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 TGFBR2 7048 broad.mit.edu 37 3 30713755 30713758 + Frame_Shift_Del DEL CCTC CCTC - TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 CCTC - CCTC CCTC Valid Somatic Phase_I WXS targeted Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr3:30713755_30713758delCCTC ENST00000295754.5 + 4 1462_1465 c.1080_1083delCCTC c.(1078-1083)cacctcfs p.HL360fs TGFBR2_ENST00000359013.4_Frame_Shift_Del_p.HL385fs NM_003242.5 NP_003233.4 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II (70/80kDa) 53 GGATTGCTCACCTCCACAGTGATC 0.608000 0 SO:0001589 frameshift_variant ENST00000295754.5 1 1 hg19 CCDS2648.1 TCGA-2L-AAQL-01A-11D-A38G-08 TGFBR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252994.2 1 0 0 84 539 1 224 0 5.086617e-02 0 3 1 224 2 1 1 135 554 0 336 2 1 1.000000 103 543 2 218 16 0 0 0 0 0 0 -3.318799 1 1 0 0 1 0 1 1 1.703696 1 0.380000 1.790000 0.234568 0.560000 4.600000e-01 0.690000 0.570000 0.576759 0.560000 0 0.510000 0.630000 FLNC 2318 broad.mit.edu 37 7 128495281 128495282 + Frame_Shift_Ins INS - - A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:128495281_128495282insA ENST00000325888.8 + 43 7425_7426 c.7164_7165insA c.(7165-7167)gatfs p.D2389fs RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Frame_Shift_Ins_p.D2356fs NM_001458.4 NP_001449.3 Q14315 FLNC_HUMAN filamin C, gamma 128 TCAAGTTCAATGATGAGCACAT 0.624000 0 SO:0001589 frameshift_variant ENST00000325888.8 0 1 hg19 CCDS43644.1 TCGA-2L-AAQL-01A-11D-A38G-08 FLNC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059948.3 1 0 0 59 572 0 196 0 2.442070e-01 0 10 0 196 2 0 0 0 0 1 1.000000 62 561 0 194 2 0 0 0 0 0 0 -16.845870 1 1 0 0 1 1 2 3 2.121637 0 0.380000 1.790000 0.386988 0.490000 3.800000e-01 1.000000 0.500000 0.526627 0.490000 0 0.430000 0.580000 KNDC1 85442 broad.mit.edu 37 10 135009218 135009218 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr10:135009218G>A ENST00000304613.3 + 10 1648 c.1627G>A c.(1627-1629)Gtc>Atc p.V543I KNDC1_ENST00000368572.2_Missense_Mutation_p.V543I|KNDC1_ENST00000368571.2_Missense_Mutation_p.V478I Q76NI1 VKIND_HUMAN kinase non-catalytic C-lobe domain (KIND) containing 1 60 all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203) CAAGTTCAGCGTCCCCCGCAA 0.687000 0 SO:0001583 missense ENST00000304613.3 1 1 hg19 CCDS7674.1 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 G 1.067 -0.671207 0.03403 2.27E-4 3.49E-4 ENSG00000171798 ENST00000304613;ENST00000368572;ENST00000368571 T;T;T 0.32272 1.46;1.46;1.46 4.63 -5.31 0.02730 KIND (2); 0.976965 0.08346 N 0.960109 T 0.13415 0.0325 N 0.15975 0.35 0.09310 N 1 B;B 0.17465 0.022;0.005 B;B 0.09377 0.004;0.002 T 0.28138 -1.0053 10 0.27082 T 0.32 -20.5636 5.616 0.17432 0.5361:0.0:0.2633:0.2006 . 478;543 Q76NI1-2;Q76NI1 .;VKIND_HUMAN I 543;543;478 ENSP00000304437:V543I;ENSP00000357561:V543I;ENSP00000357560:V478I ENSP00000304437:V543I V + 1 0 KNDC1 134859208 0.000000 0.05858 0.002000 0.10522 0.026000 0.11368 -0.398000 0.07259 -0.658000 0.05366 -0.692000 0.03713 GTC TCGA-2L-AAQL-01A-11D-A38G-08 KNDC1-006 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000277044.3 1 0 1 26 90 0 42 0 0 0 1 0 42 2 0 0 0 0 0 2 1 1.000000 26 90 0 42 2 0 0 0 0 42 2 -20.000000 1 1 121322 7 40 1 1 2 3 2.117198 0 0.380000 1.790000 0.385835 0.990000 8.200000e-01 1.000000 1.000000 0.985433 0.990000 1 0.990000 1.000000 CUBN 8029 broad.mit.edu 37 10 17169885 17169885 + Silent SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr10:17169885C>A ENST00000377833.4 - 3 356 c.291G>T c.(289-291)ggG>ggT p.G97G CUBN_ENST00000377823.1_Silent_p.G97G NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CAATTGCACTCCCTTTTAACT 0.323000 0 SO:0001819 synonymous_variant ENST00000377833.4 1 1 hg19 CCDS7113.1 TCGA-2L-AAQL-01A-11D-A38G-08 CUBN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047009.1 1 0 1 101 589 0 212 0 0 0 0 212 2 0 0 0 0 0 2 1 1.000000 99 577 0 208 2 0 0 0 0 212 2 -20.000000 1 1 0 0 1 1 2 3 2.117198 0 0.380000 1.790000 0.385835 0.770000 6.400000e-01 1.000000 0.780000 0.789605 0.770000 0 0.700000 0.860000 TLL2 7093 broad.mit.edu 37 10 98157035 98157035 + Missense_Mutation SNP G G A rs142713663 byFrequency TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr10:98157035G>A ENST00000357947.3 - 11 1517 c.1292C>T c.(1291-1293)cCg>cTg p.P431L TLL2_ENST00000469598.1_5'UTR NM_012465.3 NP_036597.1 Q9Y6L7 TLL2_HUMAN tolloid-like 2 58 Colorectal(252;0.0846) GAGGGGCTCCGGGATCTTATC 0.577000 0 SO:0001583 missense ENST00000357947.3 1 1 hg19 CCDS7449.1 . . . . . . . . . . G 19.66 3.868544 0.72065 0.0 0.001047 ENSG00000095587 ENST00000357947 T 0.39406 1.08 5.11 5.11 0.69529 CUB (5); 0.000000 0.45361 D 0.000368 T 0.72590 0.3479 M 0.92268 3.29 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.76716 -0.2857 10 0.40728 T 0.16 . 17.7077 0.88313 0.0:0.0:1.0:0.0 . 431 Q9Y6L7 TLL2_HUMAN L 431 ENSP00000350630:P431L ENSP00000350630:P431L P - 2 0 TLL2 98147025 1.000000 0.71417 0.486000 0.27416 0.177000 0.22998 9.464000 0.97655 2.654000 0.90174 0.650000 0.86243 CCG TCGA-2L-AAQL-01A-11D-A38G-08 TLL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049608.1 0 0 1 20 166 0 65 0 0 1 0 0 65 2 0 0 0 0 0 2 1 0.999996 20 163 0 65 2 0 0 0 0 65 2 -3.075081 1 1 121412 77 49 1 1 2 3 2.117198 0 0.380000 1.790000 0.385835 0.580000 3.600000e-01 1.000000 0.570000 0.603999 0.580000 0 0.460000 0.730000 NCAM1 4684 broad.mit.edu 37 11 113078701 113078701 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr11:113078701C>T ENST00000533760.1 + 7 1138 c.539C>T c.(538-540)gCg>gTg p.A180V NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.A297V|NCAM1_ENST00000316851.7_Missense_Mutation_p.A288V NM_001242608.1 NP_001229537.1 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 49 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) GAGCAGGATGCGACCATCCAC 0.537000 0 SO:0001583 missense ENST00000533760.1 1 1 hg19 . . . . . . . . . . C 21.1 4.105555 0.77096 . . ENSG00000149294 ENST00000531044;ENST00000401611;ENST00000316851 T;T 0.69040 -0.37;-0.37 5.71 4.75 0.60458 Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.205034 0.50627 D 0.000106 T 0.72293 0.3442 . . . 0.80722 D 1 D;D;D;D;D 0.76494 0.999;0.999;0.999;0.999;0.97 P;P;P;P;B 0.51657 0.612;0.612;0.609;0.676;0.329 T 0.75260 -0.3380 9 0.56958 D 0.05 -40.4986 15.5067 0.75745 0.1389:0.8611:0.0:0.0 . 298;298;298;298;298 P13591-5;P13591-1;P13591;P13591-3;P13591-6 .;.;NCAM1_HUMAN;.;. V 180;297;288 ENSP00000384055:A297V;ENSP00000318472:A288V ENSP00000318472:A288V A + 2 0 NCAM1 112583911 0.996000 0.38824 0.946000 0.38457 0.966000 0.64601 4.470000 0.60175 2.710000 0.92621 0.655000 0.94253 GCG TCGA-2L-AAQL-01A-11D-A38G-08 NCAM1-003 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000394068.2 0 0 0 4 60 0 22 0 0 0 1 0 22 2 0 0 0 0 0 2 1 0.892544 4 60 0 21 2 0 0 0 0 22 2 -8.011300 1 1 0 0 1 0 1 1 1.900546 0 0.380000 1.790000 0.324839 0.320000 1.100000e-01 0.670000 0.290000 0.354389 0.320000 0 0.200000 0.500000 OR4D5 219875 broad.mit.edu 37 11 123810974 123810974 + Silent SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr11:123810974G>A ENST00000307033.2 + 1 725 c.651G>A c.(649-651)tcG>tcA p.S217S NM_001001965.1 NP_001001965.1 Q8NGN0 OR4D5_HUMAN olfactory receptor, family 4, subfamily D, member 5 41 Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22) TTCTGGGATCGTACACAGCAC 0.512000 0 SO:0001819 synonymous_variant ENST00000307033.2 0 1 hg19 CCDS31699.1 TCGA-2L-AAQL-01A-11D-A38G-08 OR4D5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387263.1 0 0 0 8 814 0 324 0 0 0 0 324 2 0 0 0 0 0 2 1 0.988035 8 791 0 321 2 0 0 0 0 324 2 -2.142773 0 1 121412 6 41 1 0 1 1 1.900546 0 0.380000 1.790000 0.324839 0.040000 1.000000e-02 0.090000 0.050000 0.052671 0.040000 0 0.020000 0.070000 OPCML 4978 broad.mit.edu 37 11 132307148 132307148 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr11:132307148G>A ENST00000331898.7 - 4 1210 c.632C>T c.(631-633)cCc>cTc p.P211L OPCML_ENST00000524381.1_Missense_Mutation_p.P204L|OPCML_ENST00000541867.1_Missense_Mutation_p.P211L|OPCML_ENST00000374778.4_Missense_Mutation_p.P170L|OPCML_ENST00000529038.1_5'UTR NM_002545.3 NP_002536.1 Q14982 OPCM_HUMAN opioid binding protein/cell adhesion molecule-like 47 all_hematologic(175;0.019) all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129) CCGCACATCGGGCGCAGCGAC 0.542000 0 SO:0001583 missense ENST00000331898.7 1 1 hg19 CCDS8492.1 . . . . . . . . . . G 19.43 3.825927 0.71143 . . ENSG00000183715 ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867 T;T;T;T 0.59224 0.29;0.28;1.19;1.19 5.95 5.95 0.96441 Immunoglobulin-like (1); 0.000000 0.85682 D 0.000000 T 0.77980 0.4212 M 0.75085 2.285 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;0.999;1.0 D;D;D;D 0.85130 0.997;0.997;0.995;0.997 T 0.78640 -0.2125 10 0.87932 D 0 -13.4278 19.9958 0.97383 0.0:0.0:1.0:0.0 . 