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 RASGEF1A 221002 broad.mit.edu 37 10 43701485 43701485 + Missense_Mutation SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr10:43701485C>T ENST00000395809.1 - 2 2586 c.80G>A c.(79-81)cGt>cAt p.R27H RASGEF1A_ENST00000374459.1_Missense_Mutation_p.R35H|RASGEF1A_ENST00000395810.1_Missense_Mutation_p.R27H|RASGEF1A_ENST00000472864.1_5'Flank Q8N9B8 RGF1A_HUMAN RasGEF domain family, member 1A p.R27H(1) 11 CCCGCCTCCACGCTCCCCCAT 0.637000 1 Substitution - Missense(1) SO:0001583 missense ENST00000395809.1 0 1 hg19 CCDS7202.2 . . . . . . . . . . c 15.65 2.896724 0.52121 . . ENSG00000198915 ENST00000374459;ENST00000395810;ENST00000395809 T;T;T 0.71579 -0.56;-0.58;-0.58 5.49 3.63 0.41609 . 0.397928 0.18488 N 0.139733 T 0.54775 0.1879 N 0.22421 0.69 0.26555 N 0.973839 B;B 0.10296 0.002;0.003 B;B 0.08055 0.001;0.003 T 0.49606 -0.8922 10 0.45353 T 0.12 . 9.9083 0.41390 0.0:0.7883:0.0:0.2117 . 27;35 Q8N9B8;Q8N9B8-2 RGF1A_HUMAN;. H 35;27;27 ENSP00000363583:R35H;ENSP00000379155:R27H;ENSP00000379154:R27H ENSP00000363583:R35H R - 2 0 RASGEF1A 43021491 0.769000 0.28531 0.691000 0.30163 0.786000 0.44442 1.601000 0.36773 1.344000 0.45657 -0.119000 0.15052 CGT TCGA-3E-AAAY-01A-11D-A38G-08 RASGEF1A-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000313989.1 0 0 1 6 50 0 20 0 4.418469e-02 0 3 0 20 2 0 0 0 0 0 2 1 0.963922 5 49 0 18 2 0 0 0 0 20 2 -12.258250 1 1 121094 9 38 1 0 1 1 2.001307 0 0.110000 1.860000 0.101600 0.990000 0.700000 1.000000 1.000000 0.977917 0.990000 1 0.990000 1.000000 RTKN2 219790 broad.mit.edu 37 10 64005797 64005797 + Missense_Mutation SNP T T C TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr10:64005797T>C ENST00000373789.3 - 3 373 c.277A>G c.(277-279)Aaa>Gaa p.K93E RTKN2_ENST00000395260.3_Missense_Mutation_p.K93E|RTKN2_ENST00000395265.1_Missense_Mutation_p.K93E NM_145307.2 NP_660350.2 Q8IZC4 RTKN2_HUMAN rhotekin 2 21 Prostate(12;0.0297)|all_hematologic(501;0.215) GTTCGTTCTTTACTTTCAAAT 0.279000 0 SO:0001583 missense ENST00000373789.3 1 1 hg19 CCDS7263.1 . . . . . . . . . . T 4.450 0.083293 0.08533 . . ENSG00000182010 ENST00000395265;ENST00000373789;ENST00000395260 T;T;T 0.41758 1.6;1.6;0.99 5.38 1.67 0.24075 . 0.457220 0.27932 N 0.017279 T 0.28333 0.0700 L 0.48362 1.52 0.19300 N 0.999979 B;B 0.06786 0.001;0.0 B;B 0.09377 0.004;0.002 T 0.20042 -1.0287 10 0.13853 T 0.58 -0.4111 5.9418 0.19198 0.0:0.1462:0.1373:0.7165 . 93;93 Q8IZC4-3;Q8IZC4 .;RTKN2_HUMAN E 93 ENSP00000378682:K93E;ENSP00000362894:K93E;ENSP00000378678:K93E ENSP00000362894:K93E K - 1 0 RTKN2 63675803 0.949000 0.32298 0.294000 0.24946 0.859000 0.49053 1.602000 0.36783 0.337000 0.23665 0.528000 0.53228 AAA TCGA-3E-AAAY-01A-11D-A38G-08 RTKN2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000091618.1 0 0 0 7 205 0 119 1 9.923676e-02 6 8 0 119 2 0 0 0 0 0 2 1 0.980136 7 202 0 119 2 0 0 0 0 119 2 -9.121509 1 1 0 0 1 0 1 1 2.001307 0 0.110000 1.860000 0.101600 0.610000 0.270000 1.000000 1.000000 0.636064 0.610000 0 0.420000 0.850000 ROBO3 64221 broad.mit.edu 37 11 124743218 124743218 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr11:124743218G>A ENST00000397801.1 + 10 1741 c.1549G>A c.(1549-1551)Ggc>Agc p.G517S ROBO3_ENST00000538940.1_Missense_Mutation_p.G495S NM_022370.3 NP_071765.2 Q96MS0 ROBO3_HUMAN roundabout, axon guidance receptor, homolog 3 (Drosophila) 35 all_hematologic(175;0.215) Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112) GATGGACATGGGCTTCTACAG 0.542000 0 SO:0001583 missense ENST00000397801.1 0 1 hg19 CCDS44755.1 . . . . . . . . . . G 21.7 4.186181 0.78789 . . ENSG00000154134 ENST00000397801;ENST00000538940 T;T 0.60171 0.21;0.21 4.89 4.89 0.63831 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.197564 0.25478 N 0.030400 D 0.84696 0.5529 H 0.97465 4.01 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.90158 0.4226 10 0.87932 D 0 . 16.9991 0.86377 0.0:0.0:1.0:0.0 . 517 Q96MS0 ROBO3_HUMAN S 517;495 ENSP00000380903:G517S;ENSP00000441797:G495S ENSP00000380903:G517S G + 1 0 ROBO3 124248428 1.000000 0.71417 0.107000 0.21349 0.762000 0.43233 8.485000 0.90448 2.548000 0.85928 0.455000 0.32223 GGC TCGA-3E-AAAY-01A-11D-A38G-08 ROBO3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387091.1 0 0 0 3 59 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 0.802062 3 57 0 25 2 0 0 0 0 25 2 -4.236343 1 1 0 0 1 0 1 1 2.007625 0 0.110000 1.860000 0.103094 0.880000 0.270000 1.000000 1.000000 0.800659 0.880000 1 0.510000 1.000000 PIK3C2A 5286 broad.mit.edu 37 11 17156533 17156533 + Silent SNP T T C TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr11:17156533T>C ENST00000265970.7 - 10 1940 c.1941A>G c.(1939-1941)caA>caG p.Q647Q PIK3C2A_ENST00000540361.1_Silent_p.Q267Q|PIK3C2A_ENST00000531428.1_Intron NM_002645.2 NP_002636.2 O00443 P3C2A_HUMAN phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha 58 CTGCAGTTAATTGGTTTATGC 0.373000 0 SO:0001819 synonymous_variant ENST00000265970.7 1 1 hg19 CCDS7824.1 TCGA-3E-AAAY-01A-11D-A38G-08 PIK3C2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387553.1 1 0 0 31 425 0 191 0 4.979723e-03 0 2 0 191 2 0 0 0 0 0 2 1 1.000000 31 418 0 191 2 0 0 0 0 191 2 -8.146276 1 1 121412 151 54 1 1 2 3 2.018697 0 0.110000 1.860000 0.115835 0.990000 0.870000 1.000000 1.000000 0.991727 0.990000 1 0.990000 1.000000 IGF2 3481 broad.mit.edu 37 11 2154783 2154783 + Silent SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr11:2154783G>A ENST00000416167.2 - 3 1436 c.270C>T c.(268-270)tcC>tcT p.S90S IGF2_ENST00000381389.1_Silent_p.S90S|IGF2_ENST00000381395.1_Silent_p.S90S|IGF2_ENST00000381406.4_Silent_p.S93S|IGF2_ENST00000300632.5_Silent_p.S90S|IGF2_ENST00000418738.2_Silent_p.S90S|IGF2_ENST00000434045.2_Silent_p.S146S|MIR483_ENST00000385070.1_RNA|IGF2_ENST00000381392.1_Silent_p.S93S P01344 IGF2_HUMAN insulin-like growth factor 2 6 all_epithelial(84;5.04e-06)|Breast(177;0.000777)|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;0.0179)|COAD - Colon adenocarcinoma(6;0.029) CGTCCCTCTCGGACTTGGCGG 0.652000 0 SO:0001819 synonymous_variant ENST00000416167.2 1 1 hg19 CCDS7728.1 TCGA-3E-AAAY-01A-11D-A38G-08 IGF2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000026053.2 1 0 0 10 96 0 55 0 2.722885e-01 0 10 0 55 2 0 0 0 0 0 2 1 0.996416 9 91 0 52 2 0 0 0 0 55 2 -15.704970 1 1 121334 10 37 1 1 2 3 2.018697 0 0.110000 1.860000 0.115835 0.990000 0.880000 1.000000 1.000000 0.993015 0.990000 1 0.990000 1.000000 INS-IGF2 723961 broad.mit.edu 37 11 2182109 2182109 + Silent SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 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-3E-AAAY-01A-11D-A38G-08 INS-IGF2-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000388404.1 0 0 0 7 194 0 95 1 1 4 7436 0 95 2 0 0 0 0 0 2 0 0.387947 8 191 1 93 9 0 0 0 0 95 2 -3.066688 1 1 121154 3 34 1 1 2 3 2.018697 0 0.110000 1.860000 0.115835 0.690000 0.300000 1.000000 1.000000 0.708609 0.690000 0 0.460000 1.000000 ABTB2 25841 broad.mit.edu 37 11 34218927 34218927 + Nonsense_Mutation SNP C C A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr11:34218927C>A ENST00000435224.2 - 3 1613 c.1189G>T c.(1189-1191)Gag>Tag p.E397* ABTB2_ENST00000298992.2_Nonsense_Mutation_p.E211*|ABTB2_ENST00000530814.1_5'UTR NM_145804.2 NP_665803.2 Q8N961 ABTB2_HUMAN ankyrin repeat and BTB (POZ) domain containing 2 25 Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691) TCCATGGACTCCATCTGTGGA 0.632000 0 SO:0001587 stop_gained ENST00000435224.2 0 1 hg19 CCDS7890.2 . . . . . . . . . . C 43 10.292513 0.99377 . . ENSG00000166016 ENST00000435224;ENST00000298992 . . . 