 1 0.220000 3.280000 0.220000 0.170000 0.050000 0.380000 0.160000 0.195388 0.170000 0 1.000000e-01 2.800000e-01 SSPO 23145 broad.mit.edu 37 7 149500902 149500902 + RNA SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr7:149500902G>T ENST00000378016.2 + 0 8219 A2VEC9 SSPO_HUMAN SCO-spondin Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CCAGGTTCAGGTGTGCGACAG 0.697000 0 ENST00000378016.2 1 0 hg19 TCGA-IB-A6UG-01A-32D-A33T-08 SSPO-202 KNOWN basic processed_transcript processed_transcript 1 0 1 25 104 0 26 0 0 0 0 26 2 0 0 0 0 0 2 1 1.000000 25 104 0 26 2 0 0 0 0 26 2 -20.000000 1 1 0 0 1 1 2 3 1.942062 0 0.220000 3.280000 0.296600 0.990000 0.990000 1.000000 1.000000 0.999968 0.990000 1 9.900000e-01 1 FER1L6 654463 broad.mit.edu 37 8 125035751 125035751 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a 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 29.0 4.971850 0.92919 0.0 1.2E-4 ENSG00000214814 ENST00000522917;ENST00000399018 T;T 0.79352 -1.26;-1.26 5.81 5.81 0.92471 Ferlin B-domain (1); 0.162857 0.34435 U 0.003970 D 0.89550 0.6747 M 0.91663 3.23 0.58432 D 0.999998 D 0.76494 0.999 D 0.70935 0.971 D 0.91017 0.4854 10 0.72032 D 0.01 . 12.8851 0.58038 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 1.000000 0.71417 0.981000 0.43875 0.968000 0.65278 9.072000 0.93986 2.751000 0.94390 0.555000 0.69702 CGC TCGA-IB-A6UG-01A-32D-A33T-08 FER1L6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381400.1 0 0 0 8 702 0 87 0 5.263936e-04 0 3 0 87 2 0 0 0 0 0 2 1 0.988974 9 694 0 87 2 0 0 0 0 87 2 -2.094368 0 1 120906 9 42 1 3 4 7 2.619755 1 0.220000 3.280000 0.476334 0.160000 0.060000 1.000000 0.140000 0.244907 0.160000 0 1.000000e-01 2.600000e-01 COL22A1 169044 broad.mit.edu 37 8 139737642 139737642 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr8:139737642C>T ENST00000303045.6 - 24 2627 c.2181G>A c.(2179-2181)ccG>ccA p.P727P COL22A1_ENST00000435777.1_Silent_p.P727P NM_152888.1 NP_690848.1 Q8NFW1 COMA1_HUMAN collagen, type XXII, alpha 1 211 all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0517) GAGAACCTCCCGGTCCAGGGG 0.582000 HNSCC(7;0.00092) 0 SO:0001819 synonymous_variant ENST00000303045.6 1 1 hg19 CCDS6376.1 TCGA-IB-A6UG-01A-32D-A33T-08 COL22A1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000315905.2 1 0 1 170 544 0 91 1 8.513645e-01 9 4 0 91 2 0 0 0 0 0 2 1 1.000000 167 534 0 91 2 0 0 0 0 91 2 -4.408309 1 1 121410 7 42 1 3 4 7 2.619755 1 0.220000 3.280000 0.476334 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ADRA1A 148 broad.mit.edu 37 8 26627895 26627895 + Missense_Mutation SNP G G A rs151273238 by1000genomes TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr8:26627895G>A ENST00000519229.1 - 2 1178 c.1172C>T c.