211;204;210;211 B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982 .;.;.;OPCM_HUMAN L 211;204;170;178;211 ENSP00000330862:P211L;ENSP00000434750:P204L;ENSP00000363910:P170L;ENSP00000445496:P211L ENSP00000330862:P211L P - 2 0 OPCML 131812358 1.000000 0.71417 0.320000 0.25306 0.040000 0.13550 9.476000 0.97823 2.825000 0.97269 0.655000 0.94253 CCC TCGA-2L-AAQL-01A-11D-A38G-08 OPCML-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374689.3 1 0 1 40 295 0 129 0 0 0 0 129 2 0 0 0 0 0 2 1 1.000000 40 287 0 127 2 0 0 0 0 129 2 -3.221909 1 1 0 0 1 0 1 1 1.900546 0 0.380000 1.790000 0.324839 0.570000 4.200000e-01 0.750000 0.570000 0.584373 0.570000 0 0.490000 0.670000 FAT3 120114 broad.mit.edu 37 11 92532543 92532543 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr11:92532543G>A ENST00000298047.6 + 9 6381 c.6364G>A c.(6364-6366)Gtc>Atc p.V2122I FAT3_ENST00000525166.1_Missense_Mutation_p.V1972I|FAT3_ENST00000409404.2_Missense_Mutation_p.V2122I Q8TDW7 FAT3_HUMAN FAT atypical cadherin 3 p.V2122L(2) 85 Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858) AGTGACCTATGTCCTGCAGGA 0.423000 TCGA Ovarian(4;0.039) 2 Substitution - Missense(2) SO:0001583 missense ENST00000298047.6 1 1 hg19 . . . . . . . . . . G 6.771 0.511125 0.12883 . . ENSG00000165323 ENST00000298047;ENST00000409404;ENST00000525166 T;T;T 0.01767 4.65;4.65;4.65 5.9 0.248 0.15526 . . . . . T 0.00936 0.0031 N 0.12853 0.265 0.80722 D 1 B 0.02656 0.0 B 0.04013 0.001 T 0.53464 -0.8435 9 0.23302 T 0.38 . 0.7489 0.00987 0.2335:0.2878:0.2715:0.2072 . 2122 Q8TDW7-3 . I 2122;2122;1972 ENSP00000298047:V2122I;ENSP00000387040:V2122I;ENSP00000432586:V1972I ENSP00000298047:V2122I V + 1 0 FAT3 92172191 0.011000 0.17503 0.983000 0.44433 0.964000 0.63967 0.949000 0.29109 0.412000 0.25729 -0.136000 0.14681 GTC TCGA-2L-AAQL-01A-11D-A38G-08 FAT3-201 KNOWN basic protein_coding protein_coding 1 0 1 23 108 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 1.000000 23 106 0 42 2 0 0 0 0 42 2 -20.000000 1 1 0 0 1 0 1 1 1.900546 0 0.380000 1.790000 0.324839 0.840000 5.600000e-01 1.000000 1.000000 0.840859 0.840000 0 0.690000 1.000000 KRAS 3845 broad.mit.edu 37 12 25380276 25380276 + Missense_Mutation SNP T T C rs121913240 TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 T C T T Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr12:25380276T>C ENST00000256078.4 - 3 245 c.182A>G c.(181-183)cAa>cGa p.Q61R KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.Q61L(73)|p.Q61R(56)|p.Q61P(12) 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) GTACTCCTCTTGACCTGCTGT 0.418000 Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_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 141 Substitution - Missense(141) 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 . . . . . . . . . . T 20.6 4.022613 0.75275 . . ENSG00000133703 ENST00000311936;ENST00000256078 D;D 0.83673 -1.75;-1.75 5.77 5.77 0.91146 Small GTP-binding protein domain (1); 0.049057 0.85682 D 0.000000 D 0.88358 0.6415 M 0.92367 3.3 0.80722 D 1 B;B 0.26744 0.158;0.026 B;B 0.32805 0.135;0.153 D 0.87885 0.2680 10 0.66056 D 0.02 . 15.5753 0.76373 0.0:0.0:0.0:1.0 . 61;61 P01116-2;P01116 .;RASK_HUMAN R 61 ENSP00000308495:Q61R;ENSP00000256078:Q61R ENSP00000256078:Q61R Q - 2 0 KRAS 25271543 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.983000 0.88140 2.326000 0.78906 0.533000 0.62120 CAA TCGA-2L-AAQL-01A-11D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 68 298 0 102 0 6.358014e-01 1 10 0 102 2 1 1 107 675 0 451 2 1 1.000000 66 293 0 102 2 1 1 1264 6758 0 102 2 -20.000000 1 1 0 0 1 0 0 0 2.018804 0 0.380000 1.790000 0.358045 0.930000 7.400000e-01 1.000000 1.000000 0.927625 0.930000 1 0.840000 1.000000 AHNAK2 113146 broad.mit.edu 37 14 105413912 105413912 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr14:105413912C>T ENST00000333244.5 - 7 7995 c.7876G>A c.(7876-7878)Gat>Aat p.D2626N AHNAK2_ENST00000557457.1_Intron NM_138420.2 NP_612429.2 Q8IVF2 AHNK2_HUMAN AHNAK nucleoprotein 2 33 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116) CGCGCACCATCCAGCTTTGCT 0.592000 0 SO:0001583 missense ENST00000333244.5 0 1 hg19 CCDS45177.1 . . . . . . . . . . c 13.05 2.120665 0.37436 . . ENSG00000185567 ENST00000333244 T 0.01629 4.72 2.6 2.6 0.31112 . . . . . T 0.02156 0.0067 M 0.70903 2.155 0.09310 N 1 P 0.40834 0.73 B 0.34385 0.181 T 0.42582 -0.9443 9 0.21540 T 0.41 . 4.3944 0.11356 0.0:0.7139:0.0:0.2861 . 2626 Q8IVF2 AHNK2_HUMAN N 2626 ENSP00000353114:D2626N ENSP00000353114:D2626N D - 1 0 AHNAK2 104484957 0.000000 0.05858 0.005000 0.12908 0.015000 0.08874 -0.581000 0.05820 1.000000 0.39049 0.306000 0.20318 GAT TCGA-2L-AAQL-01A-11D-A38G-08 AHNAK2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000410300.1 0 0 0 9 1282 0 583 0 0 0 0 583 2 0 0 0 0 0 2 1 0.992519 9 1211 0 582 2 0 0 0 0 583 2 -2.875356 1 1 0 0 1 0 1 1 1.727848 1 0.380000 1.790000 0.241683 0.020000 0 0.060000 0.030000 0.033207 0.020000 0 0.010000 0.040000 TEP1 7011 broad.mit.edu 37 14 20869179 20869179 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr14:20869179G>A ENST00000262715.5 - 9 1553 c.1513C>T c.(1513-1515)Cgg>Tgg p.R505W TEP1_ENST00000556935.1_Missense_Mutation_p.R397W NM_007110.4 NP_009041.2 Q99973 TEP1_HUMAN telomerase-associated protein 1 96 all_cancers(95;0.00123) all_lung(585;0.235) Epithelial(56;7.42e-08)|all cancers(55;6.46e-07) TTGTTCCCCCGTAGGCTCAGC 0.542000 0 SO:0001583 missense ENST00000262715.5 0 1 hg19 CCDS9548.1 . . . . . . . . . . G 15.53 2.860278 0.51482 . . ENSG00000129566 ENST00000262715;ENST00000359243;ENST00000556935 T;T 0.15718 2.4;2.4 5.71 2.77 0.32553 TROVE (2); 0.542528 0.20377 N 0.093526 T 0.17789 0.0427 M 0.64997 1.995 0.20307 N 0.999916 B;B 0.22346 0.022;0.068 B;B 0.17722 0.008;0.019 T 0.18335 -1.0340 10 0.87932 D 0 -9.617 8.5605 0.33507 0.0721:0.0:0.4738:0.4541 . 397;505 G3V5X7;Q99973 .;TEP1_HUMAN W 505;505;397 ENSP00000262715:R505W;ENSP00000452574:R397W ENSP00000262715:R505W R - 1 2 TEP1 19939019 0.002000 0.14202 0.333000 0.25482 0.410000 0.31052 0.233000 0.17911 0.752000 0.32923 0.555000 0.69702 CGG TCGA-2L-AAQL-01A-11D-A38G-08 TEP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000073563.2 0 0 0 4 303 0 97 0 0 0 1 0 97 2 0 0 0 0 0 2 1 0.886320 4 297 0 96 2 0 0 0 0 97 2 -2.721050 1 1 121412 4 35 1 1 2 3 2.137626 0 0.380000 1.790000 0.389283 0.070000 2.000000e-02 1.000000 0.070000 0.144784 0.070000 0 0.040000 0.140000 CHD8 57680 broad.mit.edu 37 14 21875121 21875121 + Missense_Mutation SNP C C G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr14:21875121C>G ENST00000557364.1 - 14 3064 c.2801G>C c.(2800-2802)tGt>tCt p.C934S CHD8_ENST00000430710.3_Missense_Mutation_p.C655S|CHD8_ENST00000399982.2_Missense_Mutation_p.C934S|CHD8_ENST00000555962.1_Intron Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 85 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) AAGCTCAGGACAATCTGACAA 0.438000 0 SO:0001583 missense ENST00000557364.1 1 1 hg19 CCDS53885.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 24.5|24.5 4.542986|4.542986 0.86022|0.86022 .|. .|. ENSG00000100888|ENSG00000100888 ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935 D;D;D|. 0.93019|. -3.15;-3.15;-3.15|. 5.41|5.41 5.41|5.41 0.78517|0.78517 DEAD-like helicase (2);SNF2-related (1);|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.34193|0.34193 0.0889|0.0889 N|N 0.02334|0.02334 -0.595|-0.595 0.80722|0.80722 D|D 1|1 B;P|. 0.36633|. 0.236;0.562|. B;B|. 0.43950|. 0.345;0.437|. T|T 0.30357|0.30357 -0.9981|-0.9981 10|5 0.27785|. T|. 0.31|. -17.6138|-17.6138 18.1343|18.1343 0.89612|0.89612 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 934;655|. Q9HCK8;Q9HCK8-2|. CHD8_HUMAN;.|. S|F 655;934;654;934|159 ENSP00000406288:C655S;ENSP00000382863:C934S;ENSP00000451601:C934S|. ENSP00000262707:C654S|. C|L -|- 2|3 0|2 CHD8|CHD8 20944961|20944961 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.995000|0.995000 0.86356|0.86356 5.932000|5.932000 0.70121|0.70121 2.816000|2.816000 0.96949|0.96949 0.561000|0.561000 0.74099|0.74099 TGT|TTG TCGA-2L-AAQL-01A-11D-A38G-08 CHD8-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000410436.1 1 0 1 16 82 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999952 16 80 0 32 2 0 0 0 0 32 2 -20.000000 1 1 0 0 1 1 2 3 2.137626 0 0.380000 1.790000 0.389283 0.890000 5.400000e-01 1.000000 1.000000 0.864814 0.890000 1 0.700000 1.000000 SYNE2 23224 broad.mit.edu 37 14 64468799 64468799 + Splice_Site SNP G G C TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr14:64468799G>C ENST00000344113.4 + 29 3998 c.3786G>C c.(3784-3786)agG>agC p.R1262S SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Splice_Site_p.R1262S|SYNE2_ENST00000554584.1_Splice_Site_p.R1262S NM_015180.4 NP_055995.4 Q8WXH0 SYNE2_HUMAN spectrin repeat containing, nuclear envelope 2 224 AACACCTAAGGGTAAGTATAT 0.368000 0 SO:0001630 splice_region_variant ENST00000344113.4 1 0 hg19 CCDS41963.1 . . . . . . . . . . G 12.13 1.844143 0.32606 . . ENSG00000054654 ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678 T;T;T 0.59224 0.66;0.66;0.28 5.41 5.41 0.78517 . 