5.6 5.6 0.85130 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.87932 D 0 -12.6082 19.6195 0.95650 0.0:1.0:0.0:0.0 . . . . X 397;211 . ENSP00000298992:E211X E - 1 0 ABTB2 34175503 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.818000 0.86416 2.633000 0.89246 0.561000 0.74099 GAG TCGA-3E-AAAY-01A-11D-A38G-08 ABTB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388703.3 1 0 0 10 226 0 113 0 5.233446e-02 0 8 0 113 2 0 0 0 0 0 2 1 0.996575 9 220 0 112 2 0 0 0 0 113 2 -11.684580 1 1 0 0 1 1 2 3 2.018697 0 0.110000 1.860000 0.115835 0.820000 0.410000 1.000000 1.000000 0.804304 0.820000 0 0.590000 1.000000 FAT3 120114 broad.mit.edu 37 11 92577822 92577822 + Silent SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr11:92577822G>A ENST00000298047.6 + 18 11306 c.11289G>A c.(11287-11289)gcG>gcA p.A3763A FAT3_ENST00000525166.1_Silent_p.A3613A|FAT3_ENST00000533797.1_Silent_p.A98A|FAT3_ENST00000409404.2_Silent_p.A3763A Q8TDW7 FAT3_HUMAN FAT atypical cadherin 3 85 Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858) ATTCCCACGCGCTCATGACCT 0.532000 TCGA Ovarian(4;0.039) 0 SO:0001819 synonymous_variant ENST00000298047.6 0 1 hg19 TCGA-3E-AAAY-01A-11D-A38G-08 FAT3-201 KNOWN basic protein_coding protein_coding 0 0 0 4 62 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 0.885132 4 60 0 22 2 0 0 0 0 22 2 -4.311882 1 1 121156 1 34 1 0 1 1 2.007625 0 0.110000 1.860000 0.103094 0.990000 0.380000 1.000000 1.000000 0.877956 0.990000 1 0.660000 1.000000 SRRM4 84530 broad.mit.edu 37 12 119568524 119568524 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr12:119568524G>A ENST00000267260.4 + 8 1044 c.656G>A c.(655-657)cGa>cAa p.R219Q SRRM4_ENST00000537597.1_3'UTR NM_194286.3 NP_919262.2 A7MD48 SRRM4_HUMAN serine/arginine repetitive matrix 4 24 AAGTCCCGCCGAAGGCACTCC 0.657000 0 SO:0001583 missense ENST00000267260.4 0 1 hg19 CCDS44994.1 . . . . . . . . . . G 17.32 3.360937 0.61403 . . ENSG00000139767 ENST00000267260 T 0.24723 1.84 5.07 4.18 0.49190 . 0.282843 0.28403 N 0.015470 T 0.25344 0.0616 L 0.50333 1.59 0.31952 N 0.609555 P 0.48998 0.918 B 0.44278 0.445 T 0.23119 -1.0197 10 0.25751 T 0.34 -2.736 10.6863 0.45846 0.0886:0.0:0.9114:0.0 . 219 A7MD48 SRRM4_HUMAN Q 219 ENSP00000267260:R219Q ENSP00000267260:R219Q R + 2 0 SRRM4 118052907 0.951000 0.32395 0.966000 0.40874 0.950000 0.60333 1.852000 0.39348 1.135000 0.42183 0.448000 0.29417 CGA TCGA-3E-AAAY-01A-11D-A38G-08 SRRM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401640.2 0 0 0 4 74 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.879395 3 71 0 41 2 0 0 0 0 42 2 -8.032464 1 0 120776 3 30 1 0 1 1 2.008853 0 0.110000 1.860000 0.103094 0.920000 0.330000 1.000000 1.000000 0.831459 0.920000 1 0.580000 1.000000 HPD 3242 broad.mit.edu 37 12 122292622 122292622 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr12:122292622G>A ENST00000289004.4 - 7 436 c.401C>T c.(400-402)gCt>gTt p.A134V HPD_ENST00000543163.1_Missense_Mutation_p.A95V|RP11-7M8.2_ENST00000543848.1_RNA NM_002150.2 NP_002141 P32754 HPPD_HUMAN 4-hydroxyphenylpyruvate dioxygenase 18 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) Nitisinone(DB00348) CTGCAGCACAGCAAACTTCAC 0.597000 0 SO:0001583 missense ENST00000289004.4 0 1 hg19 CCDS9224.1 . . . . . . . . . . G 18.63 3.665066 0.67700 . . ENSG00000158104 ENST00000289004;ENST00000545969;ENST00000543163 T;T 0.65732 -0.17;-0.17 5.29 4.38 0.52667 . 0.301114 0.35151 N 0.003416 T 0.71702 0.3371 M 0.90425 3.115 0.80722 D 1 B 0.33280 0.405 B 0.37144 0.242 T 0.76599 -0.2900 10 0.87932 D 0 -7.5669 14.9723 0.71243 0.0:0.1435:0.8565:0.0 . 134 P32754 HPPD_HUMAN V 134;131;95 ENSP00000289004:A134V;ENSP00000441677:A95V ENSP00000289004:A134V A - 2 0 HPD 120777005 1.000000 0.71417 0.987000 0.45799 0.993000 0.82548 9.210000 0.95106 1.203000 0.43233 0.467000 0.42956 GCT TCGA-3E-AAAY-01A-11D-A38G-08 HPD-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402184.1 0 0 0 7 529 1 225 0 3.531803e-03 0 6 1 225 2 0 0 0 0 0 2 0 0.306196 7 525 1 224 10 0 0 0 1 225 2 -2.016036 0 1 0 0 1 0 1 1 2.008853 0 0.110000 1.860000 0.103094 0.240000 0.100000 0.450000 0.230000 0.263934 0.240000 0 0.160000 0.350000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 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 1 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-3E-AAAY-01A-11D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 0 0 9 271 0 123 1 1.846200e-02 2 4 0 123 2 1 9.930780e-01 11 256 0 212 2 1 0.993740 9 264 0 122 2 1 1 581 7441 0 123 2 -3.791404 1 1 121404 2 44 1 0 1 1 2.008853 0 0.110000 1.860000 0.103094 0.590000 0.290000 1.000000 1.000000 0.616008 0.590000 0 0.420000 0.800000 KCNH3 23416 broad.mit.edu 37 12 49950199 49950199 + Missense_Mutation SNP T T C TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr12:49950199T>C ENST00000257981.6 + 13 2775 c.2515T>C c.(2515-2517)Ttc>Ctc p.F839L MCRS1_ENST00000547182.1_5'Flank NM_012284.1 NP_036416.1 Q9ULD8 KCNH3_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 3 36 CCAGCCCAAGTTCTCTTTCCG 0.622000 0 SO:0001583 missense ENST00000257981.6 1 1 hg19 CCDS8786.1 . . . . . . . . . . T 32 5.153821 0.94645 . . ENSG00000135519 ENST00000257981 D 0.99239 -5.61 6.04 6.04 0.98038 . 0.000000 0.49305 D 0.000159 D 0.97885 0.9305 N 0.08118 0 0.39148 D 0.962164 P 0.49447 0.924 P 0.57776 0.827 D 0.98971 1.0801 10 0.44086 T 0.13 . 12.9803 0.58559 0.0:0.0:0.0:1.0 . 839 Q9ULD8 KCNH3_HUMAN L 839 ENSP00000257981:F839L ENSP00000257981:F839L F + 1 0 KCNH3 48236466 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 4.896000 0.63222 2.317000 0.78254 0.460000 0.39030 TTC TCGA-3E-AAAY-01A-11D-A38G-08 KCNH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404571.2 0 0 0 12 299 0 141 0 1.682052e-02 0 5 0 141 2 0 0 0 0 0 2 1 0.998999 12 290 0 137 2 0 0 0 0 141 2 -13.217620 1 1 0 0 1 0 1 1 2.008853 0 0.110000 1.860000 0.103094 0.700000 0.380000 1.000000 1.000000 0.717593 0.700000 0 0.520000 0.910000 IPO5 3843 broad.mit.edu 37 13 98671972 98671972 + Missense_Mutation SNP G G T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr13:98671972G>T ENST00000490680.1 + 24 3039 c.2974G>T c.(2974-2976)Gtc>Ttc p.V992F IPO5_ENST00000539640.1_Missense_Mutation_p.V867F|IPO5_ENST00000261574.5_Missense_Mutation_p.V1010F O00410 IPO5_HUMAN importin 5 27 CGTTGAAGAGGTCCTTCCACA 0.413000 0 SO:0001583 missense ENST00000490680.1 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 13.24|13.24 2.176764|2.176764 0.38413|0.38413 .|. .|. ENSG00000065150|ENSG00000065150 ENST00000469360|ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640 .|T;T;T;T .|0.16073 .|2.39;2.39;2.39;2.37 5.95|5.95 1.82|1.82 0.25136|0.25136 .|. .|0.289846 .|0.38959 .|N .|0.001514 T|T 0.29321|0.29321 0.0730|0.0730 M|M 0.80616|0.80616 2.505|2.505 0.58432|0.58432 D|D 0.999997|0.999997 .|P .|0.36048 .|0.534 .|B .|0.43916 .|0.436 T|T 0.17349|0.17349 -1.0372|-1.0372 5|10 .|0.87932 .|D .|0 -19.4383|-19.4383 11.6613|11.6613 0.51347|0.51347 0.2788:0.0:0.7212:0.0|0.2788:0.0:0.7212:0.0 .|. .|1010 .|O00410-3 .|. S|F 993|1010;992;992;867 .|ENSP00000261574:V1010F;ENSP00000350219:V992F;ENSP00000418393:V992F;ENSP00000445126:V867F .|ENSP00000261574:V1010F R|V +|+ 3|1 2|0 IPO5|IPO5 97469973|97469973 1.000000|1.000000 0.71417|0.71417 0.015000|0.015000 0.15790|0.15790 0.547000|0.547000 0.35210|0.35210 2.700000|2.700000 0.47085|0.47085 0.426000|0.426000 0.26116|0.26116 -0.145000|-0.145000 0.13849|0.13849 AGG|GTC TCGA-3E-AAAY-01A-11D-A38G-08 IPO5-006 NOVEL alternative_5_UTR|basic|appris_principal protein_coding protein_coding OTTHUMT00000354655.1 1 0 1 32 424 0 197 1 9.994488e-01 24 128 0 197 2 0 0 0 0 0 2 1 1.000000 32 417 0 197 2 0 0 0 0 197 2 -20.000000 1 1 0 0 1 1 2 3 2.054353 0 0.110000 1.860000 0.123498 0.990000 0.920000 1.000000 1.000000 0.995629 0.990000 1 0.990000 1.000000 VPS13C 54832 broad.mit.edu 37 15 62283987 62283987 + Silent SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr15:62283987C>T ENST00000261517.5 - 17 1441 c.1368G>A c.