(1171-1173)aCg>aTg p.T391M ADRA1A_ENST00000380581.2_Intron|ADRA1A_ENST00000380573.3_Missense_Mutation_p.T391M|ADRA1A_ENST00000380582.3_Missense_Mutation_p.T391M|ADRA1A_ENST00000354550.4_Missense_Mutation_p.T391M|ADRA1A_ENST00000380587.1_Intron|ADRA1A_ENST00000380586.1_Missense_Mutation_p.T391M|ADRA1A_ENST00000276393.4_Missense_Mutation_p.T391M P25100 ADA1D_HUMAN adrenoceptor alpha 1A 36 all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118) Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694) AACGCCATCCGTCTTGGAGAT 0.562000 0 SO:0001583 missense ENST00000519229.1 1 1 hg19 2 9.157509157509158E-4 1 0.0020325203252032522 0 0.0 1 0.0017482517482517483 0 0.0 G 14.75 2.627392 0.46944 4.54E-4 2.33E-4 ENSG00000120907 ENST00000380586;ENST00000380582;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573 T;T;T;T;T;T 0.62941 2.02;0.07;0.05;-0.01;0.06;0.06 5.96 5.06 0.68205 . 0.667620 0.14213 N 0.333955 T 0.64159 0.2573 L 0.51422 1.61 0.80722 D 1 P;P;P;D 0.54772 0.521;0.954;0.851;0.968 B;P;B;B 0.46049 0.128;0.502;0.332;0.374 T 0.67122 -0.5750 10 0.72032 D 0.01 . 16.2148 0.82198 0.0:0.0:0.8577:0.1423 . 391;391;391;391 P35348;P35348-4;P35348-3;B0ZBD3 ADA1A_HUMAN;.;.;. M 391 ENSP00000369960:T391M;ENSP00000369956:T391M;ENSP00000430793:T391M;ENSP00000346557:T391M;ENSP00000276393:T391M;ENSP00000369947:T391M ENSP00000276393:T391M T - 2 0 ADRA1A 26683812 1.000000 0.71417 0.954000 0.39281 0.837000 0.47467 4.852000 0.62904 1.445000 0.47624 0.655000 0.94253 ACG TCGA-IB-A6UG-01A-32D-A33T-08 ADRA1A-009 PUTATIVE not_organism_supported|basic|exp_conf protein_coding protein_coding OTTHUMT00000376207.1 1 0 1 74 566 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 1.000000 74 562 0 132 2 0 0 0 0 133 2 -11.297450 1 1 121412 23 49 1 1 2 3 1.792119 0 0.220000 3.280000 0.230997 0.990000 0.850000 1.000000 1.000000 0.983539 0.990000 1 9.500000e-01 1 FZD3 7976 broad.mit.edu 37 8 28385210 28385210 + Missense_Mutation SNP G G T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr8:28385210G>T ENST00000240093.3 + 5 1411 c.933G>T c.(931-933)tgG>tgT p.W311C FZD3_ENST00000537916.1_Missense_Mutation_p.W311C|RNA5SP259_ENST00000365541.1_RNA NM_017412.3 NP_059108.1 Q9NPG1 FZD3_HUMAN frizzled class receptor 3 41 Ovarian(32;2.06e-05) CCATCACATGGTTTTTAGCAG 0.433000 0 SO:0001583 missense ENST00000240093.3 1 1 hg19 CCDS6069.1 . . . . . . . . . . G 17.79 3.476133 0.63737 . . ENSG00000104290 ENST00000537916;ENST00000240093 D;D 0.91464 -2.85;-2.85 5.32 5.32 0.75619 GPCR, family 2-like (1); 0.000000 0.85682 D 0.000000 D 0.96765 0.8944 H 0.94925 3.6 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.97815 1.0253 10 0.87932 D 0 . 17.5384 0.87840 0.0:0.0:1.0:0.0 . 311 Q9NPG1 FZD3_HUMAN C 311 ENSP00000437489:W311C;ENSP00000240093:W311C ENSP00000240093:W311C W + 3 0 FZD3 28441129 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.869000 0.99810 2.482000 0.83794 0.563000 0.77884 TGG TCGA-IB-A6UG-01A-32D-A33T-08 FZD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219986.2 1 0 1 53 379 0 80 0 1.655719e-01 0 6 0 80 2 0 0 0 0 0 2 1 1.000000 53 378 0 78 2 0 0 0 0 80 2 -19.954380 1 1 0 0 1 1 2 3 1.792119 0 0.220000 3.280000 0.230997 0.990000 0.870000 1.000000 1.000000 0.989439 0.990000 1 9.900000e-01 1 MRPL15 29088 broad.mit.edu 37 8 55049226 55049226 + Splice_Site SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr8:55049226G>A ENST00000260102.4 + 2 337 c.e2+1 NM_014175.3 NP_054894.1 Q9P015 RM15_HUMAN mitochondrial ribosomal protein L15 10 Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181) OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458) AAGGACATAGGTAAGGTTGCT 0.418000 0 SO:0001630 splice_region_variant ENST00000260102.4 1 1 hg19 CCDS6158.1 . . . . . . . . . . G 18.54 3.645927 0.67358 . . ENSG00000137547 ENST00000260102;ENST00000519831 . . . 