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 C16orf72 29035 broad.mit.edu 37 16 9210640 9210640 + Frame_Shift_Del DEL T T - TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr16:9210640delT ENST00000327827.7 + 4 1096 c.699delT c.(697-699)gatfs p.D233fs NM_014117.2 NP_054836.2 Q14CZ0 CP072_HUMAN chromosome 16 open reading frame 72 8 ATGATGTCGATTTGAACACTT 0.478000 0 SO:0001589 frameshift_variant ENST00000327827.7 1 0 hg19 CCDS10538.1 TCGA-HZ-A49G-01A-11D-A26I-08 C16orf72-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000440760.2 1 0 0 85 845 0 87 1 9.758052e-01 2 58 0 87 2 0 0 0 0 0 0 1 1.000000 112 838 1 87 32 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 2.024092 0 0.150000 1.820000 0.146158 0.990000 0.970000 1.000000 1.000000 0.998483 0.990000 1 0.990000 1.000000 ANXA11 311 broad.mit.edu 37 10 81930573 81930573 + Missense_Mutation SNP C C A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr10:81930573C>A ENST00000438331.1 - 5 636 c.154G>T c.(154-156)Gac>Tac p.D52Y ANXA11_ENST00000372231.3_Missense_Mutation_p.D52Y|ANXA11_ENST00000463657.1_5'Flank|ANXA11_ENST00000422982.3_Missense_Mutation_p.D52Y|ANXA11_ENST00000535999.1_Missense_Mutation_p.D52Y|ANXA11_ENST00000360615.4_Missense_Mutation_p.D52Y|ANXA11_ENST00000537102.1_Missense_Mutation_p.D19Y|ANXA11_ENST00000265447.4_Missense_Mutation_p.D52Y NM_145869.1 NP_665876.1 P50995 ANX11_HUMAN annexin A11 17 Prostate(51;0.00985)|all_epithelial(25;0.0951) Colorectal(32;0.109) GAGAGATAGTCCTGGTTGAAC 0.652000 0 SO:0001583 missense ENST00000438331.1 1 1 hg19 CCDS7364.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 12.29|12.29 1.893491|1.893491 0.33442|0.33442 .|. .|. ENSG00000122359|ENSG00000122359 ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000537102;ENST00000445524;ENST00000437799|ENST00000424188 T;T;T;T;T;T;T|. 0.02140|. 4.5;4.5;4.5;4.5;4.5;4.5;4.43|. 4.69|4.69 3.77|3.77 0.43336|0.43336 .|. 1.397770|. 0.04356|. N|. 0.356611|. T|T 0.38612|0.38612 0.1047|0.1047 L|L 0.36672|0.36672 1.1|1.1 0.27665|0.27665 N|N 0.946935|0.946935 D;P;P|. 0.58970|. 0.984;0.826;0.826|. P;B;B|. 0.54372|. 0.75;0.367;0.367|. T|T 0.31971|0.31971 -0.9924|-0.9924 10|6 0.52906|0.87932 T|D 0.07|0 .|. 7.2398|7.2398 0.26090|0.26090 0.0:0.7252:0.1762:0.0986|0.0:0.7252:0.1762:0.0986 .|. 152;52;52|. B7Z6L0;Q5T0G8;P50995|. .;.;ANX11_HUMAN|. Y|S 52;52;52;52;52;52;52;19;52;52|7 ENSP00000361305:D52Y;ENSP00000404412:D52Y;ENSP00000398610:D52Y;ENSP00000353827:D52Y;ENSP00000265447:D52Y;ENSP00000441748:D52Y;ENSP00000441400:D19Y|. ENSP00000265447:D52Y|ENSP00000410826:R7S D|R -|- 1|3 0|2 ANXA11|ANXA11 81920553|81920553 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.671000|0.671000 0.39405|0.39405 1.595000|1.595000 0.36708|0.36708 2.326000|2.326000 0.78906|0.78906 0.443000|0.443000 0.29094|0.29094 GAC|AGG TCGA-HZ-A49G-01A-11D-A26I-08 ANXA11-003 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000049044.1 1 0 1 19 331 0 52 1 9.999999e-01 55 504 0 52 2 0 0 0 0 0 2 1 0.999992 19 331 0 52 2 0 0 0 0 52 2 -19.935120 1 1 119964 1 29 1 0 0 0 1.944076 0 0.150000 1.820000 0.109948 0.680000 0.430000 1.000000 1.000000 0.703896 0.680000 0 0.540000 0.850000 CTR9 9646 broad.mit.edu 37 11 10785352 10785352 + Missense_Mutation SNP A A C TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr11:10785352A>C ENST00000361367.2 + 9 1546 c.1120A>C c.(1120-1122)Aat>Cat p.N374H NM_014633.3 NP_055448.1 Q6PD62 CTR9_HUMAN CTR9, Paf1/RNA polymerase II complex component 40 TTATCCTAATAATTACGAAAC 0.358000 0 SO:0001583 missense ENST00000361367.2 1 1 hg19 CCDS7805.1 . . . . . . . . . . A 22.5 4.294603 0.81025 . . ENSG00000198730 ENST00000361367 T 0.52983 0.64 5.62 5.62 0.85841 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1); 0.000000 0.85682 D 0.000000 T 0.72811 0.3507 M 0.88181 2.935 0.80722 D 1 D 0.89917 1.0 D 0.75484 0.986 T 0.74833 -0.3530 10 0.33940 T 0.23 -32.6144 16.1172 0.81314 1.0:0.0:0.0:0.0 . 374 Q6PD62 CTR9_HUMAN H 374 ENSP00000355013:N374H ENSP00000355013:N374H N + 1 0 CTR9 10741928 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.156000 0.94705 2.266000 0.75297 0.533000 0.62120 AAT TCGA-HZ-A49G-01A-11D-A26I-08 CTR9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000386215.1 1 0 0 28 504 0 46 1 5.503940e-01 4 30 0 46 2 0 0 0 0 0 2 1 1.000000 28 503 0 46 2 0 0 0 0 46 2 -20.000000 1 1 0 0 1 0 0 0 1.947351 0 0.150000 1.820000 0.111343 0.660000 0.450000 0.920000 0.670000 0.681717 0.660000 0 0.550000 0.800000 CD44 960 broad.mit.edu 37 11 35227738 35227738 + Silent SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr11:35227738C>T ENST00000428726.2 + 11 1485 c.1362C>T c.(1360-1362)ttC>ttT p.F454F CD44_ENST00000433354.2_Silent_p.F455F|CD44_ENST00000526669.2_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000449691.2_Silent_p.F411F|CD44_ENST00000434472.2_Intron|CD44_ENST00000437706.2_Silent_p.F454F|CD44_ENST00000263398.6_Intron|CD44_ENST00000415148.2_Silent_p.F411F|CD44_ENST00000433892.2_Intron|CD44_ENST00000278386.6_Intron NM_000610.3 NP_000601.3 P16070 CD44_HUMAN CD44 molecule (Indian blood group) 23 all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112) all_hematologic(20;0.107) STAD - Stomach adenocarcinoma(6;0.00731) Hyaluronan(DB08818) CTGATTTCTTCAACCCAATCT 0.468000 0 SO:0001819 synonymous_variant ENST00000428726.2 1 1 hg19 CCDS7897.1 . . . . . . . . . . C 0.021 -1.427132 0.01117 . . ENSG00000026508 ENST00000526553 . . . 4.76 -4.84 0.03151 . . . . . . . . . . . 0.09310 N 0.999999 . . . . . . . . . . . . . -16.0397 6.5665 0.22515 0.0:0.3178:0.3143:0.3678 . . . . X 107 . . Q + 1 0 CD44 35184314 0.015000 0.18098 0.007000 0.13788 0.000000 0.00434 -1.469000 0.02348 -1.229000 0.02564 -0.797000 0.03246 CAA TCGA-HZ-A49G-01A-11D-A26I-08 CD44-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000388927.1 1 0 1 51 609 0 56 1 9.200194e-01 9 44 0 56 2 0 0 0 0 0 2 1 1.000000 51 599 0 54 2 0 0 0 0 56 2 -11.898880 1 0 0 0 1 0 0 0 1.947351 0 0.150000 1.820000 0.111343 0.970000 0.740000 1.000000 1.000000 0.942136 0.970000 1 0.850000 1.000000 CKAP5 9793 broad.mit.edu 37 11 46782199 46782199 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr11:46782199G>A ENST00000529230.1 - 33 4403 c.4357C>T c.(4357-4359)Cgc>Tgc p.R1453C SNORD67_ENST00000516618.1_RNA|CKAP5_ENST00000312055.5_Missense_Mutation_p.R1453C|CKAP5_ENST00000415402.1_Missense_Mutation_p.R1453C|SNORD67_ENST00000390833.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.R1453C Q14008 CKAP5_HUMAN cytoskeleton associated protein 5 p.R1453C(1) 43 GGTCCCTTGCGTAACATGTTG 0.483000 Ovarian(4;85 273 2202 4844 13323) 1 Substitution - Missense(1) SO:0001583 missense ENST00000529230.1 0 1 hg19 CCDS31477.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 20.7|20.7 4.036557|4.036557 0.75617|0.75617 .|. .|. ENSG00000175216|ENSG00000175216 ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876|ENST00000527333 T;T;T;T|. 0.51071|. 0.72;0.74;0.74;0.74|. 6.03|6.03 5.12|5.12 0.69794|0.69794 Armadillo-like helical (1);Armadillo-type fold (1);|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.56455|0.56455 0.1986|0.1986 L|L 0.32530|0.32530 0.975|0.975 0.80722|0.80722 D|D 1|1 D;B;B|. 0.89917|. 1.0;0.004;0.002|. D;B;B|. 0.72625|. 0.978;0.001;0.0|. T|T 0.52866|0.52866 -0.8518|-0.8518 10|5 0.59425|. D|. 0.04|. -10.0088|-10.0088 15.5956|15.5956 0.76578|0.76578 0.0658:0.0:0.9342:0.0|0.0658:0.0:0.9342:0.0 .|. 1453;1453;1453|. Q14008-3;Q14008-2;Q14008|. .;.;CKAP5_HUMAN|. C|M 1453;1453;1453;1453;176|1 ENSP00000432768:R1453C;ENSP00000395302:R1453C;ENSP00000310227:R1453C;ENSP00000346566:R1453C|. ENSP00000310227:R1453C|. R|T -|- 1|2 0|0 CKAP5|CKAP5 46738775|46738775 1.000000|1.000000 0.71417|0.71417 0.939000|0.939000 0.37840|0.37840 0.997000|0.997000 0.91878|0.91878 5.506000|5.506000 0.66993|0.66993 1.556000|1.556000 0.49512|0.49512 0.655000|0.655000 0.94253|0.94253 CGC|ACG TCGA-HZ-A49G-01A-11D-A26I-08 CKAP5-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390679.1 1 0 0 36 307 1 38 1 4.285205e-01 7 33 1 38 5 0 0 0 0 0 2 1 0.939787 35 304 1 38 25 0 0 0 1 38 2 -13.585080 1 1 121410 2 36 1 0 0 0 1.947351 0 0.150000 1.820000 0.111343 0.990000 0.920000 1.000000 1.000000 0.995795 0.990000 1 0.990000 1.000000 CNGA4 1262 broad.mit.edu 37 11 6262838 6262838 + Silent SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr11:6262838G>A ENST00000379936.2 + 5 1210 c.1095G>A c.