(1366-1368)ggG>ggA p.G456G VPS13C_ENST00000395896.4_Silent_p.G456G|VPS13C_ENST00000395898.3_Silent_p.G413G|VPS13C_ENST00000249837.3_Silent_p.G413G NM_020821.2 NP_065872.1 vacuolar protein sorting 13 homolog C (S. cerevisiae) p.G456G(1) 117 TTAATTTTTGCCCAGACCGAA 0.383000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000261517.5 0 1 hg19 CCDS32257.1 TCGA-3E-AAAY-01A-11D-A38G-08 VPS13C-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000415997.1 0 0 0 6 508 0 272 0 0 0 0 272 2 0 0 0 0 0 2 1 0.961595 6 493 0 267 2 0 0 0 0 272 2 -1.761338 0 1 121412 10 43 1 1 2 3 2.015703 0 0.110000 1.860000 0.114868 0.230000 0.090000 1.000000 0.210000 0.305435 0.230000 0 0.150000 0.380000 MAZ 4150 broad.mit.edu 37 16 29819148 29819148 + Splice_Site SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr16:29819148C>T ENST00000322945.6 + 2 1207 c.1042C>T c.(1042-1044)Cgg>Tgg p.R348W MAZ_ENST00000562337.1_Intron|MAZ_ENST00000566906.2_Intron|AC009133.20_ENST00000569039.1_RNA|MAZ_ENST00000568282.1_5'Flank|AC009133.14_ENST00000563806.1_RNA|MAZ_ENST00000568544.1_5'Flank|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000545521.1_Splice_Site_p.R325W|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000563402.1_Intron|MAZ_ENST00000569978.1_5'Flank|MAZ_ENST00000219782.6_Splice_Site_p.R348W NM_002383.2 NP_002374.2 P56270 MAZ_HUMAN MYC-associated zinc finger protein (purine-binding transcription factor) 10 GAGCTTCTCCCGGTGTGCACG 0.701000 Colon(72;875 1167 15364 30899 37091) 0 SO:0001630 splice_region_variant ENST00000322945.6 1 0 hg19 CCDS42143.1 . . . . . . . . . . C 18.35 3.603964 0.66445 . . ENSG00000103495 ENST00000545521;ENST00000322945;ENST00000219782;ENST00000544343 T;T;T 0.58210 3.17;3.17;0.35 2.69 2.69 0.31865 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.64402 U 0.000001 T 0.64907 0.2641 L 0.60067 1.865 0.80722 D 1 D;D;P;D 0.89917 1.0;1.0;0.951;1.0 D;D;P;D 0.91635 0.996;0.999;0.818;0.998 T 0.64050 -0.6498 10 0.38643 T 0.18 -5.0701 11.6094 0.51052 0.0:1.0:0.0:0.0 . 325;113;348;348 C6G496;Q59GP8;P56270;G5E927 .;.;MAZ_HUMAN;. W 325;348;348;123 ENSP00000443956:R325W;ENSP00000313362:R348W;ENSP00000219782:R348W ENSP00000219782:R348W R + 1 2 MAZ 29726649 0.772000 0.28567 1.000000 0.80357 0.693000 0.40251 0.202000 0.17295 1.459000 0.47892 0.435000 0.28638 CGG TCGA-3E-AAAY-01A-11D-A38G-08 MAZ-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000435536.1 1 0 0 15 187 0 79 1 9.999997e-01 73 313 0 79 2 0 0 0 0 0 2 1 0.999878 15 184 0 78 2 0 0 0 0 79 2 -2.879664 1 1 0 0 1 0 1 1 2.006578 0 0.110000 1.860000 0.103094 0.990000 0.780000 1.000000 1.000000 0.982998 0.990000 1 0.990000 1.000000 COL1A1 1277 broad.mit.edu 37 17 48273541 48273541 + Missense_Mutation SNP C C T rs72645356 TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr17:48273541C>T ENST00000225964.5 - 15 1095 c.977G>A c.(976-978)gGt>gAt p.G326D NM_000088.3 NP_000079 P02452 CO1A1_HUMAN collagen, type I, alpha 1 COL1A1/PDGFB(429) 71 Collagenase(DB00048) ACCAGTAGCACCATCATTTCC 0.632000 T PDGFB, USP6 dermatofibrosarcoma protuberans, aneurysmal bone cyst Osteogenesis imperfecta Dom yes 17 17q21.31-q22 1277 collagen, type I, alpha 1 yes M 0 GRCh37 CM070721 COL1A1 M rs72645356 SO:0001583 missense ENST00000225964.5 1 1 hg19 CCDS11561.1 . . . . . . . . . . C 22.8 4.334954 0.81801 . . ENSG00000108821 ENST00000225964 D 0.99619 -6.28 5.1 5.1 0.69264 . 0.000000 0.85682 D 0.000000 D 0.99840 0.9927 H 0.99130 4.44 0.80722 D 1 D 0.76494 0.999 D 0.97110 1.0 D 0.96436 0.9323 10 0.87932 D 0 . 17.3045 0.87191 0.0:1.0:0.0:0.0 . 326 P02452 CO1A1_HUMAN D 326 ENSP00000225964:G326D ENSP00000225964:G326D G - 2 0 COL1A1 45628540 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.737000 0.84957 2.382000 0.81193 0.650000 0.86243 GGT TCGA-3E-AAAY-01A-11D-A38G-08 COL1A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000309036.2 1 0 0 9 119 0 60 1 1 5 2133 0 60 2 0 0 0 0 0 2 1 0.994565 9 118 0 60 2 0 0 0 0 60 2 -13.394600 1 1 0 0 1 1 2 3 2.080272 0 0.110000 1.860000 0.128690 0.990000 0.690000 1.000000 1.000000 0.974299 0.990000 1 0.990000 1.000000 ACE 1636 broad.mit.edu 37 17 61558987 61558987 + Missense_Mutation SNP T T C TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr17:61558987T>C ENST00000290866.4 + 7 1030 c.1006T>C c.(1006-1008)Tcc>Ccc p.S336P ACE_ENST00000584529.1_3'UTR|ACE_ENST00000428043.1_Missense_Mutation_p.S336P|ACE_ENST00000538928.1_Missense_Mutation_p.S336P NM_000789.3 NP_000780.1 P12821 ACE_HUMAN angiotensin I converting enzyme 51 Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519) CCTGGAGCTCTCCCCCATGCC 0.657000 0 SO:0001583 missense ENST00000290866.4 0 1 hg19 CCDS11637.1 . . . . . . . . . . t 3.965 -0.009611 0.07727 . . ENSG00000159640 ENST00000538928;ENST00000290866;ENST00000428043 T;T;T 0.32023 1.47;1.47;1.47 4.48 -4.34 0.03666 . 1.422290 0.04337 N 0.353487 T 0.12646 0.0307 N 0.04787 -0.16 0.09310 N 1 P;B;B 0.44006 0.824;0.283;0.008 B;B;B 0.33799 0.17;0.111;0.022 T 0.22800 -1.0206 10 0.30854 T 0.27 -0.4851 10.3367 0.43854 0.0:0.6211:0.1276:0.2513 . 336;336;336 F5H1K1;P12821-2;P12821 .;.;ACE_HUMAN P 336 ENSP00000439591:S336P;ENSP00000290866:S336P;ENSP00000397593:S336P ENSP00000290866:S336P S + 1 0 ACE 58912719 0.000000 0.05858 0.001000 0.08648 0.009000 0.06853 -0.457000 0.06745 -0.775000 0.04584 -0.360000 0.07572 TCC TCGA-3E-AAAY-01A-11D-A38G-08 ACE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000337675.2 0 0 0 4 120 0 56 0 2.888618e-01 0 27 0 56 2 0 0 0 0 0 2 1 0.887743 4 118 0 55 2 0 0 0 0 56 2 -6.789107 1 1 0 0 1 0 1 1 1.937262 0 0.110000 1.860000 0.058201 0.530000 0.190000 0.940000 0.500000 0.556357 0.530000 0 0.330000 0.770000 TP53 7157 broad.mit.edu 37 17 7577058 7577058 + Nonsense_Mutation SNP C C A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr17:7577058C>A ENST00000269305.4 - 8 1069 c.880G>T c.(880-882)Gag>Tag p.E294* TP53_ENST00000445888.2_Nonsense_Mutation_p.E294*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.E294*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E294*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E294*|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.E294*(46)|p.E294fs*51(9)|p.K291fs*48(8)|p.0?(8)|p.E294K(3)|p.E294fs*12(3)|p.?(2)|p.E294Q(2)|p.L265_K305del41(1)|p.E294>*(1)|p.G293fs*1(1)|p.R290fs*50(1)|p.R290_P295>X(1)|p.E294fs*11(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TGGTGAGGCTCCCCTTTCTTG 0.567000 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 87 Substitution - Nonsense(46)|Deletion - Frameshift(20)|Whole gene deletion(8)|Substitution - Missense(5)|Insertion - Frameshift(3)|Unknown(2)|Deletion - In frame(1)|Complex - deletion inframe(1)|Complex - compound substitution(1) SO:0001587 stop_gained Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 0 hg19 CCDS11118.1 . . . . . . . . . . C 32 5.130179 0.94473 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 . . . 5.26 4.29 0.51040 . 0.702099 0.13430 N 0.388474 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.10902 T 0.67 -17.6918 13.5106 0.61511 0.0:0.8337:0.1663:0.0 . . . . X 294;294;294;294;294;283;162 . ENSP00000269305:E294X E - 1 0 TP53 7517783 0.019000 0.18553 0.006000 0.13384 0.253000 0.25986 1.700000 0.37815 1.441000 0.47550 0.561000 0.74099 GAG TCGA-3E-AAAY-01A-11D-A38G-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 18 159 0 81 0 8.854256e-01 1 35 0 81 2 1 1 77 759 0 749 2 1 0.999984 18 155 0 81 2 0 0 0 0 81 2 -20.000000 1 1 0 0 1 0 1 1 1.947990 0 0.110000 1.860000 0.058201 0.930000 0.710000 1.000000 0.990000 0.915232 0.930000 1 0.830000 0.990000 ST8SIA5 29906 broad.mit.edu 37 18 44268880 44268880 + Missense_Mutation SNP G G C rs151163620 TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr18:44268880G>C ENST00000315087.7 - 4 974 c.314C>G c.(313-315)tCt>tGt p.S105C ST8SIA5_ENST00000538168.1_Missense_Mutation_p.S141C|ST8SIA5_ENST00000590497.1_Intron|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.S74C NM_013305.4 NP_037437.2 O15466 SIA8E_HUMAN ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5 22 GGACAGAGTAGACCTGCCAGG 0.587000 0 SO:0001583 missense ENST00000315087.7 1 1 hg19 CCDS11930.1 . . . . . . . . . . G 21.2 4.120457 0.77323 . . ENSG00000101638 ENST00000315087;ENST00000538168;ENST00000536490 T;T;T 0.48201 0.83;0.82;1.44 5.48 5.48 0.80851 . 