0.323796 0.26446 N 0.024340 T 0.48732 0.1516 L 0.47716 1.5 0.80722 D 1 P;P 0.38504 0.501;0.634 B;B 0.28011 0.039;0.085 T 0.51450 -0.8704 10 0.39692 T 0.17 . 17.3435 0.87304 0.0:0.0:1.0:0.0 . 1262;1262 Q8WXH0;Q8WXH0-2 SYNE2_HUMAN;. S 1262 ENSP00000350719:R1262S;ENSP00000341781:R1262S;ENSP00000452570:R1262S ENSP00000261678:R1262S R + 3 2 SYNE2 63538552 1.000000 0.71417 0.941000 0.38009 0.045000 0.14185 5.812000 0.69194 2.709000 0.92574 0.655000 0.94253 AGG TCGA-2L-AAQL-01A-11D-A38G-08 SYNE2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276994.2 1 0 1 80 317 0 168 0 0 0 0 168 2 0 0 0 0 0 2 1 1.000000 78 312 0 166 2 0 0 0 0 168 2 -3.267440 1 1 0 0 1 0 1 1 1.727848 1 0.380000 1.790000 0.241683 0.850000 6.900000e-01 1.000000 0.860000 0.860600 0.850000 1 0.770000 0.940000 SPESP1 246777 broad.mit.edu 37 15 69238112 69238112 + Missense_Mutation SNP A A G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr15:69238112A>G ENST00000310673.3 + 2 393 c.239A>G c.(238-240)cAt>cGt p.H80R SPESP1_ENST00000560188.1_3'UTR|NOX5_ENST00000260364.5_Intron|NOX5_ENST00000448182.3_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000455873.3_Intron NM_145658.3 NP_663633.1 Q6UW49 SPESP_HUMAN sperm equatorial segment protein 1 19 CTAGTTACACATGGAGACGCT 0.403000 0 SO:0001583 missense ENST00000310673.3 0 1 hg19 CCDS10230.1 . . . . . . . . . . A 1.739 -0.492198 0.04322 . . ENSG00000258484 ENST00000310673 T 0.20738 2.05 4.62 -1.08 0.09936 . 0.742875 0.11558 N 0.552026 T 0.14614 0.0353 L 0.32530 0.975 0.09310 N 1 B 0.32160 0.358 B 0.33521 0.165 T 0.25779 -1.0122 10 0.41790 T 0.15 -0.9374 7.6284 0.28226 0.3289:0.5445:0.0:0.1265 . 80 Q6UW49 SPESP_HUMAN R 80 ENSP00000312284:H80R ENSP00000312284:H80R H + 2 0 SPESP1 67025166 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 0.104000 0.15313 -0.050000 0.13356 -0.313000 0.08912 CAT TCGA-2L-AAQL-01A-11D-A38G-08 SPESP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257125.1 0 0 0 9 415 0 141 0 8.415348e-03 0 6 0 141 2 0 0 0 0 0 2 1 0.994077 9 411 0 139 2 0 0 0 0 141 2 -3.404401 1 1 0 0 1 0 2 2 2.115839 1 0.380000 1.790000 0.380000 0.110000 5.000000e-02 0.200000 0.110000 0.123056 0.110000 0 0.070000 0.160000 AKAP13 11214 broad.mit.edu 37 15 86124353 86124353 + Silent SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr15:86124353G>A ENST00000394518.2 + 7 3149 c.3054G>A c.(3052-3054)gtG>gtA p.V1018V AKAP13_ENST00000361243.2_Silent_p.V1018V|RP11-815J21.2_ENST00000561409.1_RNA NM_001270546.1|NM_007200.4 NP_001257475.1|NP_009131.2 Q12802 AKP13_HUMAN A kinase (PRKA) anchor protein 13 98 AGAGCCTGGTGCCACCAGGAG 0.572000 Melanoma(94;603 1453 3280 32295 32951) 0 SO:0001819 synonymous_variant ENST00000394518.2 0 1 hg19 CCDS32319.1 TCGA-2L-AAQL-01A-11D-A38G-08 AKAP13-004 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000417318.1 0 0 0 5 298 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 0.932972 5 289 0 119 2 0 0 0 0 121 2 -5.980025 1 1 0 0 1 0 2 2 2.102882 1 0.380000 1.790000 0.380000 0.090000 3.000000e-02 0.190000 0.080000 0.102966 0.090000 0 0.050000 0.140000 IGFALS 3483 broad.mit.edu 37 16 1843655 1843655 + Translation_Start_Site SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr16:1843655C>A ENST00000215539.3 - 0 109 IGFALS_ENST00000568221.1_Intron|IGFALS_ENST00000415638.3_De_novo_Start_InFrame P35858 ALS_HUMAN insulin-like growth factor binding protein, acid labile subunit 8 CAGGGCCATCCTGCATGCAGG 0.716000 0 ENST00000215539.3 0 1 hg19 CCDS10446.1 TCGA-2L-AAQL-01A-11D-A38G-08 IGFALS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250509.2 0 0 0 7 32 0 10 0 4.181185e-02 1 1 0 10 2 0 0 0 0 0 2 1 0.982476 7 31 0 10 2 0 0 0 0 10 2 -15.078530 1 1 0 0 1 1 2 3 2.123545 0 0.380000 1.790000 0.386988 0.980000 4.600000e-01 1.000000 1.000000 0.880501 0.980000 1 0.690000 1.000000 TMC5 79838 broad.mit.edu 37 16 19488791 19488791 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr16:19488791G>A ENST00000396229.2 + 13 2869 c.2120G>A c.(2119-2121)gGc>gAc p.G707D TMC5_ENST00000381414.4_Missense_Mutation_p.G707D|TMC5_ENST00000542583.2_Missense_Mutation_p.G707D|TMC5_ENST00000561503.1_Missense_Mutation_p.G348D|TMC5_ENST00000219821.5_Missense_Mutation_p.G461D|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000541464.1_Missense_Mutation_p.G655D|TMC5_ENST00000564959.1_Missense_Mutation_p.G390D NM_001105248.1 NP_001098718.1 Q6UXY8 TMC5_HUMAN transmembrane channel-like 5 31 TCAATCATTGGCATTCTTTGT 0.383000 0 SO:0001583 missense ENST00000396229.2 1 1 hg19 CCDS45431.1 . . . . . . . . . . G 18.05 3.537353 0.65085 . . ENSG00000103534 ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743 T;T;T;T;T 0.69561 -0.41;-0.03;-0.03;-0.03;-0.03 4.33 4.33 0.51752 . 0.193755 0.43579 D 0.000559 T 0.81781 0.4895 M 0.81802 2.56 0.51233 D 0.99991 D;D;D;D;D;D 0.89917 1.0;0.996;0.999;0.998;0.999;1.0 D;D;D;D;D;D 0.81914 0.992;0.954;0.982;0.94;0.981;0.995 T 0.82625 -0.0365 10 0.38643 T 0.18 -14.3434 16.7528 0.85490 0.0:0.0:1.0:0.0 . 655;390;461;461;707;707 F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2 .;.;.;.;TMC5_HUMAN;. D 655;707;707;707;461;390 ENSP00000441227:G655D;ENSP00000370822:G707D;ENSP00000379531:G707D;ENSP00000446274:G707D;ENSP00000219821:G461D ENSP00000219821:G461D G + 2 0 TMC5 19396292 1.000000 0.71417 0.998000 0.56505 0.422000 0.31414 7.615000 0.83006 2.112000 0.64535 0.655000 0.94253 GGC TCGA-2L-AAQL-01A-11D-A38G-08 TMC5-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000435888.1 1 0 1 111 495 0 223 1 9.929468e-01 11 25 0 223 2 0 0 0 0 0 2 1 1.000000 108 482 0 222 2 0 0 0 0 223 2 -20.000000 1 1 0 0 1 1 2 3 2.123545 0 0.380000 1.790000 0.386988 0.970000 8.100000e-01 1.000000 1.000000 0.956426 0.970000 1 0.890000 1.000000 ADCY9 115 broad.mit.edu 37 16 4164208 4164208 + Silent SNP G G A rs73492586 byFrequency TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr16:4164208G>A ENST00000294016.3 - 2 1774 c.1236C>T c.(1234-1236)gcC>gcT p.A412A NM_001116.3 NP_001107.2 O60503 ADCY9_HUMAN adenylate cyclase 9 47 CCAGGGCGTGGGCAGACTTGT 0.512000 0 SO:0001819 synonymous_variant ENST00000294016.3 1 0 hg19 CCDS32382.1 TCGA-2L-AAQL-01A-11D-A38G-08 ADCY9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438076.1 1 0 1 68 278 0 104 0 0 0 1 0 104 2 0 0 0 0 0 2 1 1.000000 66 268 0 102 2 0 0 0 0 104 2 -2.705214 1 1 121408 217 55 1 1 2 3 2.123545 0 0.380000 1.790000 0.386988 0.990000 8.300000e-01 1.000000 1.000000 0.977301 0.990000 1 0.930000 1.000000 FOXF1 2294 broad.mit.edu 37 16 86544569 86544569 + Missense_Mutation SNP T T C TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr16:86544569T>C ENST00000262426.4 + 1 437 c.394T>C c.(394-396)Ttc>Ctc p.F132L FENDRR_ENST00000595886.1_lincRNA NM_001451.2 NP_001442.2 Q12946 FOXF1_HUMAN forkhead box F1 12 CGAGTTCATGTTCGAGGAGGG 0.632000 0 SO:0001583 missense ENST00000262426.4 1 1 hg19 CCDS10957.2 . . . . . . . . . . T 28.1 4.887395 0.91814 . . ENSG00000103241 ENST00000262426 T 0.36340 1.26 4.51 4.51 0.55191 Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3); 0.000000 0.85682 D 0.000000 T 0.49915 0.1585 L 0.45285 1.41 0.80722 D 1 D 0.55605 0.972 D 0.66716 0.946 T 0.52563 -0.8559 10 0.87932 D 0 . 12.9875 0.58599 0.0:0.0:0.0:1.0 . 132 Q12946 FOXF1_HUMAN L 132 ENSP00000262426:F132L ENSP00000262426:F132L F + 1 0 FOXF1 85102070 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.653000 0.83643 1.668000 0.50843 0.528000 0.53228 TTC TCGA-2L-AAQL-01A-11D-A38G-08 FOXF1-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000269103.2 1 0 0 141 450 0 287 0 0 0 1 0 287 2 0 0 0 0 0 2 1 1.000000 140 433 0 281 2 0 0 0 0 287 2 -20.000000 1 1 0 0 1 0 1 1 1.734762 1 0.380000 1.790000 0.241683 0.980000 8.600000e-01 1.000000 1.000000 0.968899 0.980000 1 0.920000 1.000000 ANKRD11 29123 broad.mit.edu 37 16 89350085 89350085 + Silent SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr16:89350085C>A ENST00000301030.4 - 9 3325 c.2865G>T c.(2863-2865)ctG>ctT p.L955L ANKRD11_ENST00000378330.2_Silent_p.L955L NM_001256183.1|NM_013275.5 NP_001243112.1|NP_037407.4 Q6UB99 ANR11_HUMAN ankyrin repeat domain 11 83 all_hematologic(23;0.00824)|Colorectal(91;0.0475) TGCAGCTCTCCAGGGCGTCCT 0.612000 0 SO:0001819 synonymous_variant ENST00000301030.4 1 1 hg19 CCDS32513.1 TCGA-2L-AAQL-01A-11D-A38G-08 ANKRD11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000430462.3 1 0 1 111 387 0 218 0 5.052295e-02 1 1 0 218 2 0 0 0 0 0 2 1 1.000000 110 373 0 216 2 0 0 0 0 218 2 -20.000000 1 1 0 0 1 0 1 1 1.734762 1 0.380000 1.790000 0.241683 0.930000 7.900000e-01 1.000000 1.000000 0.932835 0.930000 1 0.860000 1.000000 MYH4 4622 broad.mit.edu 37 17 10352050 10352050 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr17:10352050C>A ENST00000255381.2 - 32 4526 c.4416G>T c.(4414-4416)gaG>gaT p.E1472D RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA NM_017533.2 NP_060003.2 Q9Y623 MYH4_HUMAN myosin, heavy chain 4, skeletal muscle 149 TCTGGGAGGCCTCAAGTTCAG 0.448000 0 SO:0001583 missense ENST00000255381.2 0 1 hg19 CCDS11154.1 . . . . . . . . . . C 14.47 2.545239 0.45280 . . ENSG00000141048 ENST00000255381 T 0.77229 -1.08 4.97 0.598 0.17512 Myosin tail (1); 0.000000 0.37577 U 0.002040 T 0.66819 0.2828 L 0.35249 1.045 0.38463 D 0.947264 B 0.28760 0.221 B 0.37015 0.239 T 0.56625 -0.7948 10 0.23302 T 0.38 . 