(1093-1095)caG>caA p.Q365Q CNGA4_ENST00000533426.1_Silent_p.Q134Q NM_001037329.3 NP_001032406.1 Q8IV77 CNGA4_HUMAN cyclic nucleotide gated channel alpha 4 40 Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029) TGAAGCTGCAGCCCCAGACCT 0.567000 0 SO:0001819 synonymous_variant ENST00000379936.2 1 1 hg19 CCDS31408.1 TCGA-HZ-A49G-01A-11D-A26I-08 CNGA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383765.2 0 0 0 59 1013 1 155 0 0 0 1 155 2 0 0 0 0 0 2 1 0.999993 59 1005 1 155 22 0 0 0 1 155 2 -8.088550 1 1 121412 1 36 1 0 0 0 1.947351 0 0.150000 1.820000 0.111343 0.690000 0.530000 0.880000 0.700000 0.707134 0.690000 0 0.610000 0.790000 RTN3 10313 broad.mit.edu 37 11 63486571 63486571 + Silent SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr11:63486571G>A ENST00000377819.5 + 3 751 c.597G>A c.(595-597)ttG>ttA p.L199L RTN3_ENST00000354497.4_Intron|RTN3_ENST00000540798.1_Silent_p.L87L|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000339997.4_Silent_p.L180L|RTN3_ENST00000341307.2_Intron NM_001265589.1 NP_001252518.1 O95197 RTN3_HUMAN reticulon 3 20 AAACTGCATTGGATGCTGATG 0.413000 0 SO:0001819 synonymous_variant ENST00000377819.5 0 1 hg19 CCDS58141.1 TCGA-HZ-A49G-01A-11D-A26I-08 RTN3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000397846.1 0 0 0 8 387 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 0.989425 8 387 0 28 2 0 0 0 0 28 2 -4.117064 1 0 0 0 1 0 0 0 1.936465 0 0.150000 1.820000 0.105734 0.260000 0.120000 0.470000 0.250000 0.281170 0.260000 0 0.180000 0.370000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HZ-A49G-01A-11D-A26I-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 12 131 0 15 1 2.264209e-01 3 7 0 15 2 1 1 36 467 0 424 2 1 0.999217 12 130 0 15 2 1 1 575 7461 0 15 2 -6.683395 1 1 121404 2 44 1 0 0 0 2.008939 0 0.150000 1.820000 0.138368 0.990000 0.610000 1.000000 1.000000 0.938882 0.990000 1 0.820000 1.000000 LRRK2 120892 broad.mit.edu 37 12 40677757 40677757 + Silent SNP G G A rs146103273 byFrequency TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr12:40677757G>A ENST00000298910.7 + 19 2380 c.2322G>A c.(2320-2322)gcG>gcA p.A774A LRRK2_ENST00000343742.2_Silent_p.A774A NM_198578.3 NP_940980 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 181 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) TACGAAAAGCGTTGACGATAA 0.433000 0 SO:0001819 synonymous_variant ENST00000298910.7 1 1 hg19 CCDS31774.1 TCGA-HZ-A49G-01A-11D-A26I-08 LRRK2-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277179.1 1 0 1 70 555 0 52 0 6.637305e-02 0 4 0 52 2 0 0 0 0 0 2 1 1.000000 70 553 0 52 2 0 0 0 0 52 2 -11.715160 1 1 121412 43 50 1 0 0 0 2.008939 0 0.150000 1.820000 0.138368 0.990000 0.990000 1.000000 1.000000 0.999975 0.990000 1 0.990000 1.000000 TPP2 7174 broad.mit.edu 37 13 103299607 103299607 + Silent SNP A A G TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr13:103299607A>G ENST00000376065.4 + 21 2577 c.2541A>G c.(2539-2541)ttA>ttG p.L847L TPP2_ENST00000376052.3_Silent_p.L847L NM_003291.2 NP_003282.2 P29144 TPP2_HUMAN tripeptidyl peptidase II 52 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184) GTGAACTATTATATGAATCTG 0.368000 0 SO:0001819 synonymous_variant ENST00000376065.4 0 1 hg19 CCDS9502.1 TCGA-HZ-A49G-01A-11D-A26I-08 TPP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045683.2 1 0 0 21 217 0 19 0 7.241644e-01 1 27 0 19 2 0 0 0 0 0 2 1 0.999998 21 216 0 19 2 0 0 0 0 19 2 -20.000000 1 1 0 0 1 1 2 3 2.031075 0 0.150000 1.820000 0.154439 0.990000 0.760000 1.000000 1.000000 0.977263 0.990000 1 0.960000 1.000000 TM9SF1 10548 broad.mit.edu 37 14 24659700 24659700 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr14:24659700G>A ENST00000261789.4 - 5 1671 c.1313C>T c.(1312-1314)gCc>gTc p.A438V IPO4_ENST00000354464.6_5'Flank|TM9SF1_ENST00000528669.1_Missense_Mutation_p.A438V|TM9SF1_ENST00000530611.1_Missense_Mutation_p.A647V|TM9SF1_ENST00000556387.1_Missense_Mutation_p.A647V|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000524835.1_Missense_Mutation_p.A351V|TM9SF1_ENST00000396854.4_Missense_Mutation_p.A438V NM_006405.5 NP_006396.2 O15321 TM9S1_HUMAN transmembrane 9 superfamily member 1 24 AAAGGGGCTGGCGTTGTTCTT 0.577000 0 SO:0001583 missense ENST00000261789.4 1 1 hg19 CCDS9617.1 . . . . . . . . . . G 33 5.206576 0.95033 . . ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692 ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000530611 T;T;T;T;T;T 0.46451 0.87;0.87;0.87;0.87;0.87;0.87 5.02 5.02 0.67125 . 0.056859 0.64402 D 0.000001 T 0.51381 0.1671 M 0.66297 2.02 0.80722 D 1 P;P 0.43662 0.599;0.814 P;P 0.47346 0.472;0.544 T 0.55909 -0.8066 10 0.56958 D 0.05 -4.0085 15.8364 0.78801 0.0:0.0:1.0:0.0 . 438;438 Q86SZ6;O15321 .;TM9S1_HUMAN V 438;438;647;351;438;647 ENSP00000261789:A438V;ENSP00000432997:A438V;ENSP00000451949:A647V;ENSP00000434387:A351V;ENSP00000380063:A438V;ENSP00000433967:A647V ENSP00000433967:A647V A - 2 0 TM9SF1;RP11-468E2.1 23729540 1.000000 0.71417 0.996000 0.52242 0.982000 0.71751 8.286000 0.89916 2.317000 0.78254 0.655000 0.94253 GCC TCGA-HZ-A49G-01A-11D-A26I-08 TM9SF1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000073136.2 1 0 0 38 443 0 74 1 9.999918e-01 17 188 0 74 2 0 0 0 0 0 2 1 1.000000 36 441 0 74 2 0 0 0 0 74 2 -20.000000 1 1 0 0 1 1 2 3 2.027927 0 0.150000 1.820000 0.153808 0.990000 0.760000 1.000000 1.000000 0.966413 0.990000 1 0.900000 1.000000 WWP2 11060 broad.mit.edu 37 16 69973005 69973005 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr16:69973005G>A ENST00000359154.2 + 22 2520 c.2419G>A c.(2419-2421)Ggg>Agg p.G807R WWP2_ENST00000542271.1_Missense_Mutation_p.G691R|WWP2_ENST00000356003.2_Missense_Mutation_p.G807R|WWP2_ENST00000568684.1_Missense_Mutation_p.G368R|WWP2_ENST00000448661.1_Missense_Mutation_p.G807R|WWP2_ENST00000544162.1_3'UTR NM_001270454.1|NM_007014.4 NP_001257383.1|NP_008945.2 O00308 WWP2_HUMAN WW domain containing E3 ubiquitin protein ligase 2 42 CCTGCCCGTCGGGGGATTTGC 0.597000 0 SO:0001583 missense ENST00000359154.2 0 1 hg19 CCDS10885.1 . . . . . . . . . . G 20.8 4.058259 0.76074 . . ENSG00000198373 ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271 T;T;T;T 0.60424 0.19;0.19;0.19;0.19 5.16 5.16 0.70880 HECT (4); 0.000000 0.85682 D 0.000000 T 0.81250 0.4783 M 0.89715 3.055 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.84898 0.0840 9 . . . . 18.6562 0.91455 0.0:0.0:1.0:0.0 . 807 O00308 WWP2_HUMAN R 807;807;807;694;691 ENSP00000352069:G807R;ENSP00000396871:G807R;ENSP00000348283:G807R;ENSP00000445616:G691R . G + 1 0 WWP2 68530506 1.000000 0.71417 0.969000 0.41365 0.092000 0.18411 9.824000 0.99380 2.410000 0.81850 0.561000 0.74099 GGG TCGA-HZ-A49G-01A-11D-A26I-08 WWP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268954.1 1 0 1 8 72 0 9 1 9.940835e-01 11 78 0 9 2 1 9.999997e-01 65 770 1 721 6 1 0.988401 8 68 0 9 2 0 0 0 0 9 2 -13.546480 1 1 121280 1 21 1 1 2 3 2.029334 0 0.150000 1.820000 0.153808 0.990000 0.650000 1.000000 1.000000 0.965599 0.990000 1 0.940000 1.000000 TP53 7157 broad.mit.edu 37 17 7577114 7577114 + Missense_Mutation SNP C C A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr17:7577114C>A ENST00000269305.4 - 8 1013 c.824G>T c.(823-825)tGt>tTt p.C275F TP53_ENST00000445888.2_Missense_Mutation_p.C275F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C275F|TP53_ENST00000420246.2_Missense_Mutation_p.C275F|TP53_ENST00000359597.4_Missense_Mutation_p.C275F|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.C275Y(53)|p.C275F(37)|p.0?(8)|p.C275fs*70(3)|p.?