5.05 4.17 0.49024 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.9287 0.70898 0.0:0.0:0.8558:0.1441 . . . . . -1 . . . + . . MRPL15 55211779 1.000000 0.71417 1.000000 0.80357 0.950000 0.60333 9.855000 0.99526 1.326000 0.45319 -0.181000 0.13052 . TCGA-IB-A6UG-01A-32D-A33T-08 MRPL15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378254.1 1 0 1 80 413 0 65 1 2.705279e-02 2 0 0 65 2 0 0 0 0 0 2 1 1.000000 80 410 0 65 2 0 0 0 0 65 2 -20.000000 1 1 121412 1 28 1 3 3 6 2.268370 1 0.220000 3.280000 0.397590 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 MMP16 4325 broad.mit.edu 37 8 89198805 89198805 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr8:89198805C>T ENST00000286614.6 - 3 585 c.304G>A c.(304-306)Ggt>Agt p.G102S MMP16_ENST00000544227.1_5'UTR NM_005941.4 NP_005932.2 P51512 MMP16_HUMAN matrix metallopeptidase 16 (membrane-inserted) 81 Marimastat(DB00786) TCAGGTACACCGCATCGGGGC 0.378000 0 SO:0001583 missense ENST00000286614.6 1 1 hg19 CCDS6246.1 . . . . . . . . . . C 31 5.102432 0.94245 . . ENSG00000156103 ENST00000286614;ENST00000522726 T;T 0.65549 -0.16;-0.16 5.72 5.72 0.89469 Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.81029 0.4738 M 0.80847 2.515 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.76071 0.987;0.985 T 0.79757 -0.1669 10 0.41790 T 0.15 . 19.8778 0.96885 0.0:1.0:0.0:0.0 . 102;102 P51512-2;P51512 .;MMP16_HUMAN S 102;119 ENSP00000286614:G102S;ENSP00000429147:G119S ENSP00000286614:G102S G - 1 0 MMP16 89267921 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 7.487000 0.81328 2.710000 0.92621 0.585000 0.79938 GGT TCGA-IB-A6UG-01A-32D-A33T-08 MMP16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375304.2 1 0 0 50 769 0 113 0 0 0 1 0 113 2 0 0 0 0 0 2 1 1.000000 48 744 0 113 2 0 0 0 0 113 2 -2.402339 0 1 121410 2 35 1 3 4 7 2.619755 1 0.220000 3.280000 0.476334 0.840000 0.620000 1.000000 1.000000 0.849201 0.840000 0 7.200000e-01 1 RAD54B 25788 broad.mit.edu 37 8 95419794 95419794 + Silent SNP C C T rs113276250 byFrequency TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr8:95419794C>T ENST00000336148.5 - 5 778 c.654G>A c.(652-654)tcG>tcA p.S218S NM_012415.3 NP_036547.1 Q9Y620 RA54B_HUMAN RAD54 homolog B (S. cerevisiae) 39 Breast(36;4.5e-05) BRCA - Breast invasive adenocarcinoma(8;0.00217) GAGAAGAATGCGAGATAGCAG 0.398000 Direct reversal of damage;Homologous recombination 0 SO:0001819 synonymous_variant ENST00000336148.5 0 1 hg19 CCDS6262.1 TCGA-IB-A6UG-01A-32D-A33T-08 RAD54B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257806.3 0 0 0 5 471 0 80 0 2.631803e-03 0 6 0 80 2 0 0 0 0 0 2 1 0.936101 5 466 0 78 2 0 0 0 0 80 2 -2.382980 0 1 121408 95 53 1 3 4 7 2.619755 1 0.220000 3.280000 0.476334 0.160000 0.030000 1.000000 0.130000 0.243051 0.160000 0 9.000000e-02 2.800000e-01 PRPF4 9128 broad.mit.edu 37 9 116049072 116049072 + Missense_Mutation SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr9:116049072C>T ENST00000374198.4 + 9 1001 c.899C>T c.