9.7593 0.40522 0.0:0.6205:0.0:0.3795 . 1472 Q9Y623 MYH4_HUMAN D 1472 ENSP00000255381:E1472D ENSP00000255381:E1472D E - 3 2 MYH4 10292775 0.001000 0.12720 0.997000 0.53966 0.973000 0.67179 -1.559000 0.02162 0.222000 0.20900 0.561000 0.74099 GAG TCGA-2L-AAQL-01A-11D-A38G-08 MYH4-001 KNOWN NAGNAG_splice_site|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252731.1 0 0 0 5 315 0 154 0 0 0 0 154 2 0 0 0 0 0 2 0 0.193994 5 307 1 152 9 0 0 0 0 154 2 -3.015550 1 1 0 0 1 0 1 1 1.732470 1 0.380000 1.790000 0.238142 0.060000 2.000000e-02 0.150000 0.070000 0.079016 0.060000 0 0.040000 0.110000 TP53 7157 broad.mit.edu 37 17 7578555 7578555 + Splice_Site SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr17:7578555C>A ENST00000269305.4 - 5 565 c.e5-1 TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000413465.2_Splice_Site 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.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CAGGGGAGTACTGTAGGAAGA 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 51 Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1) SO:0001630 splice_region_variant Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 17.36 3.370877 0.61624 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591 . . . 4.87 3.9 0.45041 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 11.4246 0.50003 0.0:0.9094:0.0:0.0906 . . . . . -1 . . . - . . TP53 7519280 1.000000 0.71417 0.999000 0.59377 0.918000 0.54935 7.639000 0.83342 1.359000 0.45940 0.655000 0.94253 . TCGA-2L-AAQL-01A-11D-A38G-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 35 80 0 55 0 0 1 0 0 55 2 1 1 319 1076 0 1006 2 1 1.000000 33 73 0 53 2 0 0 0 0 55 2 -20.000000 1 1 0 0 1 0 1 1 1.732470 1 0.380000 1.790000 0.238142 0.960000 8.000000e-01 1.000000 1.000000 0.952497 0.960000 1 0.890000 1.000000 NOTUM 147111 broad.mit.edu 37 17 79914915 79914915 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr17:79914915C>T ENST00000409678.3 - 7 1114 c.731G>A c.(730-732)cGt>cAt p.R244H NM_178493.5 NP_848588.3 Q6P988 NOTUM_HUMAN notum pectinacetylesterase homolog (Drosophila) 15 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382) CTCAGCCACACGGTCCACATT 0.662000 0 SO:0001583 missense ENST00000409678.3 1 1 hg19 CCDS32771.2 . . . . . . . . . . C 11.73 1.724700 0.30593 . . ENSG00000185269 ENST00000409678;ENST00000425009 . . . 4.54 3.56 0.40772 . 0.302720 0.37483 N 0.002071 T 0.43255 0.1239 L 0.39245 1.2 0.43994 D 0.996693 B 0.28258 0.205 B 0.28139 0.086 T 0.44817 -0.9303 9 0.48119 T 0.1 . 5.0317 0.14413 0.1749:0.6566:0.0:0.1686 . 244 Q6P988 NOTUM_HUMAN H 244 . ENSP00000387310:R244H R - 2 0 NOTUM 77508205 0.958000 0.32768 0.998000 0.56505 0.611000 0.37282 2.080000 0.41586 2.055000 0.61198 0.313000 0.20887 CGT TCGA-2L-AAQL-01A-11D-A38G-08 NOTUM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335123.2 1 0 1 25 127 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 25 126 0 45 2 0 0 0 0 45 2 -20.000000 1 1 0 0 1 1 2 3 2.111665 0 0.380000 1.790000 0.384676 0.870000 5.900000e-01 1.000000 1.000000 0.866653 0.870000 1 0.720000 1.000000 DSG3 1830 broad.mit.edu 37 18 29049139 29049139 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr18:29049139G>A ENST00000257189.4 + 12 1807 c.1724G>A c.(1723-1725)cGg>cAg p.R575Q NM_001944.2 NP_001935.2 P32926 DSG3_HUMAN desmoglein 3 62 OV - Ovarian serous cystadenocarcinoma(10;0.00504) CAGAACAATCGGTGTGAGATG 0.527000 0 SO:0001583 missense ENST00000257189.4 0 1 hg19 CCDS11898.1 . . . . . . . . . . G 10.84 1.462788 0.26248 . . ENSG00000134757 ENST00000257189 T 0.58060 0.36 5.95 -11.9 0.00025 . 1.487420 0.04727 N 0.420484 T 0.23094 0.0558 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.05852 -1.0860 10 0.14252 T 0.57 . 8.0923 0.30807 0.1856:0.0:0.3465:0.4679 . 575 P32926 DSG3_HUMAN Q 575 ENSP00000257189:R575Q ENSP00000257189:R575Q R + 2 0 DSG3 27303137 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -2.230000 0.01207 -3.245000 0.00206 -1.911000 0.00521 CGG TCGA-2L-AAQL-01A-11D-A38G-08 DSG3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254949.1 0 0 0 8 514 0 223 0 0 0 1 0 223 2 0 0 0 0 0 2 1 0.988692 8 505 0 223 2 0 0 0 0 223 2 -2.028886 0 1 121412 2 40 1 0 1 1 1.729344 1 0.380000 1.790000 0.238142 0.060000 2.000000e-02 0.120000 0.070000 0.073116 0.060000 0 0.040000 0.100000 ST8SIA5 29906 broad.mit.edu 37 18 44272163 44272163 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr18:44272163C>A ENST00000315087.7 - 3 940 c.280G>T c.(280-282)Gcg>Tcg p.A94S ST8SIA5_ENST00000538168.1_Missense_Mutation_p.A130S|ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.A63S NM_013305.4 NP_037437.2 O15466 SIA8E_HUMAN ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5 22 ATGTTCATCGCCCATTTGCAC 0.522000 0 SO:0001583 missense ENST00000315087.7 1 1 hg19 CCDS11930.1 . . . . . . . . . . C 11.40 1.627958 0.28978 . . ENSG00000101638 ENST00000315087;ENST00000538168;ENST00000536490 T;T;T 0.43294 0.97;0.95;1.57 4.89 4.02 0.46733 . 0.249281 0.40064 N 0.001183 T 0.30823 0.0777 L 0.29908 0.895 0.34705 D 0.727107 B;B;B;B 0.16166 0.008;0.006;0.001;0.016 B;B;B;B 0.18561 0.017;0.004;0.003;0.022 T 0.32534 -0.9903 10 0.23302 T 0.38 . 13.3123 0.60386 0.0:0.923:0.0:0.077 . 63;130;63;94 F5H8D1;B7Z1K9;B7Z5F7;O15466 .;.;.;SIA8E_HUMAN S 94;130;63 ENSP00000321343:A94S;ENSP00000445492:A130S;ENSP00000443683:A63S ENSP00000321343:A94S A - 1 0 ST8SIA5 42526161 1.000000 0.71417 0.997000 0.53966 0.998000 0.95712 5.591000 0.67536 1.199000 0.43173 0.555000 0.69702 GCG TCGA-2L-AAQL-01A-11D-A38G-08 ST8SIA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255892.1 1 0 1 57 232 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 1.000000 57 227 0 129 2 0 0 0 0 131 2 -20.000000 1 1 0 0 1 0 1 1 1.729344 1 0.380000 1.790000 0.238142 0.830000 6.500000e-01 0.990000 0.830000 0.834387 0.830000 0 0.730000 0.930000 MALT1 10892 broad.mit.edu 37 18 56401610 56401610 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr18:56401610C>T ENST00000348428.3 + 12 1730 c.1472C>T c.(1471-1473)gCc>gTc p.A491V MALT1_ENST00000345724.3_Missense_Mutation_p.A480V|RP11-126O1.4_ENST00000588835.1_RNA NM_006785.2|NM_173844.1 NP_006776.1|NP_776216.1 Q9UDY8 MALT1_HUMAN mucosa associated lymphoid tissue lymphoma translocation gene 1 12 TTTGGATATGCCACGTAAGAA 0.403000 T BIRC3 MALT Dom yes 18 18q21 10892 mucosa associated lymphoid tissue lymphoma translocation gene 1 L 0 SO:0001583 missense ENST00000348428.3 0 1 hg19 CCDS11967.1 . . . . . . . . . . C 36 5.609673 0.96637 . . ENSG00000172175 ENST00000348428;ENST00000345724 T;T 0.56611 0.45;0.45 5.88 5.88 0.94601 Peptidase C14, caspase catalytic (1); 0.046173 0.85682 D 0.000000 T 0.78168 0.4241 M 0.88570 2.965 0.58432 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.74348 0.971;0.983 T 0.81450 -0.0927 10 0.87932 D 0 . 19.0095 0.92867 0.0:1.0:0.0:0.0 . 480;491 Q9UDY8-2;Q9UDY8 .;MALT1_HUMAN V 491;480 ENSP00000319279:A491V;ENSP00000304161:A480V ENSP00000304161:A480V A + 2 0 MALT1 54552590 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.487000 0.81328 2.779000 0.95612 0.650000 0.86243 GCC TCGA-2L-AAQL-01A-11D-A38G-08 MALT1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256132.2 0 0 0 4 219 0 81 0 0 0 1 0 81 2 0 0 0 0 0 2 1 0.884668 4 214 0 79 2 0 0 0 0 81 2 -2.777912 1 1 0 0 1 0 1 1 1.729344 1 0.380000 1.790000 0.238142 0.080000 2.000000e-02 0.180000 0.080000 0.093822 0.080000 0 0.040000 0.130000 TMX3 54495 broad.mit.edu 37 18 66377374 66377374 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr18:66377374G>A ENST00000299608.2 - 4 465 c.149C>T c.(148-150)gCg>gTg p.A50V TMX3_ENST00000562706.1_Missense_Mutation_p.A50V|TMX3_ENST00000443099.2_Missense_Mutation_p.A50V NM_019022.3 NP_061895.3 Q96JJ7 TMX3_HUMAN thioredoxin-related transmembrane protein 3 17 ACACCATGGCGCATAAAACTT 0.323000 0 SO:0001583 missense ENST00000299608.2 0 1 hg19 CCDS32840.1 . . . . . . . . . . G 28.4 4.916459 0.92249 . . ENSG00000166479 ENST00000299608;ENST00000544714;ENST00000443099 T;T;T 0.10192 2.9;2.9;2.9 5.57 5.57 0.84162 Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (3); 0.000000 0.85682 D 0.000000 T 0.47060 0.1425 H 0.94925 3.6 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 T 0.61352 -0.7080 10 0.87932 D 0 . 18.1057 0.89519 0.0:0.0:1.0:0.0 . 50;50;50 B4DIE3;Q96JJ7-2;Q96JJ7 .;.;TMX3_HUMAN V 50 ENSP00000299608:A50V;ENSP00000444954:A50V;ENSP00000402605:A50V ENSP00000299608:A50V A - 2 0 TMX3 64528354 1.000000 0.71417 1.000000 0.80357 0.798000 0.45092 9.738000 0.98835 2.619000 0.88677 0.563000 0.77884 GCG TCGA-2L-AAQL-01A-11D-A38G-08 TMX3-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000420155.1 0 0 0 4 181 0 56 0 4.871187e-03 0 4 0 56 2 0 0 0 0 0 2 1 0.884723 4 176 0 56 2 0 0 0 0 56 2 -3.115087 1 1 121396 5 24 1 0 1 1 1.729344 1 0.380000 1.790000 0.238142 0.090000 3.000000e-02 0.220000 0.090000 0.112553 0.090000 0 0.050000 0.160000 ZNF709 163051 broad.mit.edu 37 19 12576048 12576048 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr19:12576048C>T ENST00000397732.3 - 4 859 c.688G>A c.