(2)|p.C275S(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) AGGACAGGCACAAACACGCAC 0.552000 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 115 Substitution - Missense(92)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2) GRCh37 CM076568|CM951234 TP53 M SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . C 24.5 4.536533 0.85812 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99874 -7.39;-7.39;-7.39;-7.39;-7.39;-7.39 4.92 4.92 0.64577 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 0.99883 0.9944 M 0.92738 3.34 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;0.998 D;D;D;D 0.97110 0.993;1.0;0.993;0.993 D 0.96317 0.9233 10 0.87932 D 0 -17.2181 15.662 0.77193 0.0:1.0:0.0:0.0 . 275;275;275;275 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. F 275;275;275;275;275;264;143 ENSP00000352610:C275F;ENSP00000269305:C275F;ENSP00000398846:C275F;ENSP00000391127:C275F;ENSP00000391478:C275F;ENSP00000425104:C143F ENSP00000269305:C275F C - 2 0 TP53 7517839 1.000000 0.71417 0.999000 0.59377 0.904000 0.53231 7.587000 0.82613 2.556000 0.86216 0.462000 0.41574 TGT TCGA-HZ-A49G-01A-11D-A26I-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 16 199 0 18 1 9.403865e-01 13 49 0 18 2 1 1 91 869 0 1155 2 1 0.999934 16 195 0 18 2 0 0 0 0 18 2 -19.955830 1 1 0 0 1 0 1 1 1.873034 1 0.150000 1.820000 0.081081 0.810000 0.510000 0.990000 0.880000 0.803128 0.810000 0 0.660000 0.940000 S1PR2 9294 broad.mit.edu 37 19 10334708 10334708 + Missense_Mutation SNP T T C TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr19:10334708T>C ENST00000590320.1 - 2 984 c.874A>G c.(874-876)Agc>Ggc p.S292G CTD-2369P2.2_ENST00000317726.4_lincRNA NM_004230.3 NP_004221.3 O95136 S1PR2_HUMAN sphingosine-1-phosphate receptor 2 15 AGGTCCCGGCTGCGCCACGTG 0.687000 Pancreas(194;229 3020 15179 45747) 0 SO:0001583 missense ENST00000590320.1 1 1 hg19 CCDS12229.1 . . . . . . . . . . T 26.7 4.765117 0.90020 . . ENSG00000175898 ENST00000317726 . . . 5.49 5.49 0.81192 . 0.000000 0.85682 D 0.000000 T 0.66287 0.2774 L 0.34521 1.04 0.80722 D 1 D 0.69078 0.997 D 0.75020 0.985 T 0.69412 -0.5152 9 0.66056 D 0.02 . 14.5692 0.68200 0.0:0.0:0.0:1.0 . 292 O95136 S1PR2_HUMAN G 292 . ENSP00000322049:S292G S - 1 0 S1PR2 10195708 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 8.040000 0.89188 2.091000 0.63221 0.454000 0.30748 AGC TCGA-HZ-A49G-01A-11D-A26I-08 S1PR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451194.1 0 0 0 10 244 0 41 0 2.448993e-01 0 22 0 41 2 0 0 0 0 0 2 1 0.996663 10 238 0 41 2 0 0 0 0 41 2 -16.196770 1 1 0 0 1 0 0 0 1.952993 0 0.150000 1.820000 0.114122 0.510000 0.260000 0.850000 0.490000 0.532538 0.510000 0 0.370000 0.680000 TMEM145 284339 broad.mit.edu 37 19 42821981 42821981 + Missense_Mutation SNP T T A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr19:42821981T>A ENST00000301204.3 + 12 1062 c.1021T>A c.(1021-1023)Ttt>Att p.F341I TMEM145_ENST00000598766.1_Missense_Mutation_p.F365I NM_173633.2 NP_775904.2 Q8NBT3 TM145_HUMAN transmembrane protein 145 27 Prostate(69;0.00682) ACTGCGACACTTTCCTGAGAA 0.587000 0 SO:0001583 missense ENST00000301204.3 1 1 hg19 CCDS12603.1 . . . . . . . . . . T 19.70 3.875924 0.72180 . . ENSG00000167619 ENST00000301204 T 0.42900 0.96 4.55 4.55 0.56014 Rhodopsin-like GPCR transmembrane domain (1); 0.406915 0.23626 N 0.046195 T 0.38639 0.1048 L 0.50333 1.59 0.40337 D 0.978994 B 0.33413 0.411 B 0.37015 0.239 T 0.21690 -1.0238 10 0.23302 T 0.38 -16.4936 12.1572 0.54083 0.0:0.0:0.0:1.0 . 341 Q8NBT3 TM145_HUMAN I 341 ENSP00000301204:F341I ENSP00000301204:F341I F + 1 0 TMEM145 47513821 1.000000 0.71417 0.998000 0.56505 0.944000 0.59088 6.453000 0.73488 1.832000 0.53329 0.482000 0.46254 TTT TCGA-HZ-A49G-01A-11D-A26I-08 TMEM145-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463737.1 1 0 0 59 584 0 89 0 0 0 1 0 89 2 0 0 0 0 0 2 1 1.000000 59 576 0 88 2 0 0 0 0 89 2 -16.310760 1 1 0 0 1 1 2 3 2.102529 1 0.150000 1.820000 0.168704 0.990000 0.970000 1.000000 1.000000 0.998313 0.990000 1 0.990000 1.000000 PSG8 440533 broad.mit.edu 37 19 43268187 43268187 + Missense_Mutation SNP T T C TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr19:43268187T>C ENST00000306511.4 - 2 408 c.311A>G c.(310-312)aAt>aGt p.N104S PSG8_ENST00000404209.4_Missense_Mutation_p.N104S|PSG8_ENST00000406636.3_Intron|PSG8_ENST00000401467.2_Missense_Mutation_p.N104S NM_182707.2 NP_874366.1 Q9UQ74 PSG8_HUMAN pregnancy specific beta-1-glycoprotein 8 40 Prostate(69;0.00899) CAGGGATGCATTGGAATATAT 0.423000 0 SO:0001583 missense ENST00000306511.4 1 1 hg19 CCDS33037.1 . . . . . . . . . . t 12.62 1.993629 0.35131 . . ENSG00000124467 ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511 T;T;T 0.01963 4.53;4.53;4.53 1.35 1.35 0.21983 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1); . . . . T 0.11965 0.0291 M 0.89534 3.04 0.09310 N 1 D;D;D;P;P 0.71674 0.998;0.971;0.963;0.908;0.925 D;P;D;P;P 0.75020 0.985;0.831;0.945;0.716;0.813 T 0.06356 -1.0831 9 0.87932 D 0 . 4.8841 0.13694 0.0:0.0:0.0:1.0 . 104;104;104;104;104 B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3 .;PSG8_HUMAN;.;.;. S 104 ENSP00000385869:N104S;ENSP00000386090:N104S;ENSP00000305005:N104S ENSP00000305005:N104S N - 2 0 PSG8 47960027 0.108000 0.22018 0.088000 0.20740 0.189000 0.23516 0.679000 0.25291 0.879000 0.35944 0.155000 0.16302 AAT TCGA-HZ-A49G-01A-11D-A26I-08 PSG8-008 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000464526.1 1 0 0 232 2551 0 270 0 0 0 0 270 2 0 0 0 0 0 2 1 1.000000 232 2539 0 268 2 0 0 0 0 270 2 -20.000000 1 1 121408 4 44 1 1 2 3 2.102529 1 0.150000 1.820000 0.168704 0.990000 0.990000 1.000000 1.000000 0.999533 0.990000 1 0.990000 1.000000 LIG1 3978 broad.mit.edu 37 19 48654515 48654515 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr19:48654515G>A ENST00000263274.7 - 7 967 c.548C>T c.(547-549)aCg>aTg p.T183M LIG1_ENST00000599165.1_5'UTR|LIG1_ENST00000427526.2_Missense_Mutation_p.T152M|LIG1_ENST00000536218.1_Intron NM_000234.1 NP_000225.1 P18858 DNLI1_HUMAN ligase I, DNA, ATP-dependent 44 all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203) Bleomycin(DB00290) CTTGGGAGGCGTGGTGGGCTG 0.567000 Nucleotide excision repair (NER) 0 SO:0001583 missense ENST00000263274.7 1 1 hg19 CCDS12711.1 . . . . . . . . . . G 9.371 1.070591 0.20147 . . ENSG00000105486 ENST00000263274;ENST00000544761;ENST00000427526;ENST00000542460 T;T;T 0.58060 0.49;0.36;3.03 4.54 -0.526 0.11913 . 1.498560 0.03481 N 0.215059 T 0.47600 0.1454 L 0.51422 1.61 0.09310 N 1 B;B 0.13145 0.007;0.007 B;B 0.10450 0.005;0.005 T 0.39231 -0.9624 10 0.52906 T 0.07 -0.0148 7.3598 0.26739 0.4529:0.0:0.5471:0.0 . 152;183 B4DTU4;P18858 .;DNLI1_HUMAN M 183;214;152;151 ENSP00000263274:T183M;ENSP00000442841:T152M;ENSP00000445928:T151M ENSP00000263274:T183M T - 2 0 LIG1 53346327 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 0.139000 0.16036 -0.084000 0.12595 -0.254000 0.11334 ACG TCGA-HZ-A49G-01A-11D-A26I-08 LIG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465575.1 1 0 0 66 1124 0 128 1 4.873682e-01 3 26 0 128 2 0 0 0 0 0 2 1 1.000000 65 1110 0 125 2 0 0 0 0 128 2 -8.585160 1 1 121412 8 45 1 1 2 3 2.112060 1 0.150000 1.820000 0.170529 0.780000 0.590000 1.000000 0.750000 0.814782 0.780000 0 0.680000 1.000000 C3 718 broad.mit.edu 37 19 6710823 6710823 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr19:6710823G>A ENST00000245907.6 - 13 1605 c.1513C>T c.(1513-1515)Cgc>Tgc p.R505C NM_000064.2 NP_000055.2 P01024 CO3_HUMAN complement component 3 72 Intravenous Immunoglobulin(DB00028) CGCACCTGGCGTCCCGCCTTC 0.652000 0 SO:0001583 missense ENST00000245907.6 1 1 hg19 CCDS32883.1 . . . . . . . . . . G 15.92 2.976535 0.53720 . . ENSG00000125730 ENST00000245907 T 0.65178 -0.14 5.31 3.14 0.36123 Alpha-2-macroglobulin, N-terminal 2 (1); 0.050520 0.85682 N 0.000000 T 0.78477 0.4289 M 0.92026 3.265 0.19300 N 0.999976 D 0.89917 1.0 D 0.97110 1.0 T 0.68085 -0.5502 10 0.59425 D 0.04 . 3.8203 0.08833 0.082:0.1398:0.5074:0.2707 . 