(898-900)gCg>gTg p.A300V PRPF4_ENST00000374199.4_Missense_Mutation_p.A299V NM_001244926.1|NM_004697.4 NP_001231855.1|NP_004688.2 O43172 PRP4_HUMAN pre-mRNA processing factor 4 23 GCCTCTTGTGCGGCTGATGGC 0.468000 0 SO:0001583 missense ENST00000374198.4 0 1 hg19 CCDS6791.1 . . . . . . . . . . C 32 5.163644 0.94727 . . ENSG00000136875 ENST00000374199;ENST00000374198 T;T 0.61040 0.14;0.14 5.82 5.82 0.92795 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.155793 0.56097 D 0.000025 T 0.72244 0.3436 L 0.56340 1.77 0.80722 D 1 D;D 0.76494 0.999;0.992 D;P 0.65140 0.932;0.849 T 0.73040 -0.4108 10 0.72032 D 0.01 . 19.0872 0.93209 0.0:1.0:0.0:0.0 . 315;300 Q59EL4;O43172 .;PRP4_HUMAN V 299;300 ENSP00000363315:A299V;ENSP00000363313:A300V ENSP00000363313:A300V A + 2 0 PRPF4 115088893 1.000000 0.71417 1.000000 0.80357 0.956000 0.61745 7.378000 0.79679 2.752000 0.94435 0.655000 0.94253 GCG TCGA-IB-A6UG-01A-32D-A33T-08 PRPF4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053708.2 0 0 0 10 1786 0 338 0 2.782200e-02 0 41 0 338 2 0 0 0 0 0 2 1 0.996804 10 1780 0 337 2 0 0 0 0 338 2 -2.138998 0 1 121412 4 43 1 1 2 3 1.945305 0 0.220000 3.280000 0.292389 0.050000 0.010000 1.000000 0.060000 0.114169 0.050000 0 3.000000e-02 9.000000e-02 COL27A1 85301 broad.mit.edu 37 9 117029789 117029789 + Silent SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr9:117029789G>A ENST00000356083.3 + 34 3844 c.3453G>A c.(3451-3453)ccG>ccA p.P1151P NM_032888.2 NP_116277.2 Q8IZC6 CORA1_HUMAN collagen, type XXVII, alpha 1 80 TTCAGGGGCCGCCTGGTGCAG 0.562000 0 SO:0001819 synonymous_variant ENST00000356083.3 1 1 hg19 CCDS6802.1 TCGA-IB-A6UG-01A-32D-A33T-08 COL27A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053763.1 1 0 0 20 202 0 30 0 6.784022e-01 0 25 0 30 2 0 0 0 0 0 2 1 0.999996 20 201 0 30 2 0 0 0 0 30 2 -3.142705 1 1 121412 5 39 1 1 2 3 1.945305 0 0.220000 3.280000 0.292389 0.920000 0.580000 1.000000 1.000000 0.887802 0.920000 1 7.300000e-01 1 CDKN2A 1029 broad.mit.edu 37 9 21971120 21971120 + Nonsense_Mutation SNP G G A rs121913388 TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr9:21971120G>A ENST00000304494.5 - 2 508 c.238C>T c.(238-240)Cga>Tga p.R80* CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29* NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) TGCACGGGTCGGGTGAGAGTG 0.726000 R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1474 Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1) GRCh37 CM014695 CDKN2A M rs121913388 SO:0001587 stop_gained ENST00000304494.5 0 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 39|39 7.328457|7.328457 0.98214|0.98214 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 D;D|. 0.86497|. -2.13;-2.02|. 5.93|5.93 5.01|5.01 0.66863|0.66863 .|. 0.000000|. 0.37136|. N|. 0.002233|. T|. 0.44561|. 0.1299|. L|L 0.36672|0.36672 1.1|1.1 0.47511|0.47511 D|D 0.999443|0.999443 D|. 0.59357|. 0.985|. B|. 