(688-690)Ggg>Agg p.G230R ZNF709_ENST00000428311.1_Missense_Mutation_p.G230R|CTD-3105H18.18_ENST00000598753.1_Intron NM_152601.3 NP_689814.1 Q8N972 ZN709_HUMAN zinc finger protein 709 6 AACGTTTTCCCGCATTCTTTA 0.403000 GBM(33;565 669 12371 29134 51667) 0 SO:0001583 missense ENST00000397732.3 1 1 hg19 CCDS42504.1 . . . . . . . . . . C 17.47 3.397133 0.62177 . . ENSG00000242852;ENSG00000196826 ENST00000397732;ENST00000428311 T;T 0.03524 3.9;3.9 2.4 0.0633 0.14348 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.34676 N 0.003765 T 0.12732 0.0309 M 0.77616 2.38 0.30398 N 0.780325 D 0.89917 1.0 D 0.78314 0.991 T 0.01972 -1.1237 10 0.66056 D 0.02 . 6.0058 0.19544 0.0:0.6798:0.1959:0.1243 . 230 Q8N972 ZN709_HUMAN R 230 ENSP00000380840:G230R;ENSP00000404127:G230R ENSP00000404127:G230R G - 1 0 ZNF709;CTD-2192J16.17 12437048 0.059000 0.20769 0.201000 0.23476 0.396000 0.30629 1.548000 0.36201 0.097000 0.17492 0.313000 0.20887 GGG TCGA-2L-AAQL-01A-11D-A38G-08 ZNF709-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344088.1 1 0 1 127 568 0 239 0 0 0 0 239 2 0 0 0 0 0 2 1 1.000000 124 557 0 238 2 0 0 0 0 239 2 -2.520565 1 1 121390 2 33 1 1 2 3 2.107045 0 0.380000 1.790000 0.384676 0.960000 8.100000e-01 1.000000 1.000000 0.953869 0.960000 1 0.890000 1.000000 ATP8B3 148229 broad.mit.edu 37 19 1785279 1785279 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr19:1785279C>A ENST00000310127.6 - 27 3649 c.3411G>T c.(3409-3411)aaG>aaT p.K1137N ATP8B3_ENST00000539485.1_Missense_Mutation_p.K1147N|ATP8B3_ENST00000525591.1_Missense_Mutation_p.K1100N NM_138813.3 NP_620168.1 O60423 AT8B3_HUMAN ATPase, aminophospholipid transporter, class I, type 8B, member 3 23 Hepatocellular(1079;0.137) CGGTCCAGTACTTGATGATAA 0.607000 0 SO:0001583 missense ENST00000310127.6 1 1 hg19 CCDS45901.1 . . . . . . . . . . C 13.80 2.345599 0.41498 . . ENSG00000130270 ENST00000310127;ENST00000539485;ENST00000525591 D;D;D 0.88664 -2.41;-2.41;-2.41 4.49 -0.244 0.13031 . 0.488846 0.21162 N 0.079130 D 0.83594 0.5288 L 0.28694 0.88 0.21604 N 0.999627 D;D 0.54964 0.961;0.969 P;P 0.52159 0.617;0.691 T 0.75068 -0.3448 10 0.45353 T 0.12 . 5.2161 0.15344 0.1426:0.6161:0.0:0.2414 . 1137;1100 O60423;Q7Z485 AT8B3_HUMAN;. N 1137;1147;1100 ENSP00000311336:K1137N;ENSP00000443574:K1147N;ENSP00000437115:K1100N ENSP00000311336:K1137N K - 3 2 ATP8B3 1736279 0.001000 0.12720 0.070000 0.20053 0.053000 0.15095 -0.307000 0.08167 -0.219000 0.10003 -0.136000 0.14681 AAG TCGA-2L-AAQL-01A-11D-A38G-08 ATP8B3-002 KNOWN alternative_5_UTR|basic|CCDS protein_coding protein_coding OTTHUMT00000388279.1 1 0 1 15 77 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 0.999920 15 77 0 21 2 0 0 0 0 22 2 -20.000000 1 1 0 0 1 1 2 3 2.102412 0 0.380000 1.790000 0.382347 0.860000 5.200000e-01 1.000000 1.000000 0.848274 0.860000 1 0.680000 1.000000 ZNF790 388536 broad.mit.edu 37 19 37310991 37310991 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr19:37310991C>A ENST00000356725.4 - 5 375 c.255G>T c.(253-255)aaG>aaT p.K85N CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA NM_001242802.1|NM_206894.3 NP_001229731.1|NP_996777.2 Q6PG37 ZN790_HUMAN zinc finger protein 790 32 Esophageal squamous(110;0.183) COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065) GTAATAACTTCTTGGTCTGAC 0.323000 0 SO:0001583 missense ENST00000356725.4 1 1 hg19 CCDS12496.1 . . . . . . . . . . C 8.442 0.851037 0.17034 . . ENSG00000197863 ENST00000356725;ENST00000528994;ENST00000525288 T;T;T 0.07327 3.2;6.04;5.63 3.08 3.08 0.35506 . . . . . T 0.09862 0.0242 L 0.50333 1.59 0.09310 N 1 P 0.41313 0.745 B 0.41202 0.35 T 0.16482 -1.0401 9 0.52906 T 0.07 . 7.5937 0.28035 0.2541:0.7459:0.0:0.0 . 85 Q6PG37 ZN790_HUMAN N 85 ENSP00000349161:K85N;ENSP00000435944:K85N;ENSP00000433389:K85N ENSP00000349161:K85N K - 3 2 ZNF790 42002831 0.000000 0.05858 0.115000 0.21578 0.254000 0.26022 0.138000 0.16016 1.708000 0.51301 0.484000 0.47621 AAG TCGA-2L-AAQL-01A-11D-A38G-08 ZNF790-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385341.2 0 0 0 11 354 0 142 0 6.550418e-03 0 4 0 142 2 0 0 0 0 0 2 1 0.998292 11 351 0 141 2 0 0 0 0 142 2 -11.387680 1 1 0 0 1 1 2 3 2.090028 0 0.380000 1.790000 0.381176 0.160000 8.000000e-02 0.280000 0.160000 0.171654 0.160000 0 0.110000 0.220000 EEF2 1938 broad.mit.edu 37 19 3980040 3980040 + Nonsense_Mutation SNP G G C TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 G C G G Valid Somatic Phase_I WXS targeted Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr19:3980040G>C ENST00000309311.6 - 10 1459 c.1371C>G c.(1369-1371)taC>taG p.Y457* SNORD37_ENST00000384048.1_RNA NM_001961.3 NP_001952.1 P13639 EF2_HUMAN eukaryotic translation elongation factor 2 21 Hepatocellular(1079;0.137) TGGGCTCCACGTAGCGGCCCA 0.627000 Colon(165;1804 1908 4071 6587 18799) 0 SO:0001587 stop_gained ENST00000309311.6 0 1 hg19 CCDS12117.1 . . . . . . . . . . G 36 5.611568 0.96637 . . ENSG00000167658 ENST00000543343;ENST00000309311 . . . 5.45 -4.98 0.03019 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -38.4193 14.8867 0.70575 0.5244:0.0:0.4756:0.0 . . . . X 457 . ENSP00000307940:Y457X Y - 3 2 EEF2 3931040 0.000000 0.05858 0.873000 0.34254 0.950000 0.60333 -2.827000 0.00746 -0.965000 0.03591 -1.134000 0.01955 TAC TCGA-2L-AAQL-01A-11D-A38G-08 EEF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457615.2 1 0 1 18 111 0 44 1 1 4 777 0 44 2 1 1 142 619 0 473 2 1 0.999987 17 110 0 44 2 0 0 0 0 44 2 -20.000000 1 1 0 0 1 1 2 3 2.102412 0 0.380000 1.790000 0.382347 0.740000 4.600000e-01 1.000000 1.000000 0.753013 0.740000 0 0.590000 0.920000 C3 718 broad.mit.edu 37 19 6694601 6694601 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr19:6694601G>A ENST00000245907.6 - 24 3087 c.2995C>T c.(2995-2997)Cgg>Tgg p.R999W NM_000064.2 NP_000055.2 P01024 CO3_HUMAN complement component 3 72 Intravenous Immunoglobulin(DB00028) TGCTTCAGCCGTTCCGCGTCG 0.622000 0 SO:0001583 missense ENST00000245907.6 1 1 hg19 CCDS32883.1 . . . . . . . . . . G 15.71 2.913948 0.52546 . . ENSG00000125730 ENST00000245907 T 0.37584 1.19 5.67 4.61 0.57282 Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1); 0.519800 0.21650 N 0.071200 T 0.32704 0.0838 N 0.08118 0 0.20926 N 0.999829 D 0.76494 0.999 P 0.58620 0.842 T 0.13683 -1.0500 10 0.72032 D 0.01 . 10.8984 0.47036 0.0:0.0:0.6435:0.3565 . 999 P01024 CO3_HUMAN W 999 ENSP00000245907:R999W ENSP00000245907:R999W R - 1 2 C3 6645601 0.290000 0.24343 0.988000 0.46212 0.150000 0.21749 1.655000 0.37345 2.693000 0.91896 0.650000 0.86243 CGG TCGA-2L-AAQL-01A-11D-A38G-08 C3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317636.2 1 0 1 29 230 0 99 1 1 2 349 0 99 2 0 0 0 0 0 2 1 1.000000 29 224 0 99 2 0 0 0 0 99 2 -20.000000 1 1 0 0 1 1 2 3 2.107045 0 0.380000 1.790000 0.384676 0.590000 4.100000e-01 1.000000 0.590000 0.617138 0.590000 0 0.490000 0.720000 ACTL9 284382 broad.mit.edu 37 19 8807951 8807951 + Missense_Mutation SNP G G C TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr19:8807951G>C ENST00000324436.3 - 1 1221 c.1101C>G c.(1099-1101)caC>caG p.H367Q NM_178525.3 NP_848620.3 Q8TC94 ACTL9_HUMAN actin-like 9 36 CCACCACCACGTGGGTCTCGG 0.677000 0 SO:0001583 missense ENST00000324436.3 1 1 hg19 CCDS12207.1 . . . . . . . . . . g 3.006 -0.204896 0.06180 . . ENSG00000181786 ENST00000324436 T 0.07444 3.19 4.51 2.29 0.28610 . 0.738936 0.11482 U 0.559628 T 0.05227 0.0139 N 0.17564 0.495 0.09310 N 1 B 0.12630 0.006 B 0.19148 0.024 T 0.38243 -0.9670 10 0.87932 D 0 . 3.6914 0.08347 0.088:0.316:0.4331:0.1629 . 367 Q8TC94 ACTL9_HUMAN Q 367 ENSP00000316674:H367Q ENSP00000316674:H367Q H - 3 2 ACTL9 8668951 0.001000 0.12720 0.084000 0.20598 0.088000 0.18126 0.676000 0.25247 0.604000 0.29930 -0.482000 0.04802 CAC TCGA-2L-AAQL-01A-11D-A38G-08 ACTL9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459953.1 1 0 1 30 159 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 28 150 0 71 2 0 0 0 0 73 2 -20.000000 1 1 0 0 1 1 2 3 2.107045 0 0.380000 1.790000 0.384676 0.840000 5.900000e-01 1.000000 1.000000 0.845971 0.840000 0 0.710000 1.000000 S1PR1 1901 broad.mit.edu 37 1 101705012 101705012 + Missense_Mutation SNP T T G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:101705012T>G ENST00000305352.6 + 2 847 c.472T>G c.(472-474)Ttc>Gtc p.F158V S1PR1_ENST00000475821.1_3'UTR|RP4-575N6.4_ENST00000432195.1_RNA NM_001400.4 NP_001391.2 P21453 S1PR1_HUMAN sphingosine-1-phosphate receptor 1 43 GAGCAATAACTTCCGCCTCTT 0.557000 OREG0013620 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000305352.6 1 1 hg19 CCDS777.1 . . . . . . . . . . T 6.195 0.404153 0.11754 . . ENSG00000170989 ENST00000305352;ENST00000424264 T 0.36699 1.24 5.46 3.01 0.34805 GPCR, rhodopsin-like superfamily (1); 0.270993 0.42964 D 0.000624 T 0.04588 0.0125 N 0.02916 -0.46 0.31924 N 0.613066 B 0.02656 0.0 B 0.06405 0.002 T 0.38067 -0.9678 10 0.17369 T 0.5 . 