505 P01024 CO3_HUMAN C 505 ENSP00000245907:R505C ENSP00000245907:R505C R - 1 0 C3 6661823 0.662000 0.27439 0.008000 0.14137 0.008000 0.06430 1.347000 0.33975 0.608000 0.30000 0.655000 0.94253 CGC TCGA-HZ-A49G-01A-11D-A26I-08 C3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317636.2 0 0 0 13 362 0 64 0 9.999999e-01 0 981 0 64 2 0 0 0 0 0 2 1 0.999494 13 355 0 63 2 0 0 0 0 64 2 -13.084040 1 1 121408 1 24 1 0 0 0 1.952993 0 0.150000 1.820000 0.114122 0.440000 0.250000 0.710000 0.440000 0.465264 0.440000 0 0.330000 0.580000 FCGR2B 2213 broad.mit.edu 37 1 161645099 161645099 + Missense_Mutation SNP A A T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr1:161645099A>T ENST00000358671.5 + 6 894 c.813A>T c.(811-813)aaA>aaT p.K271N RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367961.4_Missense_Mutation_p.K264N|FCGR2B_ENST00000236937.9_Intron|FCGR2B_ENST00000367960.5_Missense_Mutation_p.K264N|FCGR2B_ENST00000367962.4_Missense_Mutation_p.K271N NM_001002275.2|NM_004001.4 NP_001002275.1|NP_003992.3 P31994 FCG2B_HUMAN Fc fragment of IgG, low affinity IIb, receptor (CD32) all_cancers(52;4.89e-16)|all_hematologic(112;0.0207) BRCA - Breast invasive adenocarcinoma(70;0.00376) Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072) TCCCTGAGAAACCAGGTGAGT 0.602000 T ? ALL Dom yes 1 1q23 2213 Fc fragment of IgG, low affinity IIb, receptor for (CD32) L 0 SO:0001583 missense ENST00000358671.5 0 1 hg19 CCDS30924.1 . . . . . . . . . . A 11.24 1.579357 0.28180 . . ENSG00000072694 ENST00000367962;ENST00000367960;ENST00000367961;ENST00000358671 T;T;T;T 0.32272 4.59;1.46;1.46;4.59 5.06 -5.67 0.02444 . 7.541930 0.00550 N 0.000242 T 0.03220 0.0094 N 0.08118 0 0.24714 N 0.993181 B;P 0.35011 0.063;0.48 B;B 0.21917 0.037;0.026 T 0.11108 -1.0601 10 0.38643 T 0.18 . 3.0765 0.06248 0.2125:0.2573:0.4044:0.1258 . 264;271 P31994-3;P31994 .;FCG2B_HUMAN N 271;264;264;271 ENSP00000356939:K271N;ENSP00000356937:K264N;ENSP00000356938:K264N;ENSP00000351497:K271N ENSP00000351497:K271N K + 3 2 FCGR2B 159911723 0.000000 0.05858 0.213000 0.23690 0.463000 0.32649 -1.239000 0.02916 -1.009000 0.03400 -0.466000 0.05196 AAA TCGA-HZ-A49G-01A-11D-A26I-08 FCGR2B-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000083337.4 1 0 0 11 81 0 9 0 7.100932e-01 0 20 0 9 2 0 0 0 0 0 2 1 0.996539 9 68 0 11 2 0 0 0 0 9 2 -18.203790 1 1 0 0 1 1 2 3 2.030952 0 0.150000 1.820000 0.154439 0.990000 0.850000 1.000000 1.000000 0.991478 0.990000 1 0.990000 1.000000 SOAT1 6646 broad.mit.edu 37 1 179320574 179320574 + Missense_Mutation SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr1:179320574C>T ENST00000367619.3 + 15 1716 c.1573C>T c.(1573-1575)Cgt>Tgt p.R525C SOAT1_ENST00000540564.1_Missense_Mutation_p.R467C|SOAT1_ENST00000539888.1_Missense_Mutation_p.R460C|SOAT1_ENST00000535686.1_Missense_Mutation_p.R261C NM_003101.5 NP_003092.4 P35610 SOAT1_HUMAN sterol O-acyltransferase 1 20 Ezetimibe(DB00973)|Hesperetin(DB01094) ATGGTATGCACGTCAGCACTG 0.433000 0 SO:0001583 missense ENST00000367619.3 1 1 hg19 CCDS1330.1 . . . . . . . . . . C 31 5.067359 0.93898 . . ENSG00000057252 ENST00000539888;ENST00000540564;ENST00000535686;ENST00000367619 T;T;T;T 0.37058 1.25;1.24;1.31;1.22 5.58 5.58 0.84498 . 0.175782 0.53938 N 0.000049 T 0.61726 0.2370 M 0.75615 2.305 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.76575 0.953;0.988 T 0.64753 -0.6333 10 0.87932 D 0 -6.7329 17.0671 0.86562 0.0:1.0:0.0:0.0 . 467;525 A8K3P4;P35610 .;SOAT1_HUMAN C 460;467;261;525 ENSP00000441356:R460C;ENSP00000445315:R467C;ENSP00000442503:R261C;ENSP00000356591:R525C ENSP00000356591:R525C R + 1 0 SOAT1 177587197 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.572000 0.60886 2.618000 0.88619 0.563000 0.77884 CGT TCGA-HZ-A49G-01A-11D-A26I-08 SOAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085286.2 1 0 0 86 905 0 83 1 9.999957e-01 7 173 0 83 2 0 0 0 0 0 2 1 1.000000 86 902 0 83 2 0 0 0 0 83 2 -19.841640 1 1 121412 1 35 1 1 2 3 2.030952 0 0.150000 1.820000 0.154439 0.990000 0.940000 1.000000 1.000000 0.996612 0.990000 1 0.990000 1.000000 ALDH4A1 8659 broad.mit.edu 37 1 19212958 19212958 + Splice_Site SNP C C A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr1:19212958C>A ENST00000375341.3 - 4 554 c.297G>T c.(295-297)aaG>aaT p.K99N ALDH4A1_ENST00000290597.5_Splice_Site_p.K99N|ALDH4A1_ENST00000538309.1_Splice_Site_p.K39N|ALDH4A1_ENST00000538839.1_Splice_Site_p.K99N|ALDH4A1_ENST00000454547.1_5'Flank|RP13-279N23.2_ENST00000494072.3_3'UTR NM_003748.3 NP_003739.2 P30038 AL4A1_HUMAN aldehyde dehydrogenase 4 family, member A1 15 Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255) GCTCACTCACCTTGTCTGCAT 0.587000 0 SO:0001630 splice_region_variant ENST00000375341.3 1 0 hg19 CCDS188.1 . . . . . . . . . . C 29.4 5.006620 0.93287 . . ENSG00000159423 ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375334 T;T;T;T 0.76968 -1.06;-1.06;-1.06;-1.06 5.71 5.71 0.89125 Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1); 0.046947 0.85682 D 0.000000 D 0.87676 0.6237 M 0.83852 2.665 0.80722 D 1 D 0.59357 0.985 P 0.61477 0.889 D 0.88178 0.2869 9 . . . -28.641 16.5735 0.84631 0.0:1.0:0.0:0.0 . 99 P30038 AL4A1_HUMAN N 99;99;99;39;39 ENSP00000290597:K99N;ENSP00000364490:K99N;ENSP00000446071:K99N;ENSP00000442988:K39N . K - 3 2 ALDH4A1 19085545 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 6.798000 0.75155 2.686000 0.91538 0.655000 0.94253 AAG TCGA-HZ-A49G-01A-11D-A26I-08 ALDH4A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000006954.1 1 0 0 22 208 0 26 0 4.419896e-01 0 15 0 26 2 0 0 0 0 0 2 1 0.999999 22 207 0 26 2 0 0 0 0 26 2 -2.879466 1 1 0 0 1 0 1 1 2.022039 0 0.150000 1.820000 0.145514 0.990000 0.820000 1.000000 1.000000 0.986918 0.990000 1 0.990000 1.000000 USP48 84196 broad.mit.edu 37 1 22030753 22030753 + Splice_Site SNP A A G TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr1:22030753A>G ENST00000308271.9 - 20 3164 c.e20+1 USP48_ENST00000529637.1_Splice_Site|USP48_ENST00000374732.3_Splice_Site|USP48_ENST00000400301.1_Splice_Site NM_032236.5 NP_115612.4 Q86UV5 UBP48_HUMAN ubiquitin specific peptidase 48 42 Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) ATGAAAACTTACTGGGCTCAG 0.368000 0 SO:0001630 splice_region_variant ENST00000308271.9 1 1 hg19 CCDS30623.1 . . . . . . . . . . A 20.3 3.969098 0.74131 . . ENSG00000090686 ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637 . . . 5.52 5.52 0.82312 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.8242 0.70097 1.0:0.0:0.0:0.0 . . . . . -1 . . . - . . USP48 21903340 1.000000 0.71417 1.000000 0.80357 0.936000 0.57629 7.561000 0.82288 2.094000 0.63399 0.533000 0.62120 . TCGA-HZ-A49G-01A-11D-A26I-08 USP48-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021372.1 1 0 0 36 417 0 33 1 1.909166e-02 3 0 0 33 2 0 0 0 0 0 2 1 1.000000 36 412 0 33 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 1 2 3 2.043071 0 0.150000 1.820000 0.156955 0.990000 0.770000 1.000000 1.000000 0.969413 0.990000 1 0.910000 1.000000 MACF1 23499 broad.mit.edu 37 1 39749752 39749752 + Missense_Mutation SNP G G T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr1:39749752G>T ENST00000372915.3 + 9 1032 c.945G>T c.(943-945)agG>agT p.R315S MACF1_ENST00000564288.1_Missense_Mutation_p.R310S|MACF1_ENST00000361689.2_Missense_Mutation_p.R315S|MACF1_ENST00000539005.1_Missense_Mutation_p.R315S|MACF1_ENST00000567887.1_Missense_Mutation_p.R347S|MACF1_ENST00000317713.7_Missense_Mutation_p.R315S|MACF1_ENST00000545844.1_Missense_Mutation_p.R315S Q9UPN3 MACF1_HUMAN microtubule-actin crosslinking factor 1 203 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) TGGACTCCAGGTGGCAAGAAT 0.443000 0 SO:0001583 missense ENST00000372915.3 1 1 hg19 . . . . . . . . . . G 16.69 3.192152 0.58017 . . ENSG00000127603 ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900 T;T;T;T;T;T;T 0.68025 -0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3 5.4 4.48 0.54585 . . . . . T 0.64516 0.2605 L 0.35249 1.045 0.80722 D 1 B;D 0.62365 0.066;0.991 B;P 0.54026 0.041;0.74 T 0.66995 -0.5782 9 0.87932 D 0 . 9.0036 0.36097 0.0793:0.1485:0.7721:0.0 . 