0.40602|. 0.334|. T|. 0.34825|. -0.9813|. 10|. 0.13108|0.02654 T|T 0.6|1 -2.989|-2.989 8.7197|8.7197 0.34434|0.34434 0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526 .|. 135|. Q8N726|. CD2A2_HUMAN|. L|X 135;94|80 ENSP00000355153:P135L;ENSP00000432664:P94L|. ENSP00000355153:P135L|ENSP00000307101:R80X P|R -|- 2|1 0|2 CDKN2A|CDKN2A 21961120|21961120 0.995000|0.995000 0.38212|0.38212 1.000000|1.000000 0.80357|0.80357 0.899000|0.899000 0.52679|0.52679 2.363000|2.363000 0.44178|0.44178 1.464000|1.464000 0.47987|0.47987 0.650000|0.650000 0.86243|0.86243 CCG|CGA TCGA-IB-A6UG-01A-32D-A33T-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 49 100 0 28 1 1 97 8 0 28 2 1 1 55 116 0 97 2 1 1.000000 40 83 0 25 2 0 0 0 0 28 2 -6.798055 1 1 0 0 1 0 3 3 1.930506 1 0.220000 3.280000 0.296600 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 KIAA1432 0 broad.mit.edu 37 9 5765691 5765691 + Silent SNP C C T TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr9:5765691C>T ENST00000414202.2 + 21 3221 c.3030C>T c.(3028-3030)ttC>ttT p.F1010F KIAA1432_ENST00000449720.2_Silent_p.F894F|KIAA1432_ENST00000251879.6_Silent_p.F1010F|KIAA1432_ENST00000418622.3_Silent_p.F931F|KIAA1432_ENST00000381532.2_Silent_p.F931F NM_001206557.1|NM_020829.3 NP_001193486.1|NP_065880.2 45 Acute lymphoblastic leukemia(23;0.154) GATTTGAGTTCTTCAGGAATC 0.433000 0 SO:0001819 synonymous_variant ENST00000414202.2 1 1 hg19 CCDS34982.2 . . . . . . . . . . C 9.774 1.173584 0.21704 . . ENSG00000107036 ENST00000545641 . . . 6.04 6.04 0.98038 . . . . . T 0.77336 0.4115 . . . 0.80722 D 1 . . . . . . T 0.73886 -0.3841 4 . . . -18.4469 20.5948 0.99439 0.0:1.0:0.0:0.0 . . . . F 902 . . L + 1 0 KIAA1432 5755691 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.004000 0.49513 2.873000 0.98535 0.563000 0.77884 CTT TCGA-IB-A6UG-01A-32D-A33T-08 KIAA1432-002 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051636.3 1 0 0 98 859 0 178 1 6.977822e-01 3 20 0 178 2 0 0 0 0 0 2 1 1.000000 97 849 0 178 2 0 0 0 0 178 2 -20.000000 1 1 0 0 1 0 3 3 1.930506 1 0.220000 3.280000 0.296600 0.990000 0.840000 1.000000 1.000000 0.976912 0.990000 1 9.300000e-01 1 PTPRD 5789 broad.mit.edu 37 9 8518207 8518207 + Missense_Mutation SNP G G A TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chr9:8518207G>A ENST00000381196.4 - 18 1727 c.1184C>T c.(1183-1185)gCt>gTt p.A395V PTPRD_ENST00000360074.4_Missense_Mutation_p.A382V|PTPRD_ENST00000358503.5_Missense_Mutation_p.A382V|PTPRD_ENST00000355233.5_Missense_Mutation_p.A395V|PTPRD_ENST00000356435.5_Missense_Mutation_p.A395V|PTPRD_ENST00000537002.1_Missense_Mutation_p.A392V|PTPRD_ENST00000397606.3_Missense_Mutation_p.A385V|PTPRD_ENST00000397617.3_Missense_Mutation_p.A385V|PTPRD_ENST00000540109.1_Missense_Mutation_p.A395V|PTPRD_ENST00000397611.3_Missense_Mutation_p.A392V|PTPRD_ENST00000486161.1_Missense_Mutation_p.A395V NM_002839.3 NP_002830.1 P23468 PTPRD_HUMAN protein tyrosine phosphatase, receptor type, D 168 all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824) GTTATTGACAGCAACAACCCT 0.527000 TSP Lung(15;0.13) 0 SO:0001583 missense