0.108387 0.64402 D 0.000004 T 0.53867 0.1823 L 0.43152 1.355 0.50313 D 0.999867 P;P;P 0.52577 0.797;0.954;0.832 P;P;P 0.50440 0.641;0.57;0.625 T 0.56306 -0.8001 10 0.66056 D 0.02 . 19.345 0.94359 0.0:0.0:1.0:0.0 . 74;141;105 F5H8D1;B7Z1K9;O15466 .;.;SIA8E_HUMAN C 105;141;74 ENSP00000321343:S105C;ENSP00000445492:S141C;ENSP00000443683:S74C ENSP00000321343:S105C S - 2 0 ST8SIA5 42522878 1.000000 0.71417 1.000000 0.80357 0.954000 0.61252 6.746000 0.74866 2.578000 0.87016 0.555000 0.69702 TCT TCGA-3E-AAAY-01A-11D-A38G-08 ST8SIA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255892.1 0 0 0 6 170 0 73 0 0 0 1 0 73 2 0 0 0 0 0 2 1 0.961220 6 163 0 70 2 0 0 0 0 73 2 -8.448689 1 1 0 0 1 0 0 0 1.922669 0 0.110000 1.860000 0.061478 0.570000 0.240000 0.970000 1.000000 0.597418 0.570000 0 0.390000 0.800000 ABHD8 79575 broad.mit.edu 37 19 17412369 17412369 + Silent SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:17412369G>A ENST00000247706.3 - 2 296 c.57C>T c.(55-57)aaC>aaT p.N19N MRPL34_ENST00000594999.1_5'Flank|MRPL34_ENST00000600434.1_Intron|MRPL34_ENST00000595444.1_Intron NM_024527.4 NP_078803.4 Q96I13 ABHD8_HUMAN abhydrolase domain containing 8 p.N19N(1) 9 GCCCCACGGCGTTGGGGGGCG 0.652000 Ovarian(156;1368 2543 15275 41187) 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000247706.3 1 1 hg19 CCDS12355.1 TCGA-3E-AAAY-01A-11D-A38G-08 ABHD8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462937.1 1 0 0 12 109 0 68 1 7.953371e-01 3 26 0 68 2 0 0 0 0 0 2 1 0.999112 12 105 0 68 2 0 0 0 0 68 2 -18.323130 1 1 121056 1 30 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.990000 0.990000 1.000000 1.000000 0.997195 0.990000 1 0.990000 1.000000 PDE4C 5143 broad.mit.edu 37 19 18331091 18331091 + Silent SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:18331091G>A ENST00000355502.3 - 11 1618 c.747C>T c.(745-747)tcC>tcT p.S249S PDE4C_ENST00000262805.12_Silent_p.S217S|PDE4C_ENST00000597297.1_Silent_p.S19S|PDE4C_ENST00000447275.3_Silent_p.S143S|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594617.3_Silent_p.S249S|PDE4C_ENST00000598111.2_Silent_p.S19S|PDE4C_ENST00000594465.3_Silent_p.S249S|PDE4C_ENST00000539010.1_Silent_p.S18S Q08493 PDE4C_HUMAN phosphodiesterase 4C, cAMP-specific 33 Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656) GGCTGGTTTCGGACAGGTGGG 0.597000 0 SO:0001819 synonymous_variant ENST00000355502.3 0 1 hg19 CCDS12373.1 TCGA-3E-AAAY-01A-11D-A38G-08 PDE4C-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000466295.1 0 0 0 7 625 0 268 0 0 0 1 0 268 2 0 0 0 0 0 2 1 0.978839 8 610 0 262 2 0 0 0 0 268 2 -2.172914 0 1 121412 9 44 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.230000 0.090000 1.000000 0.200000 0.341232 0.230000 0 0.150000 0.430000 SIGLEC7 27036 broad.mit.edu 37 19 51647799 51647799 + Silent SNP C C G TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:51647799C>G ENST00000317643.6 + 2 639 c.570C>G c.(568-570)tcC>tcG p.S190S SIGLEC7_ENST00000600577.1_Intron|SIGLEC7_ENST00000305628.7_Intron NM_014385.2 NP_055200.1 Q9Y286 SIGL7_HUMAN sialic acid binding Ig-like lectin 7 29 all_neural(266;0.0199) CCTCTGTGTCCCCCCTGCACC 0.662000 0 SO:0001819 synonymous_variant ENST00000317643.6 1 1 hg19 CCDS12826.1 TCGA-3E-AAAY-01A-11D-A38G-08 SIGLEC7-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464226.2 1 0 0 20 377 0 167 0 8.352146e-03 0 3 0 167 2 0 0 0 0 0 2 1 0.999995 20 373 0 164 2 0 0 0 0 167 2 -3.302928 1 1 0 0 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.970000 0.590000 1.000000 1.000000 0.906669 0.970000 1 0.760000 1.000000 ZNF613 79898 broad.mit.edu 37 19 52448449 52448449 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:52448449G>A ENST00000293471.6 + 6 1992 c.1313G>A c.(1312-1314)aGc>aAc p.S438N ZNF613_ENST00000391794.4_Missense_Mutation_p.S402N|ZNF613_ENST00000601794.1_3'UTR NM_001031721.3 NP_001026891.2 Q6PF04 ZN613_HUMAN zinc finger protein 613 19 all_neural(266;0.117) AAAGGCTTCAGCCAGAAGACA 0.443000 0 SO:0001583 missense ENST00000293471.6 1 1 hg19 CCDS33089.1 . . . . . . . . . . G 16.86 3.238490 0.58886 . . ENSG00000176024 ENST00000293471;ENST00000391794;ENST00000535279 T;T 0.19394 2.15;2.15 3.36 2.31 0.28768 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.331298 0.22091 N 0.064756 T 0.25901 0.0631 L 0.35854 1.095 0.20764 N 0.99985 D 0.63046 0.992 P 0.59288 0.855 T 0.03043 -1.1079 10 0.59425 D 0.04 . 6.1129 0.20110 0.1094:0.1914:0.6992:0.0 . 438 Q6PF04 ZN613_HUMAN N 438;402;112 ENSP00000293471:S438N;ENSP00000375671:S402N ENSP00000293471:S438N S + 2 0 ZNF613 57140261 0.000000 0.05858 0.970000 0.41538 0.981000 0.71138 -0.130000 0.10498 0.756000 0.33013 0.655000 0.94253 AGC TCGA-3E-AAAY-01A-11D-A38G-08 ZNF613-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461104.2 1 0 0 26 321 0 170 0 4.332782e-01 1 18 0 170 2 0 0 0 0 0 2 1 1.000000 26 315 0 168 2 0 0 0 0 170 2 -7.921733 1 1 0 0 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.990000 0.940000 1.000000 1.000000 0.996304 0.990000 1 0.990000 1.000000 NLRP2 55655 broad.mit.edu 37 19 55501405 55501405 + Silent SNP C C T rs148932752 TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:55501405C>T ENST00000543010.1 + 9 2525 c.2382C>T c.(2380-2382)tcC>tcT p.S794S NLRP2_ENST00000448584.2_Silent_p.S794S|NLRP2_ENST00000263437.6_Silent_p.S791S|NLRP2_ENST00000339757.7_Silent_p.S772S|NLRP2_ENST00000537859.1_Silent_p.S772S|NLRP2_ENST00000538819.1_Silent_p.S770S|NLRP2_ENST00000427260.2_Silent_p.S771S|NLRP2_ENST00000391721.4_Silent_p.S770S NM_001174081.1 NP_001167552.1 Q9NX02 NALP2_HUMAN NLR family, pyrin domain containing 2 11 BRCA - Breast invasive adenocarcinoma(297;0.163) TGTCTTGTTCCGCTACCACTC 0.512000 0 SO:0001819 synonymous_variant ENST00000543010.1 1 1 hg19 CCDS12913.1 TCGA-3E-AAAY-01A-11D-A38G-08 NLRP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396152.1 1 0 0 23 259 0 139 0 7.361060e-03 0 2 0 139 2 0 0 0 0 0 2 1 0.999999 22 252 0 139 2 0 0 0 0 139 2 -2.690404 1 1 121412 8 42 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.990000 0.990000 1.000000 1.000000 0.997975 0.990000 1 0.990000 1.000000 RETN 56729 broad.mit.edu 37 19 7735211 7735211 + Silent SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:7735211G>A ENST00000221515.2 + 4 391 c.303G>A c.(301-303)gcG>gcA p.A101A RETN_ENST00000381324.2_Silent_p.A75A NM_001193374.1|NM_020415.3 NP_001180303.1|NP_065148.1 Q9HD89 RETN_HUMAN resistin 1 GGACCGGAGCGCGCTGCTGTC 0.706000 0 SO:0001819 synonymous_variant ENST00000221515.2 0 1 hg19 CCDS12182.1 TCGA-3E-AAAY-01A-11D-A38G-08 RETN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461731.1 0 0 0 4 43 0 16 0 9.253838e-02 0 5 0 16 2 0 0 0 0 0 2 1 0.882813 4 41 0 16 2 0 0 0 0 16 2 -9.713918 1 1 0 0 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.990000 0.550000 1.000000 1.000000 0.957854 0.990000 1 0.950000 1.000000 OR7G2 390882 broad.mit.edu 37 19 9213690 9213690 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr19:9213690G>A ENST00000305456.2 - 1 292 c.293C>T c.(292-294)aCg>aTg p.T98M NM_001005193.1 NP_001005193.1 Q8NG99 OR7G2_HUMAN olfactory receptor, family 7, subfamily G, member 2 16 CTTTGGGATCGTGGTTGTGCT 0.488000 Esophageal Squamous(67;143 1448 28637 40648) 0 SO:0001583 missense ENST00000305456.2 1 1 hg19 CCDS32897.1 . . . . . . . . . . g 4.837 0.155672 0.09236 0.0 1.16E-4 ENSG00000170923 ENST00000305456 T 0.00882 5.58 3.2 3.2 0.36748 GPCR, rhodopsin-like superfamily (1); 0.201904 0.23891 N 0.043541 T 0.01870 0.0059 M 0.87900 2.915 0.09310 N 1 P 0.49961 0.93 B 0.39379 0.298 T 0.41288 -0.9517 10 0.62326 D 0.03 . 8.3321 0.32193 0.1159:0.0:0.8841:0.0 . 