7.8339 0.29360 0.0:0.0721:0.1384:0.7895 . 158 P21453 S1PR1_HUMAN V 158 ENSP00000305416:F158V ENSP00000305416:F158V F + 1 0 S1PR1 101477600 1.000000 0.71417 0.972000 0.41901 0.514000 0.34195 3.361000 0.52306 0.918000 0.36919 0.374000 0.22700 TTC TCGA-2L-AAQL-01A-11D-A38G-08 S1PR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029908.1 0 0 1 71 280 0 147 0 1.877652e-01 0 4 0 147 2 0 0 0 0 0 2 1 1.000000 68 275 0 147 2 0 0 0 0 147 2 -20.000000 1 1 0 0 1 0 1 1 1.731845 1 0.380000 1.790000 0.238142 0.850000 6.800000e-01 1.000000 0.860000 0.855459 0.850000 1 0.760000 0.940000 AMY2A 279 broad.mit.edu 37 1 104160198 104160198 + Missense_Mutation SNP T T G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 T G T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:104160198T>G ENST00000414303.2 + 1 200 c.136T>G c.(136-138)Tat>Gat p.Y46D NM_000699.2 NP_000690.1 P04746 AMYP_HUMAN amylase, alpha 2A (pancreatic) 22 all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451) Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491) ATGTGAGCGATATTTAGCTCC 0.423000 0 SO:0001583 missense ENST00000414303.2 1 1 hg19 CCDS783.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. t|t 15.43|15.43 2.831461|2.831461 0.50845|0.50845 .|. .|. ENSG00000243480|ENSG00000243480 ENST00000423678|ENST00000414303;ENST00000393932 .|D .|0.99663 .|-6.33 3.22|3.22 3.22|3.22 0.36961|0.36961 .|Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1); .|0.056220 .|0.64402 .|D .|0.000001 D|D 0.99462|0.99462 0.9809|0.9809 M|M 0.82132|0.82132 2.575|2.575 0.58432|0.58432 D|D 0.999998|0.999998 .|D;D .|0.89917 .|1.0;0.999 .|D;D .|0.97110 .|1.0;0.985 D|D 0.98570|0.98570 1.0645|1.0645 5|10 .|0.87932 .|D .|0 .|. 11.6147|11.6147 0.51083|0.51083 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. .|46;46 .|B9EJG1;P04746 .|.;AMYP_HUMAN R|D 44|46 .|ENSP00000397582:Y46D .|ENSP00000377509:Y46D I|Y +|+ 2|1 0|0 AMY2A|AMY2A 103961721|103961721 1.000000|1.000000 0.71417|0.71417 0.999000|0.999000 0.59377|0.59377 0.474000|0.474000 0.32979|0.32979 7.267000|7.267000 0.78462|0.78462 1.455000|1.455000 0.47813|0.47813 0.374000|0.374000 0.22700|0.22700 ATA|TAT TCGA-2L-AAQL-01A-11D-A38G-08 AMY2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000030315.1 0 0 1 322 1045 1 625 0 1 0 265 1 625 4 0 0 0 0 0 2 1 1.000000 195 630 2 678 9 0 0 0 1 625 2 -20.000000 1 0 0 0 1 0 1 1 1.731845 1 0.380000 1.790000 0.238142 0.970000 8.900000e-01 1.000000 1.000000 0.975165 0.970000 1 0.940000 1.000000 CLCN6 1185 broad.mit.edu 37 1 11897102 11897102 + Missense_Mutation SNP A A G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:11897102A>G ENST00000346436.6 + 19 2079 c.2027A>G c.(2026-2028)cAg>cGg p.Q676R CLCN6_ENST00000376487.3_Missense_Mutation_p.Q654R|CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376496.3_Missense_Mutation_p.Q676R NM_001286.3 NP_001277 P51797 CLCN6_HUMAN chloride channel, voltage-sensitive 6 36 Ovarian(185;0.249) Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) AAACGGAGCCAGTCCATGAAG 0.602000 0 SO:0001583 missense ENST00000346436.6 1 1 hg19 CCDS138.1 . . . . . . . . . . A 11.52 1.664137 0.29604 . . ENSG00000011021 ENST00000346436;ENST00000376487;ENST00000376496 D;D;D 0.91237 -2.8;-2.8;-2.81 5.7 5.7 0.88788 . 0.000000 0.85682 D 0.000000 D 0.85026 0.5603 L 0.34521 1.04 0.80722 D 1 B;B 0.17268 0.021;0.012 B;B 0.12837 0.008;0.004 T 0.80251 -0.1460 10 0.16420 T 0.52 -27.6288 15.1511 0.72700 1.0:0.0:0.0:0.0 . 654;676 F8W9R3;P51797 .;CLCN6_HUMAN R 676;654;676 ENSP00000234488:Q676R;ENSP00000365670:Q654R;ENSP00000365679:Q676R ENSP00000234488:Q676R Q + 2 0 CLCN6 11819689 1.000000 0.71417 1.000000 0.80357 0.953000 0.61014 8.422000 0.90262 2.189000 0.69895 0.459000 0.35465 CAG TCGA-2L-AAQL-01A-11D-A38G-08 CLCN6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000006639.2 1 0 1 70 220 0 106 0 0 0 1 0 106 2 0 0 0 0 0 2 1 1.000000 68 216 0 105 2 0 0 0 0 106 2 -20.000000 1 1 0 0 1 1 2 3 2.170676 0 0.380000 1.790000 0.393821 0.990000 9.900000e-01 1.000000 1.000000 0.999678 0.990000 1 0.990000 1.000000 ADAMTS4 9507 broad.mit.edu 37 1 161166670 161166670 + Splice_Site SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:161166670G>A ENST00000367996.5 - 2 1062 c.634C>T c.(634-636)Cgc>Tgc p.R212C NDUFS2_ENST00000367993.3_5'Flank|ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Splice_Site_p.R212C NM_005099.4 NP_005090.3 O75173 ATS4_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 4 43 all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00275) Tinzaparin(DB06822) GAAGCAAAGCGCTGTAGAGAA 0.527000 0 SO:0001630 splice_region_variant ENST00000367996.5 1 0 hg19 CCDS1223.1 . . . . . . . . . . G 20.4 3.989431 0.74589 . . ENSG00000158859 ENST00000367996;ENST00000367995 T;T 0.76839 -0.51;-1.05 4.64 4.64 0.57946 Metallopeptidase, catalytic domain (1); 0.197716 0.32548 N 0.005951 T 0.75287 0.3829 L 0.27053 0.805 0.54753 D 0.999987 D;D 0.89917 1.0;0.982 D;P 0.83275 0.996;0.75 T 0.79671 -0.1706 10 0.87932 D 0 . 11.7012 0.51571 0.0:0.0:0.823:0.177 . 212;212 Q5VTW1;O75173 .;ATS4_HUMAN C 212 ENSP00000356975:R212C;ENSP00000356974:R212C ENSP00000356974:R212C R - 1 0 ADAMTS4 159433294 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 5.564000 0.67359 2.418000 0.82041 0.650000 0.86243 CGC TCGA-2L-AAQL-01A-11D-A38G-08 ADAMTS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083066.2 1 0 1 164 772 1 282 0 0 0 1 1 282 2 0 0 0 0 0 2 1 1.000000 165 755 1 280 13 0 0 0 1 282 2 -20.000000 1 1 0 0 1 1 2 3 2.499219 1 0.380000 1.790000 0.478992 0.990000 9.400000e-01 1.000000 1.000000 0.996569 0.990000 1 0.990000 1.000000 TRIM67 440730 broad.mit.edu 37 1 231298879 231298879 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:231298879C>T ENST00000366653.5 + 1 164 c.164C>T c.(163-165)tCg>tTg p.S55L TRIM67_ENST00000449018.3_Intron|TRIM67_ENST00000366652.2_Missense_Mutation_p.S55L|TRIM67_ENST00000444294.3_Missense_Mutation_p.S55L Q6ZTA4 TRI67_HUMAN tripartite motif containing 67 29 Breast(184;0.0871) all_cancers(173;0.189)|Prostate(94;0.167) TCCCGGGGATCGGGGCTGCAG 0.741000 0 SO:0001583 missense ENST00000366653.5 0 1 hg19 CCDS44333.1 . . . . . . . . . . C 9.408 1.079775 0.20309 . . ENSG00000119283 ENST00000444294;ENST00000366652;ENST00000366653 T;T;T 0.70516 -0.49;-0.4;-0.49 4.02 4.02 0.46733 Zinc finger, RING-type (1); 2.080550 0.03330 N 0.193199 T 0.55784 0.1942 N 0.08118 0 0.09310 N 1 B 0.22851 0.076 B 0.12156 0.007 T 0.41305 -0.9516 10 0.28530 T 0.3 . 13.4243 0.61015 0.0:1.0:0.0:0.0 . 55 Q6ZTA4 TRI67_HUMAN L 55 ENSP00000412124:S55L;ENSP00000355612:S55L;ENSP00000355613:S55L ENSP00000355612:S55L S + 2 0 TRIM67 229365502 0.772000 0.28567 0.083000 0.20561 0.114000 0.19823 -0.265000 0.08644 1.949000 0.56562 0.313000 0.20887 TCG TCGA-2L-AAQL-01A-11D-A38G-08 TRIM67-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000092649.3 0 0 0 6 34 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 0.960448 6 31 0 15 2 0 0 0 0 15 2 -15.775740 1 1 0 0 1 1 2 3 2.508464 1 0.380000 1.790000 0.478992 0.970000 4.300000e-01 1.000000 1.000000 0.870693 0.970000 1 0.660000 1.000000 OR1C1 26188 broad.mit.edu 37 1 247920907 247920907 + Missense_Mutation SNP G G T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:247920907G>T ENST00000408896.2 - 1 1075 c.802C>A c.(802-804)Cct>Act p.P268T NM_012353.2 NP_036485.2 Q15619 OR1C1_HUMAN olfactory receptor, family 1, subfamily C, member 1 46 all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858) all_cancers(173;0.0247) OV - Ovarian serous cystadenocarcinoma(106;0.0168) TCGCTCTCAGGCATATGGGGG 0.517000 0 SO:0001583 missense ENST00000408896.2 1 1 hg19 CCDS41481.1 . . . . . . . . . . G 0.009 -1.835122 0.00579 . . ENSG00000221888 ENST00000408896 T 0.00207 8.55 3.22 2.29 0.28610 GPCR, rhodopsin-like superfamily (1); . . . . T 0.00109 0.0003 N 0.11313 0.125 0.09310 N 1 B 0.22800 0.075 B 0.32393 0.145 T 0.09122 -1.0689 9 0.38643 T 0.18 . 5.286 0.15702 0.1055:0.0:0.5646:0.3299 . 268 Q15619 OR1C1_HUMAN T 268 ENSP00000386138:P268T ENSP00000386138:P268T P - 1 0 OR1C1 245987530 0.000000 0.05858 0.009000 0.14445 0.036000 0.12997 -0.309000 0.08145 0.681000 0.31386 0.591000 0.81541 CCT TCGA-2L-AAQL-01A-11D-A38G-08 OR1C1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096855.1 1 0 1 119 280 0 141 0 0 0 0 141 2 0 0 0 0 0 2 1 1.000000 117 275 0 141 2 0 0 0 0 141 2 -20.000000 1 1 0 0 1 1 2 3 2.508464 1 0.380000 1.790000 0.478992 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 OR2T1 26696 broad.mit.edu 37 1 248569553 248569553 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:248569553C>A ENST00000366474.1 + 1 258 c.258C>A c.(256-258)ttC>ttA p.F86L NM_030904.1 NP_112166.1 O43869 OR2T1_HUMAN olfactory receptor, family 2, subfamily T, member 1 39 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) TCATCTTCTTCACCGCACTGA 0.443000 0 SO:0001583 missense ENST00000366474.1 1 1 hg19 CCDS31115.1 . . . . . . . . . . c 1.274 -0.612375 0.03690 . . ENSG00000175143 ENST00000366474 T 0.00672 5.89 4.71 -0.642 0.11486 . 