315;280 F8W8Q1;Q9UPN3-3 .;. S 315;315;315;331;315;315;273;464;475 ENSP00000439537:R315S;ENSP00000362006:R315S;ENSP00000354573:R315S;ENSP00000313438:R315S;ENSP00000444364:R315S;ENSP00000435070:R273S;ENSP00000437059:R464S ENSP00000313438:R315S R + 3 2 MACF1 39522339 0.999000 0.42202 1.000000 0.80357 0.998000 0.95712 0.617000 0.24359 1.249000 0.43950 0.561000 0.74099 AGG TCGA-HZ-A49G-01A-11D-A26I-08 MACF1-028 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding protein_coding OTTHUMT00000392096.1 1 0 0 28 527 0 55 0 6.274117e-02 0 8 0 55 2 1 1 23 563 0 612 2 1 1.000000 28 524 0 55 2 0 0 0 0 55 2 -20.000000 1 0 0 0 1 1 2 3 2.038492 0 0.150000 1.820000 0.155699 0.690000 0.460000 1.000000 0.670000 0.713810 0.690000 0 0.560000 0.860000 PAX1 5075 broad.mit.edu 37 20 21689881 21689881 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr20:21689881G>A ENST00000398485.2 + 4 1135 c.1081G>A c.(1081-1083)Gtg>Atg p.V361M PAX1_ENST00000460221.1_3'UTR|PAX1_ENST00000444366.2_Missense_Mutation_p.V337M NM_001257096.1|NM_006192.4 NP_001244025.1|NP_006183.2 P15863 PAX1_HUMAN paired box 1 38 CCTCTCTGCCGTGGGCGGCTT 0.697000 0 SO:0001583 missense ENST00000398485.2 1 1 hg19 CCDS13146.2 . . . . . . . . . . G 14.29 2.491158 0.44249 . . ENSG00000125813 ENST00000398485;ENST00000444366 D;D 0.98862 -4.78;-5.19 5.66 4.71 0.59529 . 0.070054 0.64402 D 0.000019 D 0.97704 0.9247 M 0.73962 2.25 0.37476 D 0.915822 D;P;D 0.57257 0.968;0.852;0.979 B;B;P 0.44518 0.332;0.079;0.452 D 0.97965 1.0340 10 0.54805 T 0.06 . 11.8979 0.52665 0.1451:0.0:0.8549:0.0 . 337;267;361 P15863-2;C9J775;P15863 .;.;PAX1_HUMAN M 361;337 ENSP00000381499:V361M;ENSP00000410355:V337M ENSP00000381499:V361M V + 1 0 PAX1 21637881 0.998000 0.40836 0.888000 0.34837 0.476000 0.33039 3.037000 0.49775 1.392000 0.46585 0.462000 0.41574 GTG TCGA-HZ-A49G-01A-11D-A26I-08 PAX1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078282.3 0 0 0 47 1318 0 153 0 0 0 0 153 2 0 0 0 0 0 2 1 1.000000 47 1299 0 148 2 0 0 0 0 153 2 -3.596617 1 1 121296 1 37 1 1 5 6 2.668018 1 0.150000 1.820000 0.346154 0.590000 0.430000 0.780000 0.600000 0.607781 0.590000 0 0.510000 0.690000 GGTLC1 92086 broad.mit.edu 37 20 23966551 23966551 + Missense_Mutation SNP C C T rs143742821 byFrequency TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr20:23966551C>T ENST00000335694.4 - 4 569 c.365G>A c.(364-366)cGg>cAg p.R122Q GGTLC1_ENST00000278765.4_Missense_Mutation_p.R122Q|GGTLC1_ENST00000286890.4_Missense_Mutation_p.R122Q NM_178311.2 NP_842563.1 Q9BX51 GGTL1_HUMAN gamma-glutamyltransferase light chain 1 15 CACCACCATCCGGACCTGGCC 0.662000 0 SO:0001583 missense ENST00000335694.4 1 1 hg19 CCDS13163.1 . . . . . . . . . . c 12.08 1.830751 0.32329 0.005956 0.0 ENSG00000149435 ENST00000286890;ENST00000278765;ENST00000335694 T;T;T 0.08370 3.1;3.1;3.1 0.844 0.844 0.18943 . 0.384153 0.26627 N 0.023330 T 0.04815 0.0130 M 0.62016 1.91 0.27078 N 0.96317 B 0.31581 0.329 B 0.25291 0.059 T 0.22347 -1.0219 10 0.38643 T 0.18 -48.6079 3.7845 0.08694 0.0:0.6622:0.0:0.3378 . 122 Q9BX51 GGTL1_HUMAN Q 122 ENSP00000286890:R122Q;ENSP00000278765:R122Q;ENSP00000337587:R122Q ENSP00000278765:R122Q R - 2 0 GGTLC1 23914551 1.000000 0.71417 0.178000 0.23040 0.195000 0.23768 1.410000 0.34691 0.088000 0.17205 0.089000 0.15464 CGG TCGA-HZ-A49G-01A-11D-A26I-08 GGTLC1-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078366.2 0 0 0 57 851 0 132 0 1.184031e-02 0 3 0 132 2 0 0 0 0 0 2 1 1.000000 49 774 0 139 2 0 0 0 0 132 2 -2.841672 1 1 121398 71 52 1 0 1 1 2.015068 0 0.150000 1.820000 0.144224 0.820000 0.630000 1.000000 1.000000 0.834756 0.820000 0 0.720000 0.940000 PTPRT 11122 broad.mit.edu 37 20 41101179 41101179 + Missense_Mutation SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr20:41101179C>T ENST00000373187.1 - 8 1176 c.1177G>A c.(1177-1179)Gtg>Atg p.V393M PTPRT_ENST00000373198.4_Missense_Mutation_p.V393M|PTPRT_ENST00000356100.2_Missense_Mutation_p.V393M|PTPRT_ENST00000373184.1_Missense_Mutation_p.V393M|PTPRT_ENST00000373201.1_Missense_Mutation_p.V393M|PTPRT_ENST00000373190.1_Missense_Mutation_p.V393M|PTPRT_ENST00000373193.3_Missense_Mutation_p.V393M O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 176 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) ACGATTTCCACGTTCTGTGGG 0.562000 0 SO:0001583 missense ENST00000373187.1 1 1 hg19 CCDS42874.1 . . . . . . . . . . C 24.9 4.577402 0.86645 . . ENSG00000196090 ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201 T;T;T;T;T;T;T 0.57436 0.4;0.4;0.4;0.4;0.4;0.4;0.4 5.71 5.71 0.89125 Fibronectin, type III (3);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.67135 0.2861 L 0.51422 1.61 0.80722 D 1 D;D 0.69078 0.997;0.994 P;P 0.61722 0.893;0.674 T 0.67684 -0.5607 10 0.66056 D 0.02 . 19.8432 0.96699 0.0:1.0:0.0:0.0 . 393;393 O14522-1;O14522 .;PTPRT_HUMAN M 393 ENSP00000362286:V393M;ENSP00000362283:V393M;ENSP00000362289:V393M;ENSP00000348408:V393M;ENSP00000362294:V393M;ENSP00000362280:V393M;ENSP00000362297:V393M ENSP00000348408:V393M V - 1 0 PTPRT 40534593 0.998000 0.40836 0.965000 0.40720 0.815000 0.46073 3.895000 0.56258 2.700000 0.92200 0.462000 0.41574 GTG TCGA-HZ-A49G-01A-11D-A26I-08 PTPRT-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000080315.1 1 0 0 13 291 0 43 0 0 0 1 0 43 2 0 0 0 0 0 2 1 0.999523 13 287 0 42 2 0 0 0 0 43 2 -14.273810 1 1 121006 1 25 1 0 1 1 2.015068 0 0.150000 1.820000 0.144224 0.570000 0.320000 0.900000 0.550000 0.593292 0.570000 0 0.430000 0.740000 PRAME 23532 broad.mit.edu 37 22 22892513 22892513 + Missense_Mutation SNP A A C TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr22:22892513A>C ENST00000398741.1 - 5 894 c.588T>G c.(586-588)atT>atG p.I196M PRAME_ENST00000543184.1_Missense_Mutation_p.I196M|PRAME_ENST00000424204.2_Missense_Mutation_p.I180M|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000398743.2_Missense_Mutation_p.I196M|PRAME_ENST00000402697.1_Missense_Mutation_p.I196M|PRAME_ENST00000405655.3_Missense_Mutation_p.I196M|PRAME_ENST00000539862.1_Missense_Mutation_p.I180M NM_206955.1 NP_996838.1 P78395 PRAME_HUMAN preferentially expressed antigen in melanoma 36 all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17) all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05) TCACTTTCTCAATGAGGTAGG 0.458000 Melanoma(73;1707 1838 15168 27201) 0 SO:0001583 missense ENST00000398741.1 1 1 hg19 CCDS13801.1 . . . . . . . . . . . 4.313 0.057476 0.08339 . . ENSG00000185686 ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204;ENST00000439106 T;T;T;T;T;T;T;T 0.15139 2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45 3.24 -5.23 0.02798 . 1.278720 0.05507 N 0.559414 T 0.10337 0.0253 N 0.17800 0.525 0.09310 N 1 B 0.28208 0.203 B 0.28465 0.09 T 0.30119 -0.9989 10 0.39692 T 0.17 . 7.634 0.28255 0.3112:0.508:0.1808:0.0 . 196 P78395 PRAME_HUMAN M 196;196;196;196;180;196;180;196 ENSP00000381728:I196M;ENSP00000445675:I196M;ENSP00000381726:I196M;ENSP00000384343:I196M;ENSP00000445097:I180M;ENSP00000385198:I196M;ENSP00000407342:I180M;ENSP00000407320:I196M ENSP00000381726:I196M I - 3 3 PRAME 21222513 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -1.489000 0.02306 -2.030000 0.00929 -1.256000 0.01477 ATT TCGA-HZ-A49G-01A-11D-A26I-08 PRAME-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321644.1 1 0 0 48 719 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 1.000000 47 717 0 80 2 0 0 0 0 80 2 -20.000000 1 1 0 0 1 0 0 0 2.005901 0 0.150000 1.820000 0.137056 0.810000 0.610000 1.000000 1.000000 0.825545 0.810000 0 0.710000 0.940000 NR4A2 4929 broad.mit.edu 37 2 157186342 157186342 + Silent SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr2:157186342C>T ENST00000339562.4 - 3 719 c.357G>A c.