ENST00000381196.4 0 1 hg19 CCDS43786.1 . . . . . . . . . . G 19.37 3.814087 0.70912 . . ENSG00000153707 ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606 T;T;T;T;T;T;T;T;T;T;T 0.68624 -0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34 5.16 5.16 0.70880 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 D 0.88104 0.6347 H 0.96239 3.79 0.80722 D 1 D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;0.999;0.999;0.999 D;D;D;D;D;D;D;D;D 0.91635 0.999;0.997;0.997;0.997;0.996;0.994;0.969;0.999;0.946 D 0.92021 0.5626 9 . . . . 18.6464 0.91411 0.0:0.0:1.0:0.0 . 385;389;395;395;392;392;382;395;395 Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468 .;.;.;.;.;.;.;.;PTPRD_HUMAN V 395;395;382;382;395;385;392;392;395;395;395;385 ENSP00000370593:A395V;ENSP00000348812:A395V;ENSP00000353187:A382V;ENSP00000351293:A382V;ENSP00000347373:A395V;ENSP00000380741:A385V;ENSP00000380735:A392V;ENSP00000440515:A392V;ENSP00000438164:A395V;ENSP00000417093:A395V;ENSP00000380731:A385V . A - 2 0 PTPRD 8508207 1.000000 0.71417 1.000000 0.80357 0.159000 0.22180 9.807000 0.99171 2.392000 0.81423 0.460000 0.39030 GCT TCGA-IB-A6UG-01A-32D-A33T-08 PTPRD-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055395.3 0 0 0 6 779 0 121 0 0 0 1 0 121 2 0 0 0 0 0 2 1 0.963779 6 770 0 121 2 0 0 0 0 121 2 -2.195254 0 1 0 0 1 0 3 3 1.930506 1 0.220000 3.280000 0.296600 0.080000 0.020000 0.170000 0.090000 0.089430 0.080000 0 4.000000e-02 1.200000e-01 SHROOM4 57477 broad.mit.edu 37 X 50376908 50376908 + Missense_Mutation SNP C C T rs3761506 byFrequency TCGA-IB-A6UG-01A-32D-A33T-08 TCGA-IB-A6UG-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0d9c69f8-3543-4192-9cc1-d843dd6cfd19 2bc45b2a-1d0c-4e9b-9d09-a72efe60fd1a g.chrX:50376908C>T ENST00000289292.7 - 4 2448 c.2165G>A c.(2164-2166)cGt>cAt p.R722H SHROOM4_ENST00000460112.3_Missense_Mutation_p.R606H|SHROOM4_ENST00000376020.2_Missense_Mutation_p.R722H Q9ULL8 SHRM4_HUMAN shroom family member 4 52 Ovarian(276;0.236) ATGACCTCCACGGACTCCACA 0.557000 0 SO:0001583 missense ENST00000289292.7 1 0 hg19 CCDS35277.1 9 0.0054249547920434 0 0.0 0 0.0 9 0.01584507042253521 0 0.0 C 0.008 -1.928348 0.00493 0.001304 0.0 ENSG00000158352 ENST00000289292;ENST00000376020;ENST00000460112 D;D;D 0.88046 -2.33;-2.33;-2.33 5.52 -2.07 0.07276 . 2.325820 0.00911 N 0.002463 T 0.65647 0.2711 L 0.29908 0.895 0.09310 N 1 B 0.17667 0.023 B 0.12837 0.008 T 0.60016 -0.7345 10 0.13470 T 0.59 . 6.0462 0.19762 0.1932:0.4336:0.0:0.3732 rs3761506;rs52829651;rs3761506 722 Q9ULL8 SHRM4_HUMAN H 722;722;606 ENSP00000289292:R722H;ENSP00000365188:R722H;ENSP00000421450:R606H ENSP00000289292:R722H R - 2 0 SHROOM4 50393648 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -0.524000 0.06222 -1.613000 0.01577 -3.241000 0.00051 CGT TCGA-IB-A6UG-01A-32D-A33T-08 SHROOM4-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056564.4 1 0 1 29 94 0 34 0 1.473866e-01 0 3 0 34 2 0 0 0 0 0 2 1 1.000000 29 91 0 33 2 0 0 0 0 34 2 -2.785289 1 1 121410 153 51 1 0 1 1 0.220000 3.280000 0.220000 0.900000 0.690000 1.000000 0.990000 0.895021 0.900000 1 8.000000e-01 9.800000e-01