0.422262 0.17374 N 0.176578 T 0.00241 0.0007 N 0.00496 -1.435 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.45323 -0.9269 10 0.02654 T 1 . 1.4067 0.02282 0.1474:0.2756:0.1437:0.4333 . 86 O43869 OR2T1_HUMAN L 86 ENSP00000355430:F86L ENSP00000355430:F86L F + 3 2 OR2T1 246636176 0.000000 0.05858 0.105000 0.21289 0.088000 0.18126 -4.701000 0.00196 0.213000 0.20722 0.557000 0.71058 TTC TCGA-2L-AAQL-01A-11D-A38G-08 OR2T1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097346.2 1 0 1 133 775 0 298 0 0 0 0 298 2 0 0 0 0 0 2 1 1.000000 129 763 0 296 2 0 0 0 0 298 2 -20.000000 1 1 0 0 1 1 3 4 2.532632 1 0.380000 1.790000 0.496672 0.970000 8.100000e-01 1.000000 1.000000 0.954059 0.970000 1 0.880000 1.000000 LEPR 3953 broad.mit.edu 37 1 66102532 66102532 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:66102532C>T ENST00000349533.6 + 20 3517 c.3332C>T c.(3331-3333)aCg>aTg p.T1111M LEPR_ENST00000406510.3_Missense_Mutation_p.T178M NM_002303.5 NP_002294.2 O15243 OBRG_HUMAN leptin receptor 36 TGTTTATTCACGGACATCAGA 0.418000 0 SO:0001583 missense ENST00000349533.6 1 1 hg19 CCDS631.1 . . . . . . . . . . C 9.281 1.048241 0.19827 . . ENSG00000116678 ENST00000349533;ENST00000406510 T 0.55760 0.5 5.37 -1.07 0.09968 . 0.746455 0.13820 N 0.360475 T 0.31765 0.0807 L 0.51422 1.61 0.09310 N 1 D 0.56287 0.975 P 0.49999 0.628 T 0.12372 -1.0550 10 0.48119 T 0.1 -4.0534 5.9674 0.19332 0.1701:0.3559:0.402:0.0719 . 1111 P48357 LEPR_HUMAN M 1111;178 ENSP00000330393:T1111M ENSP00000330393:T1111M T + 2 0 LEPR 65875120 0.038000 0.19896 0.098000 0.21074 0.002000 0.02628 0.224000 0.17738 0.136000 0.18733 -0.237000 0.12165 ACG TCGA-2L-AAQL-01A-11D-A38G-08 LEPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025275.1 1 0 1 48 177 0 82 0 0 1 0 0 82 2 0 0 0 0 0 2 1 1.000000 48 173 0 80 2 0 0 0 0 82 2 -20.000000 1 1 121412 1 25 1 0 1 1 1.731845 1 0.380000 1.790000 0.238142 0.870000 6.800000e-01 1.000000 1.000000 0.875325 0.870000 1 0.770000 0.970000 SGIP1 84251 broad.mit.edu 37 1 67147855 67147855 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:67147855C>T ENST00000371037.4 + 15 1195 c.1118C>T c.(1117-1119)cCg>cTg p.P373L SGIP1_ENST00000371036.3_Intron|SGIP1_ENST00000237247.6_Missense_Mutation_p.P377L|SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371039.1_Intron NM_032291.2 NP_115667.2 Q9BQI5 SGIP1_HUMAN SH3-domain GRB2-like (endophilin) interacting protein 1 71 GTACTATCGCCGCTCAATTTA 0.542000 0 SO:0001583 missense ENST00000371037.4 1 1 hg19 CCDS30744.1 . . . . . . . . . . C 20.9 4.068566 0.76301 . . ENSG00000118473 ENST00000237247;ENST00000371038;ENST00000407289;ENST00000371037 T;T 0.03152 4.03;4.03 5.19 4.26 0.50523 . 0.113033 0.64402 D 0.000010 T 0.07369 0.0186 L 0.47716 1.5 0.80722 D 1 D;B 0.89917 1.0;0.014 D;B 0.79108 0.992;0.005 T 0.13229 -1.0517 10 0.52906 T 0.07 -9.3174 13.4763 0.61310 0.0:0.9243:0.0:0.0757 . 376;373 A6NEV3;Q9BQI5 .;SGIP1_HUMAN L 377;376;376;373 ENSP00000237247:P377L;ENSP00000360076:P373L ENSP00000237247:P377L P + 2 0 SGIP1 66920443 0.996000 0.38824 1.000000 0.80357 0.965000 0.64279 4.809000 0.62591 2.570000 0.86706 0.455000 0.32223 CCG TCGA-2L-AAQL-01A-11D-A38G-08 SGIP1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000025395.4 1 0 1 119 435 0 232 0 0 0 0 232 2 0 0 0 0 0 2 1 1.000000 117 416 0 231 2 0 0 0 0 232 2 -20.000000 1 1 121412 4 40 1 0 1 1 1.731845 1 0.380000 1.790000 0.238142 0.900000 7.700000e-01 1.000000 1.000000 0.905272 0.900000 1 0.830000 0.970000 SLC2A7 155184 broad.mit.edu 37 1 9085071 9085071 + Silent SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr1:9085071G>A ENST00000400906.1 - 2 113 c.114C>T c.(112-114)taC>taT p.Y38Y NM_207420.2 NP_997303.2 Q6PXP3 GTR7_HUMAN solute carrier family 2 (facilitated glucose transporter), member 7 24 Ovarian(185;0.112)|all_lung(157;0.185) all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104) GGTTGTAGCCGTACTGGAAGG 0.647000 0 SO:0001819 synonymous_variant ENST00000400906.1 1 1 hg19 CCDS98.2 TCGA-2L-AAQL-01A-11D-A38G-08 SLC2A7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000127768.3 1 0 1 45 229 0 119 0 0 0 0 119 2 0 0 0 0 0 2 1 1.000000 45 223 0 117 2 0 0 0 0 119 2 -3.351963 1 1 121410 1 33 1 1 2 3 2.170676 0 0.380000 1.790000 0.393821 0.890000 6.600000e-01 1.000000 1.000000 0.890780 0.890000 1 0.770000 1.000000 C20orf26 0 broad.mit.edu 37 20 20056245 20056245 + Silent SNP C C T rs116838168 byFrequency TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr20:20056245C>T ENST00000245957.5 + 6 628 c.552C>T c.(550-552)caC>caT p.H184H C20orf26_ENST00000377306.1_Silent_p.H184H|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Silent_p.H184H|C20orf26_ENST00000377309.2_5'UTR NM_015585.3 NP_056400.3 Q8NHU2 CT026_HUMAN 77 CTCAGCTGCACGTTCGCAAAG 0.478000 0 SO:0001819 synonymous_variant ENST00000245957.5 1 1 hg19 CCDS33447.1 TCGA-2L-AAQL-01A-11D-A38G-08 C20orf26-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078228.3 1 0 0 93 439 0 176 0 0 0 0 176 2 0 0 0 0 0 2 1 1.000000 92 433 0 175 2 0 0 0 0 176 2 -4.339412 1 1 121412 50 50 1 1 2 3 2.108566 0 0.380000 1.790000 0.384676 0.920000 7.600000e-01 1.000000 1.000000 0.921920 0.920000 1 0.840000 1.000000 SIGLEC1 6614 broad.mit.edu 37 20 3687258 3687258 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr20:3687258C>T ENST00000344754.4 - 2 144 c.145G>A c.(145-147)Gtg>Atg p.V49M SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V49M NM_023068.3 NP_075556.1 Q9BZZ2 SN_HUMAN sialic acid binding Ig-like lectin 1, sialoadhesin 70 GGCACCTCCACGTCGGCAGGG 0.672000 0 SO:0001583 missense ENST00000344754.4 0 1 hg19 CCDS13060.1 . . . . . . . . . . C 15.75 2.926139 0.52759 . . ENSG00000088827 ENST00000344754;ENST00000202578 T;T 0.22336 1.96;1.96 5.01 1.48 0.22813 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1); 0.207799 0.24185 N 0.040780 T 0.36908 0.0984 M 0.70595 2.14 0.09310 N 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.997 T 0.09207 -1.0685 10 0.62326 D 0.03 . 3.7683 0.08632 0.0:0.5395:0.1965:0.2641 . 49;49 Q9BZZ2;Q9BZZ2-3 SN_HUMAN;. M 49 ENSP00000341141:V49M;ENSP00000202578:V49M ENSP00000202578:V49M V - 1 0 SIGLEC1 3635258 0.133000 0.22466 0.002000 0.10522 0.058000 0.15608 0.940000 0.28992 0.416000 0.25844 0.563000 0.77884 GTG TCGA-2L-AAQL-01A-11D-A38G-08 SIGLEC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077761.2 1 0 0 3 66 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.798246 3 63 0 29 2 0 0 0 0 30 2 -6.996989 1 1 121180 1 25 1 1 2 3 2.108566 0 0.380000 1.790000 0.384676 0.270000 7.000000e-02 1.000000 0.230000 0.312303 0.270000 0 0.150000 0.450000 MMP9 4318 broad.mit.edu 37 20 44639630 44639630 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr20:44639630G>A ENST00000372330.3 + 4 609 c.590G>A c.(589-591)gGc>gAc p.G197D RP11-465L10.10_ENST00000535913.1_RNA NM_004994.2 NP_004985.2 P14780 MMP9_HUMAN matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) 46 Myeloproliferative disorder(115;0.0122) Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017) CCTGGCCCCGGCATTCAGGGA 0.602000 0 SO:0001583 missense ENST00000372330.3 0 1 hg19 CCDS13390.1 . . . . . . . . . . G 32 5.125006 0.94429 . . ENSG00000100985 ENST00000372330 T 0.23754 1.89 4.62 4.62 0.57501 Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.47414 0.1444 M 0.76328 2.33 0.80722 D 1 P 0.40660 0.726 P 0.53649 0.731 T 0.50642 -0.8804 10 0.87932 D 0 . 16.9809 0.86327 0.0:0.0:1.0:0.0 . 197 P14780 MMP9_HUMAN D 197 ENSP00000361405:G197D ENSP00000361405:G197D G + 2 0 MMP9 44073037 1.000000 0.71417 0.997000 0.53966 0.992000 0.81027 9.601000 0.98297 2.553000 0.86117 0.650000 0.86243 GGC TCGA-2L-AAQL-01A-11D-A38G-08 MMP9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080337.1 0 0 0 7 403 1 162 0 8.874123e-02 0 25 1 162 2 0 0 0 0 0 2 0 0.226476 8 396 1 157 11 0 0 0 1 162 2 -2.281619 0 1 0 0 1 1 2 3 2.108566 0 0.380000 1.790000 0.384676 0.090000 3.000000e-02 1.000000 0.090000 0.128405 0.090000 0 0.060000 0.140000 RNF114 55905 broad.mit.edu 37 20 48561946 48561946 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr20:48561946G>A ENST00000244061.2 + 3 321 c.319G>A c.(319-321)Gtg>Atg p.V107M NM_018683.3 NP_061153.1 Q9Y508 RN114_HUMAN ring finger protein 114 5 CCGGTCCCACGTGGCTACTTG 0.458000 0 SO:0001583 missense ENST00000244061.2 1 1 hg19 CCDS33482.1 . . . . . . . . . . G 14.31 2.496437 0.44352 . . ENSG00000124226 ENST00000449816;ENST00000244061 T 0.81078 -1.45 5.97 5.02 0.67125 . 0.234988 0.44688 D 0.000431 T 0.73984 0.3657 L 0.46157 1.445 0.26976 N 0.965477 P;B 0.52842 0.956;0.282 B;B 0.43508 0.422;0.041 T 0.70263 -0.4920 10 0.42905 T 0.14 -6.465 9.5071 0.39053 0.0741:0.0:0.7856:0.1403 . 