(355-357)tcG>tcA p.S119S NR4A2_ENST00000539077.1_Silent_p.S130S|NR4A2_ENST00000429376.1_Silent_p.S56S|NR4A2_ENST00000426264.1_Silent_p.S56S|NR4A2_ENST00000409108.2_Silent_p.S119S|NR4A2_ENST00000409572.1_Silent_p.S119S NM_006186.3 NP_006177.1 P43354 NR4A2_HUMAN nuclear receptor subfamily 4, group A, member 2 40 TGTAGTAAACCGACCCGGAGT 0.612000 0 SO:0001819 synonymous_variant ENST00000339562.4 1 1 hg19 CCDS2201.1 TCGA-HZ-A49G-01A-11D-A26I-08 NR4A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254909.2 1 0 0 47 549 0 64 0 5.539818e-02 0 5 0 64 2 0 0 0 0 0 2 1 1.000000 44 543 0 64 2 0 0 0 0 64 2 -2.920853 1 1 0 0 1 0 0 0 2.001073 0 0.150000 1.820000 0.135740 0.990000 0.770000 1.000000 1.000000 0.961683 0.990000 1 0.890000 1.000000 TTN 7273 broad.mit.edu 37 2 179476557 179476557 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr2:179476557G>A ENST00000591111.1 - 218 45780 c.45556C>T c.(45556-45558)Cgg>Tgg p.R15186W TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R14259W|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R7762W|TTN_ENST00000589042.1_Missense_Mutation_p.R16827W|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R7954W|TTN_ENST00000359218.5_Missense_Mutation_p.R7887W|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin p.R7762W(1)|p.R7954W(1)|p.R14259W(1)|p.R7887W(1) 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTTTCAGCCCGAACCTGAAAC 0.458000 4 Substitution - Missense(4) SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . G 8.954 0.968839 0.18659 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.59083 0.29;0.29;0.29;0.29 5.97 3.08 0.35506 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.72285 0.3441 M 0.78801 2.425 0.43988 D 0.996681 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.69654 0.965;0.965;0.965;0.965 T 0.73924 -0.3829 9 0.87932 D 0 . 10.0401 0.42153 0.0646:0.0:0.6758:0.2596 . 7762;7887;7954;15186 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN W 14259;7762;7954;7887;7762 ENSP00000343764:R14259W;ENSP00000434586:R7762W;ENSP00000340554:R7954W;ENSP00000352154:R7887W ENSP00000340554:R7954W R - 1 2 TTN 179184802 1.000000 0.71417 0.997000 0.53966 0.895000 0.52256 2.635000 0.46537 0.784000 0.33661 -0.188000 0.12872 CGG TCGA-HZ-A49G-01A-11D-A26I-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 39 695 0 73 0 3.023420e-03 0 2 0 73 2 0 0 0 0 0 2 1 1.000000 39 688 0 73 2 0 0 0 0 73 2 -3.221342 1 1 120840 3 35 1 0 0 0 2.012295 0 0.150000 1.820000 0.139676 0.690000 0.500000 0.920000 0.690000 0.709599 0.690000 0 0.590000 0.810000 SH3BP4 23677 broad.mit.edu 37 2 235949561 235949561 + Missense_Mutation SNP A A C rs138775253 TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr2:235949561A>C ENST00000409212.1 + 4 655 c.148A>C c.(148-150)Aac>Cac p.N50H SH3BP4_ENST00000392011.2_Missense_Mutation_p.N50H|SH3BP4_ENST00000344528.4_Missense_Mutation_p.N50H Q9P0V3 SH3B4_HUMAN SH3-domain binding protein 4 44 Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419) GCTCGTAGACAACCCCACACC 0.532000 0 SO:0001583 missense ENST00000409212.1 1 1 hg19 CCDS2513.1 . . . . . . . . . . A 14.26 2.481890 0.44147 . . ENSG00000130147 ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000444916;ENST00000446904;ENST00000454947 T;T;T;T;T 0.28895 1.59;1.59;1.59;1.59;1.59 5.44 4.25 0.50352 Src homology-3 domain (1); 0.509628 0.23624 N 0.046211 T 0.17704 0.0425 N 0.14661 0.345 0.39020 D 0.959721 P;P 0.41041 0.736;0.604 B;B 0.36885 0.235;0.235 T 0.06303 -1.0834 10 0.54805 T 0.06 0.9174 10.559 0.45133 0.8552:0.0:0.0:0.1448 . 50;50 A8K594;Q9P0V3 .;SH3B4_HUMAN H 50 ENSP00000375867:N50H;ENSP00000403251:N50H;ENSP00000386862:N50H;ENSP00000340237:N50H;ENSP00000415391:N50H ENSP00000340237:N50H N + 1 0 SH3BP4 235614300 0.997000 0.39634 0.976000 0.42696 0.823000 0.46562 3.448000 0.52943 0.859000 0.35456 0.533000 0.62120 AAC TCGA-HZ-A49G-01A-11D-A26I-08 SH3BP4-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329763.1 1 0 0 33 512 0 68 1 7.556374e-01 4 40 0 68 2 0 0 0 0 0 2 1 1.000000 33 506 0 68 2 0 0 0 0 68 2 -20.000000 1 1 0 0 1 0 0 0 2.012295 0 0.150000 1.820000 0.139676 0.790000 0.560000 1.000000 1.000000 0.803479 0.790000 0 0.670000 0.940000 CLIP4 79745 broad.mit.edu 37 2 29404502 29404502 + Missense_Mutation SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr2:29404502G>A ENST00000320081.5 + 16 2116 c.1861G>A c.(1861-1863)Gtg>Atg p.V621M CLIP4_ENST00000401617.2_Missense_Mutation_p.V514M|CLIP4_ENST00000481628.1_3'UTR|CLIP4_ENST00000404424.1_Missense_Mutation_p.V621M NM_024692.4 NP_078968.3 Q8N3C7 CLIP4_HUMAN CAP-GLY domain containing linker protein family, member 4 26 Acute lymphoblastic leukemia(172;0.155) TGAAGGGAGCGTGAAGCTGCA 0.542000 0 SO:0001583 missense ENST00000320081.5 1 1 hg19 CCDS1770.1 . . . . . . . . . . G 25.7 4.664449 0.88251 . . ENSG00000115295 ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644 T;T;T 0.77358 -1.09;-0.82;-0.82 5.6 5.6 0.85130 Cytoskeleton-associated protein, Gly-rich domain (2); 0.206120 0.41097 D 0.000956 T 0.80497 0.4634 L 0.29908 0.895 0.80722 D 1 D 0.67145 0.996 P 0.57846 0.828 T 0.80538 -0.1338 10 0.46703 T 0.11 . 19.6109 0.95606 0.0:0.0:1.0:0.0 . 621 Q8N3C7 CLIP4_HUMAN M 514;621;623;621;639;581 ENSP00000385148:V514M;ENSP00000385594:V621M;ENSP00000327009:V621M ENSP00000327009:V621M V + 1 0 CLIP4 29258006 1.000000 0.71417 0.904000 0.35570 0.887000 0.51463 7.111000 0.77077 2.653000 0.90120 0.491000 0.48974 GTG TCGA-HZ-A49G-01A-11D-A26I-08 CLIP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215123.2 0 0 0 11 389 0 42 1 4.698757e-01 2 52 0 42 2 0 0 0 0 0 2 1 0.998385 11 389 0 42 2 0 0 0 0 42 2 -10.247660 1 1 121412 4 39 1 0 0 0 1.990868 0 0.150000 1.820000 0.130435 0.360000 0.190000 0.600000 0.350000 0.382585 0.360000 0 0.270000 0.490000 CEP70 80321 broad.mit.edu 37 3 138289266 138289266 + Missense_Mutation SNP T T C rs143423470 TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr3:138289266T>C ENST00000264982.3 - 6 625 c.359A>G c.(358-360)gAa>gGa p.E120G CEP70_ENST00000542237.1_Missense_Mutation_p.E100G|CEP70_ENST00000464035.1_Missense_Mutation_p.E120G|CEP70_ENST00000481834.1_Missense_Mutation_p.E120G|CEP70_ENST00000489254.1_Intron|CEP70_ENST00000484888.1_Missense_Mutation_p.E120G|CEP70_ENST00000478673.1_5'UTR NM_024491.2 NP_077817.2 Q8NHQ1 CEP70_HUMAN centrosomal protein 70kDa 24 TTTCACACTTTCCATAATTTG 0.363000 0 SO:0001583 missense ENST00000264982.3 1 1 hg19 CCDS3102.1 . . . . . . . . . . T 11.18 1.563176 0.27915 0.0 1.16E-4 ENSG00000114107 ENST00000264982;ENST00000542237;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035 T;T;T;T;T;T;T;T 0.55052 1.18;1.19;1.18;1.19;1.17;0.6;0.59;0.54 4.98 3.83 0.44106 . 0.414678 0.25897 N 0.027597 T 0.42086 0.1187 L 0.47716 1.5 0.27515 N 0.95157 P;P;P 0.42692 0.787;0.787;0.787 B;B;B 0.39379 0.23;0.298;0.23 T 0.33979 -0.9847 10 0.41790 T 0.15 -4.5495 7.2698 0.26250 0.0:0.0985:0.0:0.9015 . 100;120;120 F5GZX8;Q8NHQ1-2;Q8NHQ1 .;.;CEP70_HUMAN G 120;100;120;102;120;99;100;120 ENSP00000264982:E120G;ENSP00000444128:E100G;ENSP00000419231:E120G;ENSP00000419833:E102G;ENSP00000417465:E120G;ENSP00000418131:E99G;ENSP00000417819:E100G;ENSP00000419743:E120G ENSP00000264982:E120G E - 2 0 CEP70 139771956 1.000000 0.71417 0.999000 0.59377 0.202000 0.24057 4.295000 0.59049 0.932000 0.37266 -0.256000 0.11100 GAA TCGA-HZ-A49G-01A-11D-A26I-08 CEP70-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000358001.1 1 0 1 104 520 0 47 1 7.044918e-01 3 11 0 47 2 0 0 0 0 0 2 1 1.000000 103 518 0 47 2 0 0 0 0 47 2 -20.000000 1 1 0 0 1 0 1 1 2.002839 1 0.150000 1.820000 0.081081 0.980000 0.930000 1.000000 0.990000 0.987383 0.980000 1 0.960000 1.000000 ZFYVE28 57732 broad.mit.edu 37 4 2341323 2341323 + Silent SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr4:2341323C>T ENST00000290974.2 - 4 717 c.378G>A c.(376-378)ccG>ccA p.P126P ZFYVE28_ENST00000509171.1_Silent_p.P79P|ZFYVE28_ENST00000515312.1_Silent_p.P56P|ZFYVE28_ENST00000503000.1_Silent_p.P126P|ZFYVE28_ENST00000515169.1_Silent_p.P56P|ZFYVE28_ENST00000511071.1_Silent_p.P126P|ZFYVE28_ENST00000505421.1_5'Flank NM_020972.2 NP_066023.2 Q9HCC9 LST2_HUMAN zinc finger, FYVE domain containing 28 31 CCTTGGCCAGCGGGCGCATGG 0.692000 0 SO:0001819 synonymous_variant ENST00000290974.2 0 1 hg19 CCDS33942.1 TCGA-HZ-A49G-01A-11D-A26I-08 ZFYVE28-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000360078.1 1 0 0 5 72 0 13 0 2.879646e-01 1 13 0 13 2 0 0 0 0 0 2 1 0.939687 5 72 0 13 2 0 0 0 0 13 2 -9.421114 1 1 121252 11 36 1 0 1 1 2.024131 0 0.150000 1.820000 0.146158 0.880000 0.350000 1.000000 1.000000 0.818086 0.880000 1 0.570000 1.000000 SLIT3 6586 broad.mit.edu 37 5 168199801 168199801 + Missense_Mutation SNP T T C TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr5:168199801T>C ENST00000519560.1 - 14 1863 c.1444A>G c.