77 Q8NG99 OR7G2_HUMAN M 98 ENSP00000303822:T98M ENSP00000303822:T98M T - 2 0 OR7G2 9074690 0.000000 0.05858 0.524000 0.27887 0.008000 0.06430 -0.287000 0.08388 2.145000 0.66743 0.494000 0.49563 ACG TCGA-3E-AAAY-01A-11D-A38G-08 OR7G2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448994.1 1 0 0 25 405 0 169 0 0 0 0 169 2 0 0 0 0 0 2 1 1.000000 23 394 0 168 2 0 0 0 0 169 2 -5.977114 1 1 121412 8 43 1 1 2 3 2.035854 0 0.110000 1.860000 0.119204 0.990000 0.720000 1.000000 1.000000 0.962532 0.990000 1 0.890000 1.000000 HP1BP3 50809 broad.mit.edu 37 1 21071440 21071440 + Silent SNP C C T rs144814158 TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr1:21071440C>T ENST00000312239.5 - 13 1651 c.1512G>A c.(1510-1512)acG>acA p.T504T HP1BP3_ENST00000375003.2_Silent_p.T352T|RP5-930J4.4_ENST00000413451.1_RNA NM_016287.3 NP_057371.2 Q5SSJ5 HP1B3_HUMAN heterochromatin protein 1, binding protein 3 16 all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255) TCTTGGCAGGCGTTTTGGCCT 0.527000 0 SO:0001819 synonymous_variant ENST00000312239.5 1 1 hg19 CCDS30621.1 TCGA-3E-AAAY-01A-11D-A38G-08 HP1BP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007457.2 0 0 0 12 336 0 165 1 9.732042e-01 30 143 0 165 2 0 0 0 0 0 2 1 0.999043 11 330 0 162 2 0 0 0 0 165 2 -3.342456 1 1 121412 15 43 1 1 2 3 2.015617 0 0.110000 1.860000 0.114868 0.660000 0.350000 1.000000 1.000000 0.687256 0.660000 0 0.490000 0.920000 PRDM16 63976 broad.mit.edu 37 1 3331138 3331138 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr1:3331138G>A ENST00000270722.5 + 10 2667 c.2618G>A c.(2617-2619)cGg>cAg p.R873Q PRDM16_ENST00000511072.1_Missense_Mutation_p.R874Q|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000514189.1_Missense_Mutation_p.R873Q|PRDM16_ENST00000378391.2_Missense_Mutation_p.R873Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R873Q|PRDM16_ENST00000441472.2_Missense_Mutation_p.R872Q|PRDM16_ENST00000442529.2_Missense_Mutation_p.R872Q Q9HAZ2 PRD16_HUMAN PR domain containing 16 59 all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111) all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134) GTAGAAAAGCGGAAGGTCACA 0.687000 T EVI1 MDS, AML Dom yes 1 1p36.23-p33 63976 PR domain containing 16 L 0 SO:0001583 missense ENST00000270722.5 0 1 hg19 CCDS41236.2 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 G 35 5.594815 0.96602 . . ENSG00000142611 ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860 T;T;T;T;T;T;T;T;T 0.06608 3.35;3.32;3.33;3.33;3.37;3.32;3.39;3.34;3.28 4.94 4.94 0.65067 . 0.000000 0.46758 D 0.000277 T 0.23330 0.0564 M 0.64404 1.975 0.58432 D 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;P 0.79108 0.992;0.955;0.965;0.903 T 0.00498 -1.1704 10 0.46703 T 0.11 . 18.1398 0.89636 0.0:0.0:1.0:0.0 . 873;873;872;872 Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5 PRD16_HUMAN;.;.;. Q 874;873;872;872;873;873;873;689;689;681 ENSP00000426975:R874Q;ENSP00000367651:R873Q;ENSP00000407968:R872Q;ENSP00000405253:R872Q;ENSP00000367643:R873Q;ENSP00000421400:R873Q;ENSP00000270722:R873Q;ENSP00000422504:R689Q;ENSP00000425796:R681Q ENSP00000270722:R873Q R + 2 0 PRDM16 3320998 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 9.341000 0.97041 2.281000 0.76405 0.511000 0.50034 CGG TCGA-3E-AAAY-01A-11D-A38G-08 PRDM16-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000001382.3 1 0 0 4 90 0 43 0 6.798549e-02 1 7 0 43 2 0 0 0 0 0 2 1 0.884144 4 87 0 42 2 0 0 0 0 43 2 -7.179940 1 1 120878 5 34 1 0 1 1 2.015160 0 0.110000 1.860000 0.105078 0.790000 0.280000 1.000000 1.000000 0.766090 0.790000 0 0.490000 1.000000 TAL1 6886 broad.mit.edu 37 1 47685731 47685731 + Silent SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr1:47685731C>T ENST00000294339.3 - 4 1233 c.657G>A c.(655-657)ccG>ccA p.P219P TAL1_ENST00000371883.3_Silent_p.P221P|TAL1_ENST00000371884.2_Silent_p.P219P|TAL1_ENST00000459729.1_5'UTR NM_003189.2 NP_003180.1 P17542 TAL1_HUMAN T-cell acute lymphocytic leukemia 1 15 GCTTCTTGTCCGGGGGATGTG 0.587000 T TRD@, SIL lymphoblastic leukemia/biphasic Dom yes 1 1p32 6886 T-cell acute lymphocytic leukemia 1 (SCL) L 0 SO:0001819 synonymous_variant ENST00000294339.3 1 1 hg19 CCDS547.1 TCGA-3E-AAAY-01A-11D-A38G-08 TAL1-002 KNOWN alternative_5_UTR|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000021640.1 1 0 0 21 310 0 138 0 1.299652e-02 0 3 0 138 2 0 0 0 0 0 2 1 0.999997 21 303 0 136 2 0 0 0 0 138 2 -2.578515 1 1 0 0 1 1 2 3 2.015617 0 0.110000 1.860000 0.114868 0.990000 0.750000 1.000000 1.000000 0.974001 0.990000 1 0.940000 1.000000 DEFB119 245932 broad.mit.edu 37 20 29965177 29965177 + Missense_Mutation SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr20:29965177C>T ENST00000376321.3 - 2 246 c.127G>A c.(127-129)Gaa>Aaa p.E43K SNORA40_ENST00000390832.1_RNA|DEFB119_ENST00000492344.1_5'UTR|DEFB119_ENST00000339144.3_3'UTR NM_153289.3 NP_695021.2 Q8N690 DB119_HUMAN defensin, beta 119 4 all_hematologic(12;0.158) Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347) TAGGGCTGTTCGTTCTTTTTG 0.433000 0 SO:0001583 missense ENST00000376321.3 1 1 hg19 CCDS13178.1 . . . . . . . . . . C 14.64 2.596310 0.46318 . . ENSG00000180483 ENST00000376321 T 0.73575 -0.76 4.31 4.31 0.51392 . . . . . D 0.84946 0.5585 . . . 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.86218 0.1629 8 0.87932 D 0 . 12.5997 0.56491 0.0:1.0:0.0:0.0 . 43 Q8N690 DB119_HUMAN K 43 ENSP00000365499:E43K ENSP00000365499:E43K E - 1 0 DEFB119 29428838 0.471000 0.25862 0.184000 0.23157 0.007000 0.05969 1.525000 0.35953 2.678000 0.91216 0.655000 0.94253 GAA TCGA-3E-AAAY-01A-11D-A38G-08 DEFB119-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078514.1 1 0 0 34 605 0 279 0 0 0 0 279 2 0 0 0 0 0 2 1 1.000000 33 590 0 280 2 0 0 0 0 279 2 -5.349535 1 1 121412 2 41 1 1 2 3 2.031726 0 0.110000 1.860000 0.118244 0.990000 0.690000 1.000000 1.000000 0.939428 0.990000 1 0.830000 1.000000 TRAPPC10 7109 broad.mit.edu 37 21 45478983 45478983 + Splice_Site SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr21:45478983G>A ENST00000291574.4 + 6 853 c.e6-1 TRAPPC10_ENST00000380221.3_Splice_Site NM_003274.4 NP_003265.3 P48553 TPC10_HUMAN trafficking protein particle complex 10 41 TGGGCGAATAGGAGGAGCTTG 0.448000 0 SO:0001630 splice_region_variant ENST00000291574.4 1 1 hg19 CCDS13704.1 . . . . . . . . . . G 19.11 3.763268 0.69763 . . ENSG00000160218 ENST00000380221;ENST00000291574 . . . 5.25 5.25 0.73442 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 18.8261 0.92119 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . TRAPPC10 44303411 1.000000 0.71417 0.995000 0.50966 0.579000 0.36224 9.523000 0.98034 2.443000 0.82685 0.561000 0.74099 . TCGA-3E-AAAY-01A-11D-A38G-08 TRAPPC10-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000195737.1 1 0 0 15 252 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 0.999874 15 249 0 103 2 0 0 0 0 104 2 -2.810242 1 1 0 0 1 1 2 3 2.085679 0 0.110000 1.860000 0.130095 0.990000 0.640000 1.000000 1.000000 0.949281 0.990000 1 0.850000 1.000000 FAM49A 81553 broad.mit.edu 37 2 16745312 16745312 + Silent SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr2:16745312C>T ENST00000381323.3 - 5 463 c.243G>A c.(241-243)gcG>gcA p.A81A FAM49A_ENST00000355549.2_Silent_p.A81A|FAM49A_ENST00000406434.1_Silent_p.A81A NM_030797.3 NP_110424.1 Q9H0Q0 FA49A_HUMAN family with sequence similarity 49, member A 23 Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088) GBM - Glioblastoma multiforme(3;0.00969) GAGGGCACACCGCATTCCAAG 0.408000 0 SO:0001819 synonymous_variant ENST00000381323.3 1 1 hg19 CCDS1688.1 TCGA-3E-AAAY-01A-11D-A38G-08 FAM49A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207203.2 0 0 0 12 254 1 132 0 2.184062e-01 1 17 1 132 2 0 0 0 0 0 2 1 0.798505 12 249 1 132 9 0 0 0 1 132 2 -2.463726 0 1 121406 21 41 1 0 1 1 1.918548 0 0.110000 1.860000 0.058201 0.720000 0.410000 0.980000 0.730000 0.723612 0.720000 0 0.550000 0.890000 SAG 6295 broad.mit.edu 37 2 234229331 234229331 + Silent SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr2:234229331C>T ENST00000409110.1 + 5 467 c.237C>T c.