(1444-1446)Aag>Gag p.K482E SLIT3_ENST00000404867.3_Missense_Mutation_p.K482E|SLIT3_ENST00000332966.8_Missense_Mutation_p.K482E NM_001271946.1|NM_003062.2 NP_001258875.1|NP_003053 O75094 SLIT3_HUMAN slit homolog 3 (Drosophila) 100 Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) CAGCGGAACTTCTTGCTCTTG 0.612000 Ovarian(29;311 847 10864 17279 24903) 0 SO:0001583 missense ENST00000519560.1 1 1 hg19 CCDS4369.1 . . . . . . . . . . T 21.3 4.135148 0.77662 . . ENSG00000184347 ENST00000519560;ENST00000332966;ENST00000404867 T;T;T 0.76060 -0.99;-0.97;-0.97 5.49 5.49 0.81192 Cysteine-rich flanking region, C-terminal (2); 0.091877 0.64402 D 0.000001 T 0.66277 0.2773 L 0.28608 0.87 0.80722 D 1 P;P;P 0.50528 0.936;0.738;0.627 B;B;B 0.42245 0.381;0.195;0.369 T 0.71906 -0.4451 10 0.66056 D 0.02 . 15.5931 0.76554 0.0:0.0:0.0:1.0 . 482;482;482 O75094-2;O75094-3;O75094 .;.;SLIT3_HUMAN E 482 ENSP00000430333:K482E;ENSP00000332164:K482E;ENSP00000384890:K482E ENSP00000332164:K482E K - 1 0 SLIT3 168132379 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.033000 0.88852 2.075000 0.62263 0.459000 0.35465 AAG TCGA-HZ-A49G-01A-11D-A26I-08 SLIT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252792.4 0 0 0 10 363 0 53 0 2.730107e-01 0 35 0 53 2 0 0 0 0 0 2 1 0.996934 10 362 0 53 2 0 0 0 0 53 2 -10.322950 1 1 0 0 1 1 2 3 2.032889 0 0.150000 1.820000 0.154439 0.370000 0.190000 1.000000 0.350000 0.421559 0.370000 0 0.270000 0.530000 LACE1 246269 broad.mit.edu 37 6 108768484 108768484 + Missense_Mutation SNP G G T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr6:108768484G>T ENST00000368977.4 + 8 1061 c.875G>T c.(874-876)gGa>gTa p.G292V NM_145315.3 NP_660358.2 Q8WV93 LACE1_HUMAN lactation elevated 1 15 all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152) CCTGCTGCAGGAAAACTCTAC 0.323000 0 SO:0001583 missense ENST00000368977.4 0 1 hg19 CCDS5067.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 13.55|13.55 2.270717|2.270717 0.40194|0.40194 .|. .|. ENSG00000135537|ENSG00000135537 ENST00000421954|ENST00000368977 .|. .|. .|. 5.73|5.73 5.73|5.73 0.89815|0.89815 .|. .|0.000000 .|0.85682 .|D .|0.000000 .|T .|0.44582 .|0.1300 L|L 0.55990|0.55990 1.75|1.75 0.80722|0.80722 D|D 1|1 .|P .|0.36837 .|0.571 .|B .|0.38921 .|0.285 .|T .|0.53844 .|-0.8381 .|9 .|0.66056 .|D .|0.02 -13.3981|-13.3981 13.1411|13.1411 0.59436|0.59436 0.0731:0.0:0.9269:0.0|0.0731:0.0:0.9269:0.0 .|. .|292 .|Q8WV93 .|LACE1_HUMAN X|V 160|292 .|. .|ENSP00000357973:G292V E|G +|+ 1|2 0|0 LACE1|LACE1 108875177|108875177 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.997000|0.997000 0.91878|0.91878 4.690000|4.690000 0.61731|0.61731 2.693000|2.693000 0.91896|0.91896 0.655000|0.655000 0.94253|0.94253 GAA|GGA TCGA-HZ-A49G-01A-11D-A26I-08 LACE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041719.4 1 0 0 23 263 0 20 1 1.408413e-01 3 5 0 20 2 0 0 0 0 0 2 1 0.999999 23 257 0 20 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 0 0 0 1.869586 1 0.150000 1.820000 0.073569 0.800000 0.570000 0.900000 0.890000 0.789551 0.800000 0 0.690000 0.870000 PDE10A 10846 broad.mit.edu 37 6 165832222 165832222 + Missense_Mutation SNP A A T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr6:165832222A>T ENST00000366882.1 - 12 1023 c.869T>A c.(868-870)tTc>tAc p.F290Y PDE10A_ENST00000354448.4_Missense_Mutation_p.F290Y|PDE10A_ENST00000539869.2_Missense_Mutation_p.F300Y Q9Y233 PDE10_HUMAN phosphodiesterase 10A 71 Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221) Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814) GTCCACCTGGAAAAGCGCACA 0.388000 Esophageal Squamous(22;308 615 5753 12038 40624) 0 SO:0001583 missense ENST00000366882.1 0 1 hg19 . . . . . . . . . . A 26.7 4.762878 0.89932 . . ENSG00000112541 ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126 T;T 0.69561 -0.41;-0.41 5.03 5.03 0.67393 GAF (2); 0.000000 0.85682 D 0.000000 T 0.73938 0.3651 M 0.63428 1.95 0.80722 D 1 D;D 0.62365 0.991;0.988 D;D 0.76071 0.982;0.987 T 0.76887 -0.2793 10 0.54805 T 0.06 . 14.784 0.69787 1.0:0.0:0.0:0.0 . 300;290 Q9ULW9;Q9Y233 .;PDE10_HUMAN Y 290;318;300;290;289 ENSP00000355847:F290Y;ENSP00000346435:F290Y ENSP00000341187:F300Y F - 2 0 PDE10A 165752212 1.000000 0.71417 0.978000 0.43139 0.995000 0.86356 8.749000 0.91619 1.903000 0.55091 0.459000 0.35465 TTC TCGA-HZ-A49G-01A-11D-A26I-08 PDE10A-001 PUTATIVE basic protein_coding protein_coding OTTHUMT00000043031.1 1 0 1 30 270 0 17 0 1.578555e-01 0 7 0 17 2 0 0 0 0 0 2 1 1.000000 30 267 0 17 2 0 0 0 0 17 2 -20.000000 1 1 0 0 1 0 0 0 1.855863 1 0.150000 1.820000 0.065934 0.750000 0.620000 1.000000 0.790000 0.758965 0.750000 0 0.690000 0.790000 COL9A1 1297 broad.mit.edu 37 6 70935662 70935662 + Missense_Mutation SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr6:70935662C>T ENST00000357250.6 - 37 2712 c.2554G>A c.(2554-2556)Ggt>Agt p.G852S COL9A1_ENST00000320755.7_Missense_Mutation_p.G609S|COL9A1_ENST00000370499.4_Missense_Mutation_p.G609S|RP1-149L1.1_ENST00000522264.1_RNA|COL9A1_ENST00000489611.1_5'UTR NM_001851.4 NP_001842.3 P20849 CO9A1_HUMAN collagen, type IX, alpha 1 80 CCAGGCAAACCGTTGGGACCT 0.428000 0 SO:0001583 missense ENST00000357250.6 1 1 hg19 CCDS4971.1 . . . . . . . . . . C 22.5 4.304275 0.81136 . . ENSG00000112280 ENST00000357250;ENST00000320755;ENST00000370499 D;D;D 0.99329 -5.75;-5.75;-5.75 5.43 5.43 0.79202 . 0.000000 0.85682 D 0.000000 D 0.99704 0.9887 H 0.96777 3.88 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;1.0 D 0.97485 1.0050 10 0.87932 D 0 . 19.2294 0.93831 0.0:1.0:0.0:0.0 . 852;609;401 P20849;P20849-2;B3KWS8 CO9A1_HUMAN;.;. S 852;609;609 ENSP00000349790:G852S;ENSP00000315252:G609S;ENSP00000359530:G609S ENSP00000315252:G609S G - 1 0 COL9A1 70992383 1.000000 0.71417 0.999000 0.59377 0.950000 0.60333 7.313000 0.78978 2.557000 0.86248 0.591000 0.81541 GGT TCGA-HZ-A49G-01A-11D-A26I-08 COL9A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041131.2 0 0 0 19 453 0 47 0 2.471478e-02 0 6 0 47 2 0 0 0 0 0 2 1 0.999990 19 449 0 46 2 0 0 0 0 47 2 -2.675507 1 1 0 0 1 1 2 3 2.029128 0 0.150000 1.820000 0.153808 0.550000 0.340000 1.000000 0.530000 0.579224 0.550000 0 0.430000 0.710000 ABCB5 340273 broad.mit.edu 37 7 20768012 20768012 + Missense_Mutation SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr7:20768012C>T ENST00000404938.2 + 23 3453 c.2801C>T c.(2800-2802)gCg>gTg p.A934V ABCB5_ENST00000258738.6_Missense_Mutation_p.A489V NM_001163941.1 NP_001157413.1 Q2M3G0 ABCB5_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 5 p.A489V(1) 77 TTTGCCTATGCGGCAGGGTTT 0.423000 1 Substitution - Missense(1) SO:0001583 missense ENST00000404938.2 1 1 hg19 CCDS55090.1 . . . . . . . . . . C 22.6 4.306909 0.81247 0.0 1.16E-4 ENSG00000004846 ENST00000404938;ENST00000258738 D;D 0.90133 -2.62;-2.62 3.91 3.91 0.45181 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.000000 0.52532 D 0.000062 D 0.95689 0.8598 M 0.91300 3.195 0.51012 D 0.999903 D;D;D 0.89917 0.999;1.0;0.995 D;P;P 0.67103 0.949;0.904;0.899 D 0.96323 0.9238 10 0.87932 D 0 . 14.2264 0.65863 0.0:1.0:0.0:0.0 . 934;112;489 A7BKA4;A0ASV4;Q2M3G0 .;.;ABCB5_HUMAN V 934;489 ENSP00000384881:A934V;ENSP00000258738:A489V ENSP00000258738:A489V A + 2 0 ABCB5 20734537 1.000000 0.71417 0.943000 0.38184 0.979000 0.70002 5.943000 0.70211 2.472000 0.83506 0.655000 0.94253 GCG TCGA-HZ-A49G-01A-11D-A26I-08 ABCB5-004 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000326736.2 1 0 0 53 531 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 53 529 0 44 2 0 0 0 0 44 2 -3.318794 1 1 121410 1 37 1 1 2 3 2.032143 0 0.150000 1.820000 0.154439 0.990000 0.920000 1.000000 1.000000 0.995868 0.990000 1 0.990000 1.000000 DPYS 1807 broad.mit.edu 37 8 105456665 105456665 + Splice_Site SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr8:105456665C>T ENST00000351513.2 - 4 736 c.604G>A c.(604-606)Gga>Aga p.G202R NM_001385.2 NP_001376.1 Q14117 DPYS_HUMAN dihydropyrimidinase 41 OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229) TTCTTTGCTCCCTAAAAAGAC 0.478000 0 SO:0001630 splice_region_variant ENST00000351513.2 1 0 hg19 CCDS6302.1 . . . . . . . . . . C 18.23 3.578794 0.65878 . . ENSG00000147647 ENST00000351513;ENST00000521573 D;D 0.89485 -2.52;-2.15 5.67 5.67 0.87782 Amidohydrolase 1 (1); 0.171294 0.49916 D 0.000126 D 0.84701 0.5530 N 0.16130 0.375 0.58432 D 0.999998 P 0.44816 0.844 P 0.51453 0.67 T 0.81309 -0.0991 10 0.13108 T 0.6 -10.9332 14.9731 0.71249 0.0:0.9298:0.0:0.0702 . 202 Q14117 DPYS_HUMAN R 202;149 ENSP00000276651:G202R;ENSP00000430246:G149R ENSP00000276651:G202R G - 1 0 DPYS 105525841 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 4.482000 0.60257 2.666000 0.90696 0.655000 0.94253 GGA TCGA-HZ-A49G-01A-11D-A26I-08 DPYS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380814.1 1 0 0 13 209 0 29 0 0 0 1 0 29 2 0 0 0 0 0 2 1 0.999568 13 208 0 28 2 0 0 0 0 29 2 -3.322268 1 1 0 0 1 1 2 3 2.050686 0 0.150000 1.820000 0.158207 0.830000 0.450000 1.000000 1.000000 0.815817 0.830000 0 0.620000 1.000000 SPATC1 375686 broad.mit.edu 37 8 145096207 145096207 + Missense_Mutation SNP A A G TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr8:145096207A>G ENST00000377470.3 + 4 1483 c.1381A>G c.(1381-1383)Atc>Gtc p.I461V SPATC1_ENST00000447830.2_Intron NM_198572.2 NP_940974.2 Q76KD6 SPERI_HUMAN spermatogenesis and centriole associated 1 15 all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105) CCTGTCCAGCATCTTCCCAGA 0.632000 0 SO:0001583 missense ENST00000377470.3 1 1 hg19 CCDS6413.2 . . . . . . . . . . A 15.33 2.802272 0.50315 . . ENSG00000186583 ENST00000377470 T 0.39056 1.1 4.48 4.48 0.54585 . 0.219834 0.35615 N 0.003091 T 0.40932 0.1137 L 0.42581 1.335 0.80722 D 1 P 0.42584 0.784 P 0.48166 0.569 T 0.12734 -1.0536 10 0.20519 T 0.43 -18.189 10.4401 0.44460 1.0:0.0:0.0:0.0 . 461 Q76KD6 SPERI_HUMAN V 461 ENSP00000366690:I461V ENSP00000366690:I461V I + 1 0 SPATC1 145168195 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 2.117000 0.41939 1.794000 0.52575 0.379000 0.24179 ATC TCGA-HZ-A49G-01A-11D-A26I-08 SPATC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000346926.1 1 0 0 18 194 0 36 0 8.182601e-03 0 2 0 36 2 0 0 0 0 0 2 1 0.999983 18 191 0 36 2 0 0 0 0 36 2 -19.999980 1 1 0 0 1 1 2 3 2.050686 0 0.150000 1.820000 0.158207 0.990000 0.720000 1.000000 1.000000 0.968298 0.990000 1 0.920000 1.000000 CDKN2A 1029 broad.mit.edu 37 9 21971003 21971003 + Missense_Mutation SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr9:21971003C>T ENST00000304494.5 - 2 625 c.355G>A c.(355-357)Gag>Aag p.E119K CDKN2A_ENST00000530628.2_Silent_p.*133*|CDKN2A_ENST00000498124.1_Missense_Mutation_p.E119K|CDKN2A_ENST00000579755.1_Silent_p.*133*|CDKN2A_ENST00000494262.1_Missense_Mutation_p.E68K|CDKN2A_ENST00000497750.1_Missense_Mutation_p.E68K|CDKN2A_ENST00000578845.2_Missense_Mutation_p.E68K|CDKN2A_ENST00000446177.1_Missense_Mutation_p.E119K|CDKN2A_ENST00000361570.3_Silent_p.*174*|CDKN2A_ENST00000498628.2_Missense_Mutation_p.E68K|CDKN2A_ENST00000579122.1_Missense_Mutation_p.E119K|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Missense_Mutation_p.E68K NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.E119*(4)|p.E119Q(2)|p.0(1)|p.A118fs*10(1)|p.A118fs*27(1)|p.*174L(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) CCCAGCTCCTCAGCCAGGTCC 0.726000 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1369 Whole gene deletion(1316)|Unknown(44)|Substitution - Nonsense(4)|Substitution - Missense(2)|Deletion - Frameshift(1)|Complex - frameshift(1)|Nonstop extension(1) SO:0001583 missense ENST00000304494.5 1 1 hg19 CCDS6510.1 . . . . . . . . . . C 9.497 1.102324 0.20632 . . ENSG00000147889 ENST00000304494;ENST00000446177 T;T 0.64085 -0.08;-0.08 5.93 2.91 0.33838 Ankyrin repeat-containing domain (4); . . . . T 0.69504 0.3118 . . . 0.21220 N 0.999751 D 0.71674 0.998 D 0.74023 0.982 T 0.56498 -0.7969 8 0.20519 T 0.43 -4.2732 8.4897 0.33093 0.0:0.4925:0.4233:0.0842 . 119 P42771 CD2A1_HUMAN K 119 ENSP00000307101:E119K;ENSP00000394932:E119K ENSP00000307101:E119K E - 1 0 CDKN2A 21961003 0.002000 0.14202 0.998000 0.56505 0.865000 0.49528 0.628000 0.24522 0.816000 0.34421 0.655000 0.94253 GAG TCGA-HZ-A49G-01A-11D-A26I-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 1 22 206 0 30 1 4.120908e-01 3 11 0 30 2 1 1 44 434 0 441 2 1 0.999999 22 204 0 30 2 0 0 0 0 30 2 -9.131699 1 1 0 0 1 0 1 1 1.867881 1 0.150000 1.820000 0.081081 0.900000 0.660000 1.000000 0.990000 0.889158 0.900000 1 0.790000 0.980000 INSL4 3641 broad.mit.edu 37 9 5233847 5233847 + Silent SNP C C T TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chr9:5233847C>T ENST00000239316.4 + 2 495 c.390C>T c.(388-390)gaC>gaT p.D130D NM_002195.1 NP_002186.1 Q14641 INSL4_HUMAN insulin-like 4 (placenta) 6 all_hematologic(13;0.137) Acute lymphoblastic leukemia(23;0.158) TAATTTGTGACGATGGAACTT 0.378000 0 SO:0001819 synonymous_variant ENST00000239316.4 0 1 hg19 CCDS6459.1 TCGA-HZ-A49G-01A-11D-A26I-08 INSL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051616.2 1 0 0 12 193 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 0.999127 11 191 0 18 2 0 0 0 0 18 2 -5.147433 1 1 121400 12 39 1 0 1 1 1.867881 1 0.150000 1.820000 0.081081 0.680000 0.380000 0.960000 0.690000 0.694832 0.680000 0 0.520000 0.860000 BEX2 84707 broad.mit.edu 37 X 102564742 102564742 + Missense_Mutation SNP G G A rs149711551 byFrequency TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chrX:102564742G>A ENST00000372677.3 - 3 430 c.163C>T c.(163-165)Cgg>Tgg p.R55W BEX2_ENST00000372674.1_Missense_Mutation_p.R55W|BEX2_ENST00000536889.1_Missense_Mutation_p.R87W NM_032621.3 NP_116010.1 Q9BXY8 BEX2_HUMAN brain expressed X-linked 2 3 ACGCGGAACCGCCTACGGTTT 0.478000 0 SO:0001583 missense ENST00000372677.3 1 1 hg19 CCDS14505.1 . . . . . . . . . . G 14.90 2.672757 0.47781 . . ENSG00000133134 ENST00000372677;ENST00000536889;ENST00000372674;ENST00000449185 T;T;T;T 0.12361 2.69;2.69;2.69;2.69 4.01 -1.23 0.09465 . 0.689247 0.12748 N 0.442385 T 0.26810 0.0656 M 0.81497 2.545 0.09310 N 1 D;D 0.76494 0.999;0.999 P;D 0.63488 0.828;0.915 T 0.18713 -1.0328 10 0.87932 D 0 . 0.4238 0.00460 0.2149:0.1628:0.2858:0.3364 . 55;87 Q9BXY8;F5H7H5 BEX2_HUMAN;. W 55;87;55;55 ENSP00000361762:R55W;ENSP00000442521:R87W;ENSP00000361759:R55W;ENSP00000394915:R55W ENSP00000361759:R55W R - 1 2 BEX2 102451398 0.766000 0.28496 0.031000 0.17742 0.715000 0.41141 0.716000 0.25836 -0.425000 0.07371 0.600000 0.82982 CGG TCGA-HZ-A49G-01A-11D-A26I-08 BEX2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057702.1 0 0 0 43 932 1 98 0 3.461783e-01 0 66 1 98 4 0 0 0 0 0 2 1 0.961286 44 924 1 98 29 0 0 0 1 98 2 -4.948481 1 1 121410 129 55 1 0 1 1 0.150000 1.820000 0.150000 0.580000 0.430000 0.770000 0.580000 0.596982 0.580000 0 0.500000 0.680000 ARX 170302 broad.mit.edu 37 X 25033684 25033684 + Silent SNP G G A TCGA-HZ-A49G-01A-11D-A26I-08 TCGA-HZ-A49G-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b69d58f0-e51c-470b-bcb3-743fb4cede11 6b9bda12-72ab-4d91-a3e5-df702e7cf48e g.chrX:25033684G>A ENST00000379044.4 - 1 381 c.171C>T c.(169-171)cgC>cgT p.R57R NM_139058.2 NP_620689.1 Q96QS3 ARX_HUMAN aristaless related homeobox 4 CCGGGTCGGCGCGGCTGGTCA 0.627000 0 SO:0001819 synonymous_variant ENST00000379044.4 0 1 hg19 CCDS14215.1 TCGA-HZ-A49G-01A-11D-A26I-08 ARX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056109.1 1 0 1 13 97 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 0.999621 13 96 0 19 2 0 0 0 0 19 2 -19.897360 1 1 0 0 1 0 1 1 0.150000 1.820000 0.150000 0.990000 0.870000 1.000000 1.000000 0.992853 0.990000 1 0.990000 1.000000