(235-237)atC>atT p.I79I SAG_ENST00000461532.1_3'UTR|SAG_ENST00000449594.2_5'UTR NM_000541.4 NP_000532.2 P10523 ARRS_HUMAN S-antigen; retina and pineal gland (arrestin) 9 Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054) TTGACGTGATCGGCTTGACCT 0.607000 0 SO:0001819 synonymous_variant ENST00000409110.1 0 1 hg19 CCDS46545.1 TCGA-3E-AAAY-01A-11D-A38G-08 SAG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330126.1 1 0 1 6 50 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 0.961766 6 47 0 21 2 0 0 0 0 21 2 -6.127719 1 1 121162 8 36 1 1 2 3 2.042421 0 0.110000 1.860000 0.120640 0.990000 0.800000 1.000000 1.000000 0.988569 0.990000 1 0.990000 1.000000 FBXL5 26234 broad.mit.edu 37 4 15627448 15627448 + Missense_Mutation SNP A A G TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr4:15627448A>G ENST00000341285.3 - 9 1401 c.1277T>C c.(1276-1278)aTt>aCt p.I426T FBXL5_ENST00000412094.2_Missense_Mutation_p.I409T|FBXL5_ENST00000382358.4_Missense_Mutation_p.I300T NM_001193534.1|NM_001193535.1|NM_012161.3 NP_001180463.1|NP_001180464.1|NP_036293.1 Q9UKA1 FBXL5_HUMAN F-box and leucine-rich repeat protein 5 13 AGTTGAAGTAATTTTGCTTGT 0.393000 0 SO:0001583 missense ENST00000341285.3 1 1 hg19 CCDS3415.1 . . . . . . . . . . A 0.449 -0.894587 0.02491 . . ENSG00000118564 ENST00000341285;ENST00000412094;ENST00000382358 T;T;T 0.30182 1.57;1.57;1.54 5.92 -0.683 0.11335 . 0.891429 0.10025 N 0.725521 T 0.10294 0.0252 N 0.08118 0 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.32052 -0.9921 10 0.09338 T 0.73 -0.7497 0.2314 0.00180 0.2771:0.162:0.2613:0.2996 . 409;426 Q9UKA1-2;Q9UKA1 .;FBXL5_HUMAN T 426;409;300 ENSP00000344866:I426T;ENSP00000408679:I409T;ENSP00000371795:I300T ENSP00000344866:I426T I - 2 0 FBXL5 15236546 0.000000 0.05858 0.000000 0.03702 0.492000 0.33523 -0.249000 0.08842 -0.087000 0.12528 0.528000 0.53228 ATT TCGA-3E-AAAY-01A-11D-A38G-08 FBXL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214235.2 1 0 1 35 323 0 183 1 9.933099e-01 11 63 0 183 2 0 0 0 0 0 2 1 1.000000 33 322 0 183 2 0 0 0 0 183 2 -20.000000 1 1 0 0 1 1 2 3 2.043877 0 0.110000 1.860000 0.121118 0.990000 0.990000 1.000000 1.000000 0.999979 0.990000 1 0.990000 1.000000 REEP2 51308 broad.mit.edu 37 5 137777145 137777145 + Silent SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr5:137777145C>T ENST00000254901.5 + 3 299 c.177C>T c.(175-177)ctC>ctT p.L59L REEP2_ENST00000506158.1_Silent_p.L21L|REEP2_ENST00000464751.2_3'UTR|REEP2_ENST00000378339.2_Silent_p.L59L NM_016606.2 NP_057690.2 Q9BRK0 REEP2_HUMAN receptor accessory protein 2 12 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) ATATAGTGCTCTCCTGGTGAG 0.592000 0 SO:0001819 synonymous_variant ENST00000254901.5 0 1 hg19 CCDS4205.1 . . . . . . . . . . C 9.842 1.191368 0.21954 . . ENSG00000132563 ENST00000512126 . . . 4.01 -4.81 0.03180 . . . . . T 0.50769 0.1635 . . . 0.80722 D 1 . . . . . . T 0.52426 -0.8577 4 . . . -4.1558 8.4986 0.33144 0.0:0.2491:0.5241:0.2268 . . . . F 97 . . S + 2 0 REEP2 137805044 0.915000 0.31059 0.934000 0.37439 0.986000 0.74619 -0.207000 0.09384 -0.560000 0.06102 0.455000 0.32223 TCT TCGA-3E-AAAY-01A-11D-A38G-08 REEP2-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251284.1 0 0 0 8 164 0 77 0 9.570907e-02 0 10 0 77 2 0 0 0 0 0 2 1 0.989134 8 161 0 76 2 0 0 0 0 77 2 -3.354106 1 1 0 0 1 1 2 3 2.015560 0 0.110000 1.860000 0.114868 0.900000 0.420000 1.000000 1.000000 0.840956 0.900000 1 0.620000 1.000000 PCDHB3 56132 broad.mit.edu 37 5 140481822 140481822 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr5:140481822G>A ENST00000231130.2 + 1 1589 c.1589G>A c.(1588-1590)cGc>cAc p.R530H AC005754.7_ENST00000607216.1_RNA NM_018937.2 NP_061760.1 Q9Y5E6 PCDB3_HUMAN protocadherin beta 3 p.R530H(1) 72 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) TTCGAGTTCCGCGTGGGCGCC 0.667000 1 Substitution - Missense(1) SO:0001583 missense ENST00000231130.2 1 1 hg19 CCDS4245.1 . . . . . . . . . . G 0.185 -1.058176 0.01950 . . ENSG00000113205 ENST00000231130 T 0.01767 4.65 4.14 1.03 0.20045 Cadherin (5);Cadherin-like (1); . . . . T 0.01092 0.0036 N 0.11064 0.09 0.09310 N 1 B 0.12630 0.006 B 0.13407 0.009 T 0.48854 -0.8998 9 0.15499 T 0.54 . 6.6896 0.23163 0.1992:0.224:0.5769:0.0 . 530 Q9Y5E6 PCDB3_HUMAN H 530 ENSP00000231130:R530H ENSP00000231130:R530H R + 2 0 PCDHB3 140462006 0.000000 0.05858 0.989000 0.46669 0.065000 0.16274 -0.362000 0.07602 0.834000 0.34852 0.650000 0.86243 CGC TCGA-3E-AAAY-01A-11D-A38G-08 PCDHB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251817.2 1 0 0 28 342 0 172 0 7.516577e-02 0 6 0 172 2 0 0 0 0 0 2 1 0.999536 28 326 1 183 9 0 0 0 0 172 2 -3.318788 1 1 0 0 1 1 2 3 2.015560 0 0.110000 1.860000 0.114868 0.990000 0.950000 1.000000 1.000000 0.996819 0.990000 1 0.990000 1.000000 RASGEF1C 255426 broad.mit.edu 37 5 179548100 179548100 + Missense_Mutation SNP A A C TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr5:179548100A>C ENST00000393371.2 - 6 1060 c.764T>G c.(763-765)tTc>tGc p.F255C RASGEF1C_ENST00000522500.1_Missense_Mutation_p.F104C|RASGEF1C_ENST00000519883.1_5'UTR|RASGEF1C_ENST00000361132.4_Missense_Mutation_p.F255C Q8N431 RGF1C_HUMAN RasGEF domain family, member 1C 12 all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137) all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) CAGCCTGTTGAACCATTTCAC 0.557000 0 SO:0001583 missense ENST00000393371.2 1 1 hg19 CCDS4452.1 . . . . . . . . . . A 15.78 2.934399 0.52866 . . ENSG00000146090 ENST00000361132;ENST00000393371;ENST00000522500 T;T;T 0.39787 1.06;1.06;1.06 3.64 3.64 0.41730 Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1); 0.059111 0.64402 D 0.000002 T 0.62575 0.2439 M 0.78223 2.4 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 T 0.67745 -0.5591 10 0.87932 D 0 . 11.5493 0.50711 1.0:0.0:0.0:0.0 . 255 Q8N431 RGF1C_HUMAN C 255;255;104 ENSP00000354963:F255C;ENSP00000377037:F255C;ENSP00000429114:F104C ENSP00000354963:F255C F - 2 0 RASGEF1C 179480706 1.000000 0.71417 1.000000 0.80357 0.430000 0.31655 5.407000 0.66363 1.677000 0.50941 0.254000 0.18369 TTC TCGA-3E-AAAY-01A-11D-A38G-08 RASGEF1C-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253506.2 1 0 0 16 288 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 0.999920 16 278 0 99 2 0 0 0 0 99 2 -18.389890 1 1 0 0 1 1 2 3 2.015560 0 0.110000 1.860000 0.114868 0.990000 0.580000 1.000000 1.000000 0.910360 0.990000 1 0.760000 1.000000 AIM1 202 broad.mit.edu 37 6 106987390 106987390 + Missense_Mutation SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr6:106987390C>T ENST00000369066.3 + 7 4094 c.3607C>T c.(3607-3609)Cgg>Tgg p.R1203W AIM1_ENST00000535438.1_5'Flank NM_001624.2 NP_001615 Q9UMX9 S45A2_HUMAN absent in melanoma 1 69 Breast(9;0.0138)|all_epithelial(6;0.169) all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473) Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305) TGGATCCATGCGGCCTCTGAA 0.438000 0 SO:0001583 missense ENST00000369066.3 0 1 hg19 CCDS34506.1 . . . . . . . . . . C 18.67 3.674524 0.67928 2.27E-4 0.0 ENSG00000112297 ENST00000369066 D 0.82344 -1.6 5.66 3.67 0.42095 Beta/gamma crystallin (4);Gamma-crystallin-related (1); 0.094954 0.64402 D 0.000002 D 0.90728 0.7090 M 0.91140 3.18 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 D 0.92760 0.6223 10 0.87932 D 0 . 13.4764 0.61312 0.4327:0.5673:0.0:0.0 . 1203 Q9Y4K1 AIM1_HUMAN W 1203 ENSP00000358062:R1203W ENSP00000358062:R1203W R + 1 2 AIM1 107094083 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 1.275000 0.33144 1.360000 0.45960 0.655000 0.94253 CGG TCGA-3E-AAAY-01A-11D-A38G-08 AIM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041669.1 0 0 0 6 425 0 201 0 1.448882e-02 0 11 0 201 2 0 0 0 0 0 2 1 0.962874 6 416 0 199 2 0 0 0 0 201 2 -2.223643 0 1 121412 2 36 1 0 0 0 1.958727 0 0.110000 1.860000 0.078580 0.250000 0.100000 0.490000 0.240000 0.276203 0.250000 0 0.170000 0.370000 DNAH11 8701 broad.mit.edu 37 7 21628848 21628848 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr7:21628848G>A ENST00000409508.3 + 12 2027 c.1996G>A c.(1996-1998)Gct>Act p.A666T DNAH11_ENST00000328843.6_Missense_Mutation_p.A666T NM_001277115.1 NP_001264044.1 Q96DT5 DYH11_HUMAN dynein, axonemal, heavy chain 11 230 TCCTGATCACGCTTTAGTTTA 0.303000 Kartagener syndrome 0 SO:0001583 missense Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000409508.3 1 1 hg19 . . . . . . . . . . G 4.091 0.014837 0.07959 . . ENSG00000105877 ENST00000328843 T 0.55413 0.52 5.58 3.79 0.43588 Dynein heavy chain, domain-1 (1); 0.823945 0.11127 N 0.596763 T 0.38612 0.1047 . . . 0.09310 N 0.999998 B 0.11235 0.004 B 0.04013 0.001 T 0.26815 -1.0092 9 0.41790 T 0.15 . 6.2505 0.20843 0.1557:0.0:0.6953:0.149 . 666 Q96DT5 DYH11_HUMAN T 666 ENSP00000330671:A666T ENSP00000330671:A666T A + 1 0 DNAH11 21595373 0.022000 0.18835 0.476000 0.27291 0.043000 0.13939 1.048000 0.30379 0.731000 0.32448 0.650000 0.86243 GCT TCGA-3E-AAAY-01A-11D-A38G-08 DNAH11-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000326582.6 0 0 0 15 201 1 85 0 0 0 1 85 2 0 0 0 0 0 2 1 0.883000 15 198 1 85 10 0 0 0 1 85 2 -6.240001 1 1 0 0 1 1 2 3 2.047513 0 0.110000 1.860000 0.122072 0.990000 0.770000 1.000000 1.000000 0.982963 0.990000 1 0.990000 1.000000 BAZ1B 9031 broad.mit.edu 37 7 72892025 72892025 + Missense_Mutation SNP T T G TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr7:72892025T>G ENST00000339594.4 - 7 2104 c.1766A>C c.(1765-1767)aAc>aCc p.N589T BAZ1B_ENST00000404251.1_Missense_Mutation_p.N589T NM_032408.3 NP_115784.1 Q9UIG0 BAZ1B_HUMAN bromodomain adjacent to zinc finger domain, 1B 61 Lung NSC(55;0.0659)|all_lung(88;0.152) TGCTGGAAGGTTTTTGCCAGT 0.458000 Esophageal Squamous(112;1167 1561 21085 43672 48228) 0 SO:0001583 missense ENST00000339594.4 1 1 hg19 CCDS5549.1 . . . . . . . . . . T 5.695 0.312690 0.10789 . . ENSG00000009954 ENST00000339594;ENST00000404251 T;T 0.57273 0.41;0.41 5.82 -6.38 0.01957 . 0.558505 0.22152 N 0.063904 T 0.32436 0.0829 L 0.40543 1.245 0.24006 N 0.996196 B 0.02656 0.0 B 0.01281 0.0 T 0.30736 -0.9968 10 0.14656 T 0.56 -6.4103 10.4288 0.44395 0.0:0.4925:0.284:0.2234 . 589 Q9UIG0 BAZ1B_HUMAN T 589 ENSP00000342434:N589T;ENSP00000385442:N589T ENSP00000342434:N589T N - 2 0 BAZ1B 72529961 0.003000 0.15002 0.412000 0.26496 0.974000 0.67602 -0.564000 0.05936 -1.088000 0.03077 0.533000 0.62120 AAC TCGA-3E-AAAY-01A-11D-A38G-08 BAZ1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252123.4 0 0 0 69 907 0 393 1 6.193964e-01 4 25 0 393 2 0 0 0 0 0 2 1 1.000000 69 890 0 391 2 0 0 0 0 393 2 -12.935160 1 1 0 0 1 1 2 3 2.055439 0 0.110000 1.860000 0.123498 0.990000 0.990000 1.000000 1.000000 0.999513 0.990000 1 0.990000 1.000000 ZC3H3 23144 broad.mit.edu 37 8 144620233 144620233 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr8:144620233G>A ENST00000262577.5 - 2 1335 c.1304C>T c.(1303-1305)cCg>cTg p.P435L NM_015117.2 NP_055932.2 Q8IXZ2 ZC3H3_HUMAN zinc finger CCCH-type containing 3 23 all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155) Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107) AGCCGAGAGCGGGGTCTCCCC 0.642000 0 SO:0001583 missense ENST00000262577.5 0 1 hg19 CCDS6402.1 . . . . . . . . . . G 3.338 -0.135192 0.06711 0.0 1.16E-4 ENSG00000014164 ENST00000262577 T 0.02863 4.13 5.31 4.4 0.53042 . 0.573853 0.17539 N 0.170615 T 0.02455 0.0075 L 0.47716 1.5 0.09310 N 1 P 0.37997 0.614 B 0.22152 0.038 T 0.47837 -0.9086 10 0.31617 T 0.26 -2.5276 6.5088 0.22210 0.0734:0.1267:0.6613:0.1386 . 435 Q8IXZ2 ZC3H3_HUMAN L 435 ENSP00000262577:P435L ENSP00000262577:P435L P - 2 0 ZC3H3 144691376 0.002000 0.14202 0.005000 0.12908 0.022000 0.10575 1.201000 0.32259 1.177000 0.42855 0.561000 0.74099 CCG TCGA-3E-AAAY-01A-11D-A38G-08 ZC3H3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382011.2 0 0 0 5 157 0 87 1 4.052244e-01 4 35 0 87 2 0 0 0 0 0 2 1 0.932155 5 151 0 86 2 0 0 0 0 87 2 -6.966358 1 1 121350 2 32 1 1 2 3 2.037747 0 0.110000 1.860000 0.119683 0.660000 0.240000 1.000000 1.000000 0.683308 0.660000 0 0.400000 1.000000 HOOK3 84376 broad.mit.edu 37 8 42805542 42805542 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr8:42805542G>A ENST00000307602.4 + 6 612 c.412G>A c.(412-414)Gcc>Acc p.A138T Y_RNA_ENST00000365644.1_RNA NM_032410.3 NP_115786.1 Q86VS8 HOOK3_HUMAN hook microtubule-tethering protein 3 31 Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184) all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129) Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114) GTACATCCAAGCCATTATGAT 0.353000 T RET papillary thyroid Dom yes 8 8p11.21 84376 hook homolog 3 E 0 SO:0001583 missense ENST00000307602.4 0 1 hg19 CCDS6139.1 . . . . . . . . . . G 14.28 2.487393 0.44249 . . ENSG00000168172 ENST00000307602 T 0.17370 2.28 5.7 5.7 0.88788 . 0.104415 0.64402 N 0.000006 T 0.06462 0.0166 N 0.02539 -0.55 0.40492 D 0.980557 B;B 0.18310 0.027;0.0 B;B 0.22880 0.042;0.003 T 0.40627 -0.9553 10 0.20046 T 0.44 -4.5861 7.4677 0.27330 0.1979:0.0:0.8021:0.0 . 138;138 Q2VJ45;Q86VS8 .;HOOK3_HUMAN T 138 ENSP00000305699:A138T ENSP00000305699:A138T A + 1 0 HOOK3 42924699 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.773000 0.68898 2.677000 0.91161 0.650000 0.86243 GCC TCGA-3E-AAAY-01A-11D-A38G-08 HOOK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383172.2 0 0 0 12 596 0 270 0 1.239606e-02 0 8 0 270 2 0 0 0 0 0 2 1 0.999032 12 586 0 268 2 0 0 0 0 270 2 -2.677842 1 1 0 0 1 0 0 0 1.968648 0 0.110000 1.860000 0.083797 0.350000 0.190000 0.570000 0.340000 0.369641 0.350000 0 0.260000 0.470000 ZFHX4 79776 broad.mit.edu 37 8 77767067 77767067 + Missense_Mutation SNP A A G TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr8:77767067A>G ENST00000521891.2 + 10 8358 c.7910A>G c.(7909-7911)cAt>cGt p.H2637R ZFHX4_ENST00000518282.1_Missense_Mutation_p.H2611R|ZFHX4_ENST00000050961.6_Missense_Mutation_p.H2592R|ZFHX4_ENST00000455469.2_Missense_Mutation_p.H2592R NM_024721.4 NP_078997.4 Q86UP3 ZFHX4_HUMAN zinc finger homeobox 4 432 BRCA - Breast invasive adenocarcinoma(89;0.0895) ATGCTTGATCATATTGCCCGC 0.507000 HNSCC(33;0.089) 0 SO:0001583 missense ENST00000521891.2 1 1 hg19 CCDS47878.2 . . . . . . . . . . A 8.874 0.950034 0.18431 . . ENSG00000091656 ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282 D;D;D;D 0.95788 -3.81;-3.81;-3.81;-3.81 5.32 5.32 0.75619 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.000000 0.47093 U 0.000258 D 0.89291 0.6673 N 0.01473 -0.845 0.80722 D 1 P;B;B 0.34412 0.453;0.399;0.259 B;B;B 0.42827 0.128;0.078;0.399 D 0.89968 0.4091 10 0.40728 T 0.16 . 15.4359 0.75146 1.0:0.0:0.0:0.0 . 2592;2592;2637 Q86UP3;Q86UP3-4;G3V138 ZFHX4_HUMAN;.;. R 2637;2621;2592;2592;2611 ENSP00000430497:H2637R;ENSP00000399605:H2592R;ENSP00000050961:H2592R;ENSP00000430848:H2611R ENSP00000050961:H2592R H + 2 0 ZFHX4 77929622 1.000000 0.71417 0.327000 0.25402 0.090000 0.18270 9.139000 0.94554 2.230000 0.72887 0.528000 0.53228 CAT TCGA-3E-AAAY-01A-11D-A38G-08 ZFHX4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000379197.2 1 0 0 11 188 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 0.998244 11 183 0 78 2 0 0 0 0 78 2 -14.594170 1 1 120810 1 31 1 1 2 3 2.037747 0 0.110000 1.860000 0.119683 0.990000 0.560000 1.000000 1.000000 0.925270 0.990000 1 0.790000 1.000000 TGFBR1 7046 broad.mit.edu 37 9 101891209 101891209 + Missense_Mutation SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr9:101891209C>T ENST00000374994.4 + 2 287 c.170C>T c.(169-171)tCt>tTt p.S57F TGFBR1_ENST00000552516.1_Missense_Mutation_p.S57F|TGFBR1_ENST00000374990.2_Missense_Mutation_p.S57F|TGFBR1_ENST00000550253.1_5'UTR NM_004612.2 NP_004603.1 P36897 TGFR1_HUMAN transforming growth factor, beta receptor 1 27 Acute lymphoblastic leukemia(62;0.0559) TGCTTTGTCTCTGTCACAGAG 0.408000 0 SO:0001583 missense ENST00000374994.4 1 1 hg19 CCDS6738.1 . . . . . . . . . . C 24.2 4.508992 0.85282 . . ENSG00000106799 ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000546096;ENST00000546584 D;D;D;D 0.98044 -4.68;-4.68;-4.68;-4.68 6.08 6.08 0.98989 TGF-beta receptor/activin receptor, type I/II (1); 0.334572 0.36002 N 0.002853 D 0.97012 0.9024 M 0.73430 2.235 0.80722 D 1 P;B 0.40794 0.729;0.057 B;B 0.41236 0.351;0.082 D 0.96884 0.9648 10 0.87932 D 0 . 14.3009 0.66352 0.1487:0.8513:0.0:0.0 . 57;57 P36897-3;P36897 .;TGFR1_HUMAN F 57;57;57;57;42;54 ENSP00000364133:S57F;ENSP00000364129:S57F;ENSP00000447297:S57F;ENSP00000447707:S54F ENSP00000364129:S57F S + 2 0 TGFBR1 100931030 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 5.297000 0.65704 2.894000 0.99253 0.591000 0.81541 TCT TCGA-3E-AAAY-01A-11D-A38G-08 TGFBR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053390.3 1 0 0 44 486 0 243 0 2.054057e-02 0 3 0 243 2 1 1 23 338 0 251 2 1 1.000000 43 476 0 242 2 0 0 0 0 243 2 -3.017764 1 1 0 0 1 0 1 1 1.916859 0 0.110000 1.860000 0.061478 0.990000 0.850000 1.000000 1.000000 0.979279 0.990000 1 0.940000 1.000000 C9orf24 84688 broad.mit.edu 37 9 34381395 34381395 + Silent SNP A A T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr9:34381395A>T ENST00000297623.2 - 4 642 c.444T>A c.(442-444)ccT>ccA p.P148P C9orf24_ENST00000379124.1_Silent_p.P13P|C9orf24_ENST00000379133.3_Silent_p.P13P|C9orf24_ENST00000379126.3_Silent_p.P13P|C9orf24_ENST00000379127.1_Silent_p.P13P|C9orf24_ENST00000481295.1_5'Flank NM_032596.3 NP_115985.2 Q8NCR6 SMRP1_HUMAN chromosome 9 open reading frame 24 5 LUSC - Lung squamous cell carcinoma(29;0.0107) CCGGCCTAGGAGGGCATTCCA 0.617000 0 SO:0001819 synonymous_variant ENST00000297623.2 1 1 hg19 CCDS6554.1 TCGA-3E-AAAY-01A-11D-A38G-08 C9orf24-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000001098.3 1 0 0 29 334 0 185 0 1.967078e-02 1 2 0 185 2 0 0 0 0 0 2 1 1.000000 28 328 0 181 2 0 0 0 0 185 2 -9.198959 1 1 0 0 1 0 1 1 1.916859 0 0.110000 1.860000 0.061478 0.980000 0.770000 1.000000 1.000000 0.958010 0.980000 1 0.890000 1.000000 TRPM3 80036 broad.mit.edu 37 9 73151305 73151305 + Missense_Mutation SNP G G A TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr9:73151305G>A ENST00000377110.3 - 25 4931 c.4688C>T c.(4687-4689)gCg>gTg p.A1563V TRPM3_ENST00000360823.2_Missense_Mutation_p.A1425V|TRPM3_ENST00000396285.1_Missense_Mutation_p.A1422V|TRPM3_ENST00000423814.3_Missense_Mutation_p.A1590V|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Missense_Mutation_p.A1435V|TRPM3_ENST00000377105.1_Missense_Mutation_p.A1422V|TRPM3_ENST00000358082.3_Missense_Mutation_p.A1425V|TRPM3_ENST00000408909.2_Missense_Mutation_p.A1422V|TRPM3_ENST00000396280.5_Missense_Mutation_p.A1412V|TRPM3_ENST00000377106.1_Missense_Mutation_p.A1435V|TRPM3_ENST00000357533.2_Missense_Mutation_p.A1567V Q9HCF6 TRPM3_HUMAN transient receptor potential cation channel, subfamily M, member 3 95 AGCTCTGTCCGCAATTGCTTG 0.493000 0 SO:0001583 missense ENST00000377110.3 0 1 hg19 CCDS43835.1 . . . . . . . . . . G 6.617 0.482296 0.12581 . . ENSG00000083067 ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814 T;T;T;T;T;T;T;T;T;T 0.56275 0.56;0.5;0.5;0.47;0.57;0.47;0.51;0.5;0.5;0.56 5.87 4.97 0.65823 . 0.180840 0.47093 D 0.000241 T 0.29158 0.0725 N 0.11560 0.145 0.19775 N 0.99995 B;B;B;B;B;B;B 0.06786 0.001;0.0;0.0;0.0;0.0;0.0;0.0 B;B;B;B;B;B;B 0.04013 0.001;0.001;0.0;0.0;0.001;0.001;0.0 T 0.10590 -1.0623 10 0.12766 T 0.61 -8.7036 10.1358 0.42706 0.0704:0.0:0.7916:0.138 . 1563;1553;1567;1425;1422;1535;1422 Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3 .;.;.;.;.;.;. V 1563;1435;1425;1422;1567;1422;1422;1435;1425;1590 ENSP00000366314:A1563V;ENSP00000366310:A1435V;ENSP00000354066:A1425V;ENSP00000366309:A1422V;ENSP00000350140:A1567V;ENSP00000386127:A1422V;ENSP00000379581:A1422V;ENSP00000379587:A1435V;ENSP00000350791:A1425V;ENSP00000389542:A1590V ENSP00000350140:A1567V A - 2 0 TRPM3 72341125 0.994000 0.37717 0.071000 0.20095 0.751000 0.42716 4.224000 0.58593 2.785000 0.95823 0.655000 0.94253 GCG TCGA-3E-AAAY-01A-11D-A38G-08 TRPM3-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214158.3 0 0 0 5 387 1 179 0 0 0 1 179 2 0 0 0 0 0 2 0 0.137011 5 378 1 178 10 0 0 0 1 179 2 -1.964215 0 1 121412 2 35 1 0 1 1 1.916859 0 0.110000 1.860000 0.061478 0.230000 0.080000 0.460000 0.210000 0.252366 0.230000 0 0.140000 0.350000 ZCCHC6 79670 broad.mit.edu 37 9 88938112 88938112 + Silent SNP G G A rs146207882 byFrequency TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chr9:88938112G>A ENST00000375963.3 - 13 2725 c.2553C>T c.(2551-2553)gaC>gaT p.D851D ZCCHC6_ENST00000375961.2_Silent_p.D851D|ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375960.2_Silent_p.D728D|ZCCHC6_ENST00000277141.6_Silent_p.D140D NM_001185059.1|NM_024617.3 NP_001171988.1|NP_078893.2 Q5VYS8 TUT7_HUMAN zinc finger, CCHC domain containing 6 46 cctcttcttcgtcgtcctcct 0.463000 0 SO:0001819 synonymous_variant ENST00000375963.3 1 0 hg19 CCDS35057.1 TCGA-3E-AAAY-01A-11D-A38G-08 ZCCHC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052918.1 1 0 0 13 221 0 117 1 2.242333e-01 4 11 0 117 2 0 0 0 0 0 2 1 0.850983 13 217 1 115 9 0 0 0 0 117 2 -3.298050 1 1 121404 163 54 1 0 1 1 1.916859 0 0.110000 1.860000 0.061478 0.840000 0.500000 1.000000 1.000000 0.825546 0.840000 0 0.660000 0.990000 KIF4A 24137 broad.mit.edu 37 X 69615826 69615826 + Missense_Mutation SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chrX:69615826C>T ENST00000374403.3 + 22 2498 c.2416C>T c.(2416-2418)Cgt>Tgt p.R806C KIF4A_ENST00000374388.3_Missense_Mutation_p.R806C|RNY4P23_ENST00000364507.1_RNA NM_012310.4 NP_036442.3 O95239 KIF4A_HUMAN kinesin family member 4A 51 TACTGAAGTGCGTGGTCAAGT 0.398000 0 SO:0001583 missense ENST00000374403.3 0 1 hg19 CCDS14401.1 1 6.027727546714888E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 6.236 0.411750 0.11812 . . ENSG00000090889 ENST00000374388;ENST00000374403;ENST00000544650 T;T 0.69806 -0.43;-0.37 4.78 3.92 0.45320 . 0.641178 0.13965 N 0.350586 T 0.35682 0.0940 N 0.02011 -0.69 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.20706 -1.0267 9 . . . . 7.9061 0.29763 0.0:0.886:0.0:0.114 . 806 O95239 KIF4A_HUMAN C 806;806;108 ENSP00000363509:R806C;ENSP00000363524:R806C . R + 1 0 KIF4A 69532551 0.999000 0.42202 0.001000 0.08648 0.223000 0.24884 3.801000 0.55545 1.133000 0.42147 0.594000 0.82650 CGT TCGA-3E-AAAY-01A-11D-A38G-08 KIF4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057068.1 0 0 0 5 120 0 45 0 8.401479e-02 0 10 0 45 2 0 0 0 0 0 2 1 0.936177 5 118 0 44 2 0 0 0 0 45 2 -2.998761 1 1 121410 2 30 1 0 1 1 0.110000 1.860000 0.110000 0.370000 0.140000 0.720000 0.340000 0.400970 0.370000 0 0.240000 0.550000 SRPX2 27286 broad.mit.edu 37 X 99925874 99925874 + Missense_Mutation SNP C C T TCGA-3E-AAAY-01A-11D-A38G-08 TCGA-3E-AAAY-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx e732348f-c0aa-41bb-b465-09607386d190 6eadfab7-891c-443f-bf86-e072cb8338d3 g.chrX:99925874C>T ENST00000373004.3 + 11 1716 c.1288C>T c.(1288-1290)Cgc>Tgc p.R430C RP11-524D16__A.3_ENST00000568809.1_RNA NM_014467.2 NP_055282.1 O60687 SRPX2_HUMAN sushi-repeat containing protein, X-linked 2 19 TGACCGAGACCGCTACATGGA 0.512000 OREG0019890 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000373004.3 1 1 hg19 CCDS14471.1 . . . . . . . . . . C 25.0 4.590739 0.86851 . . ENSG00000102359 ENST00000373004 T 0.54071 0.59 5.09 5.09 0.68999 . 0.000000 0.85682 D 0.000000 T 0.74419 0.3714 M 0.81497 2.545 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.76756 -0.2842 9 . . . -14.007 17.6638 0.88198 0.0:1.0:0.0:0.0 . 430 O60687 SRPX2_HUMAN C 430 ENSP00000362095:R430C . R + 1 0 SRPX2 99812530 1.000000 0.71417 1.000000 0.80357 0.792000 0.44763 5.063000 0.64332 2.357000 0.79964 0.523000 0.50628 CGC TCGA-3E-AAAY-01A-11D-A38G-08 SRPX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057486.1 1 0 1 24 143 0 75 1 9.999907e-01 12 106 0 75 2 0 0 0 0 0 2 1 1.000000 24 141 0 75 2 0 0 0 0 75 2 -2.895261 1 1 0 0 1 0 1 1 0.110000 1.860000 0.110000 0.920000 0.710000 1.000000 0.990000 0.910525 0.920000 1 0.820000 0.980000