107;107 Q9Y508-2;Q9Y508 .;RN114_HUMAN M 107 ENSP00000244061:V107M ENSP00000244061:V107M V + 1 0 RNF114 47995353 1.000000 0.71417 0.977000 0.42913 0.934000 0.57294 4.718000 0.61930 2.833000 0.97629 0.585000 0.79938 GTG TCGA-2L-AAQL-01A-11D-A38G-08 RNF114-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079663.1 1 0 1 41 178 0 78 1 9.999998e-01 32 75 0 78 2 0 0 0 0 0 2 1 1.000000 39 175 0 78 2 0 0 0 0 78 2 -19.999960 1 1 121412 2 32 1 1 2 3 2.108566 0 0.380000 1.790000 0.384676 0.990000 7.300000e-01 1.000000 1.000000 0.946522 0.990000 1 0.850000 1.000000 ARFGAP1 55738 broad.mit.edu 37 20 61906986 61906986 + Missense_Mutation SNP G G T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr20:61906986G>T ENST00000370283.4 + 2 194 c.54G>T c.(52-54)gaG>gaT p.E18D ARFGAP1_ENST00000370275.4_Missense_Mutation_p.E18D|NKAIN4_ENST00000370307.2_5'Flank|ARFGAP1_ENST00000547204.1_5'UTR|ARFGAP1_ENST00000519273.2_5'UTR|ARFGAP1_ENST00000353546.3_Missense_Mutation_p.E18D|ARFGAP1_ENST00000519604.1_Missense_Mutation_p.R2I NM_018209.2 NP_060679.1 Q8N6T3 ARFG1_HUMAN ADP-ribosylation factor GTPase activating protein 1 13 all_cancers(38;1.59e-09) TGCAGGATGAGAACAACGTAA 0.517000 0 SO:0001583 missense ENST00000370283.4 0 1 hg19 CCDS13515.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 2.379|2.379 -0.342631|-0.342631 0.05243|0.05243 .|. .|. ENSG00000101199|ENSG00000101199 ENST00000370283;ENST00000523114;ENST00000370275;ENST00000353546;ENST00000522403;ENST00000550188|ENST00000519604 T;T;T;T;T;T|T 0.46819|0.46063 0.86;0.86;0.86;0.86;0.86;0.86|0.88 4.78|4.78 0.0115|0.0115 0.14087|0.14087 .|. 0.057039|. 0.64402|. N|. 0.000002|. T|T 0.34890|0.34890 0.0913|0.0913 N|N 0.16862|0.16862 0.45|0.45 0.80722|0.80722 D|D 1|1 B;B;B|B 0.10296|0.29955 0.003;0.0;0.0|0.263 B;B;B|P 0.17098|0.46208 0.017;0.009;0.005|0.507 T|T 0.32534|0.32534 -0.9903|-0.9903 10|9 0.21014|0.87932 T|D 0.42|0 -0.3684|-0.3684 5.8773|5.8773 0.18836|0.18836 0.328:0.1544:0.5176:0.0|0.328:0.1544:0.5176:0.0 .|. 18;18;18|2 B7ZBI2;Q8N6T3;Q8N6T3-2|E7EV62 .;ARFG1_HUMAN;.|. D|I 18|2 ENSP00000359306:E18D;ENSP00000428355:E18D;ENSP00000359298:E18D;ENSP00000314615:E18D;ENSP00000430929:E18D;ENSP00000449515:E18D|ENSP00000430500:R2I ENSP00000314615:E18D|ENSP00000430500:R2I E|R +|+ 3|2 2|0 ARFGAP1|ARFGAP1 61377431|61377431 0.998000|0.998000 0.40836|0.40836 0.900000|0.900000 0.35374|0.35374 0.053000|0.053000 0.15095|0.15095 0.412000|0.412000 0.21131|0.21131 -0.161000|-0.161000 0.10983|0.10983 -0.379000|-0.379000 0.06801|0.06801 GAG|AGA TCGA-2L-AAQL-01A-11D-A38G-08 ARFGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080134.3 0 0 0 4 142 0 60 0 1.755982e-01 0 22 0 60 2 0 0 0 0 0 2 1 0.884808 4 138 0 60 2 0 0 0 0 60 2 -6.515642 1 0 0 0 1 1 2 3 2.108566 0 0.380000 1.790000 0.384676 0.160000 5.000000e-02 1.000000 0.140000 0.200893 0.160000 0 0.090000 0.260000 PLXNB2 23654 broad.mit.edu 37 22 50728171 50728171 + Silent SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr22:50728171G>A ENST00000449103.1 - 3 983 c.843C>T c.(841-843)gcC>gcT p.A281A PLXNB2_ENST00000359337.4_Silent_p.A281A O15031 PLXB2_HUMAN plexin B2 66 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) CCACGGAGGCGGCCAGGCAGG 0.662000 0 SO:0001819 synonymous_variant ENST00000449103.1 0 1 hg19 CCDS43035.1 TCGA-2L-AAQL-01A-11D-A38G-08 PLXNB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316874.3 0 0 1 24 144 1 75 0 2.183712e-01 1 5 1 75 2 1 1 38 357 0 223 2 1 0.995154 24 136 1 68 10 0 0 0 1 75 2 -20.000000 1 1 120718 7 37 1 0 1 1 1.915113 0 0.380000 1.790000 0.319205 0.680000 4.500000e-01 0.940000 0.680000 0.695196 0.680000 0 0.560000 0.820000 TTN 7273 broad.mit.edu 37 2 179455476 179455476 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr2:179455476C>T ENST00000591111.1 - 254 56277 c.56053G>A c.(56053-56055)Gct>Act p.A18685T TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A17758T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A11261T|TTN_ENST00000589042.1_Missense_Mutation_p.A20326T|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A11453T|TTN_ENST00000359218.5_Missense_Mutation_p.A11386T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTCAGGTCAGCGATAGGTGTT 0.443000 0 SO:0001583 missense ENST00000591111.1 0 1 hg19 . . . . . . . . . . C 6.198 0.404659 0.11754 0.0 1.21E-4 ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.54279 0.58;0.58;0.58;0.58 6.11 0.782 0.18567 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.35158 0.0922 N 0.13352 0.335 0.09310 N 1 B;B;B;B 0.06786 0.001;0.001;0.001;0.001 B;B;B;B 0.06405 0.002;0.002;0.002;0.002 T 0.28396 -1.0045 9 0.87932 D 0 . 11.1443 0.48422 0.0:0.2701:0.5822:0.1477 . 11261;11386;11453;18685 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN T 17758;11261;11453;11386;11259 ENSP00000343764:A17758T;ENSP00000434586:A11261T;ENSP00000340554:A11453T;ENSP00000352154:A11386T ENSP00000340554:A11453T A - 1 0 TTN 179163722 0.086000 0.21541 0.001000 0.08648 0.796000 0.44982 0.327000 0.19663 -0.131000 0.11578 0.655000 0.94253 GCT TCGA-2L-AAQL-01A-11D-A38G-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 8 484 0 188 0 0 0 0 188 2 0 0 0 0 0 2 1 0.988658 7 477 0 188 2 0 0 0 0 188 2 -2.475960 0 1 120840 27 46 1 1 2 3 2.094280 0 0.380000 1.790000 0.382347 0.080000 3.000000e-02 0.180000 0.080000 0.104789 0.080000 0 0.050000 0.130000 ASNSD1 54529 broad.mit.edu 37 2 190535201 190535201 + Silent SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr2:190535201C>T ENST00000260952.4 + 6 2094 c.1681C>T c.(1681-1683)Cta>Tta p.L561L ASNSD1_ENST00000607062.1_Silent_p.L80L NM_019048.2 NP_061921 Q9NWL6 ASND1_HUMAN asparagine synthetase domain containing 1 25 OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118) TGTCTCCTTTCTAAATTCTCT 0.353000 0 SO:0001819 synonymous_variant ENST00000260952.4 1 1 hg19 CCDS2300.1 TCGA-2L-AAQL-01A-11D-A38G-08 ASNSD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255919.3 1 0 0 99 411 0 207 1 1 19 105 0 207 2 0 0 0 0 0 2 1 1.000000 96 405 0 205 2 0 0 0 0 207 2 -20.000000 1 1 0 0 1 1 2 3 2.094280 0 0.380000 1.790000 0.382347 0.990000 8.400000e-01 1.000000 1.000000 0.976147 0.990000 1 0.930000 1.000000 PUM2 23369 broad.mit.edu 37 2 20508209 20508209 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr2:20508209G>A ENST00000361078.2 - 5 677 c.655C>T c.(655-657)Cct>Tct p.P219S PUM2_ENST00000403432.1_Missense_Mutation_p.P219S|PUM2_ENST00000420234.1_5'UTR|PUM2_ENST00000338086.5_Missense_Mutation_p.P219S|PUM2_ENST00000319801.5_Missense_Mutation_p.P219S|PUM2_ENST00000536417.1_Missense_Mutation_p.P163S Q8TB72 PUM2_HUMAN pumilio RNA-binding family member 2 42 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TGAGTTTCAGGATTTGAAAAT 0.448000 0 SO:0001583 missense ENST00000361078.2 1 1 hg19 . . . . . . . . . . G 14.59 2.581242 0.46006 . . ENSG00000055917 ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417;ENST00000442400 T;T;T;T;T;T 0.18016 2.31;2.58;2.58;2.24;2.31;2.31 6.07 4.22 0.49857 . 0.151121 0.64402 D 0.000008 T 0.08044 0.0201 N 0.08118 0 0.38222 D 0.94079 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.0;0.0;0.001 T 0.25882 -1.0119 10 0.21014 T 0.42 -4.9397 8.5974 0.33723 0.0667:0.0:0.5388:0.3945 . 163;219;219 B4E2B6;B7ZL34;Q8TB72-3 .;.;. S 219;219;219;110;219;163;219 ENSP00000338173:P219S;ENSP00000354370:P219S;ENSP00000326746:P219S;ENSP00000409905:P110S;ENSP00000385992:P219S;ENSP00000440093:P163S ENSP00000326746:P219S P - 1 0 PUM2 20371690 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 1.825000 0.39081 0.840000 0.34995 0.650000 0.86243 CCT TCGA-2L-AAQL-01A-11D-A38G-08 PUM2-202 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 1 107 525 0 201 0 0 0 0 201 2 0 0 0 0 0 2 1 1.000000 107 516 0 200 2 0 0 0 0 201 2 -20.000000 1 1 0 0 1 1 2 3 2.093014 0 0.380000 1.790000 0.381176 0.880000 7.400000e-01 1.000000 1.000000 0.892137 0.880000 1 0.810000 0.970000 CTDSP1 58190 broad.mit.edu 37 2 219266400 219266400 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr2:219266400C>T ENST00000273062.2 + 2 517 c.181C>T c.(181-183)Ccc>Tcc p.P61S MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000443891.1_Missense_Mutation_p.P61S|RP11-378A13.2_ENST00000608367.1_RNA|CTDSP1_ENST00000488627.1_3'UTR NM_021198.2|NM_182642.2 NP_067021.1|NP_872580.1 Q9GZU7 CTDS1_HUMAN CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1 8 Renal(207;0.0915) CAGCGGGGCGCCCCTGCTTGT 0.667000 0 SO:0001583 missense ENST00000273062.2 1 1 hg19 CCDS2416.1 . . . . . . . . . . C 18.16 3.561410 0.65538 . . ENSG00000144579 ENST00000443891;ENST00000273062 T;T 0.14144 2.53;2.55 5.08 4.19 0.49359 . 0.061117 0.64402 D 0.000003 T 0.19725 0.0474 M 0.74467 2.265 0.58432 D 0.999999 B;B 0.17852 0.024;0.024 B;B 0.26202 0.024;0.067 T 0.03060 -1.1077 10 0.44086 T 0.13 -16.6294 12.6141 0.56567 0.0:0.9192:0.0:0.0807 . 61;61 Q9GZU7;C9IYG0 CTDS1_HUMAN;. S 61 ENSP00000392248:P61S;ENSP00000273062:P61S ENSP00000273062:P61S P + 1 0 CTDSP1 218974644 0.543000 0.26434 0.924000 0.36721 0.734000 0.41952 3.105000 0.50314 2.362000 0.80069 0.655000 0.94253 CCC TCGA-2L-AAQL-01A-11D-A38G-08 CTDSP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256774.1 1 0 1 36 127 0 56 1 1 31 79 0 56 2 0 0 0 0 0 2 1 1.000000 35 124 0 54 2 0 0 0 0 56 2 -20.000000 1 1 0 0 1 1 2 3 2.094280 0 0.380000 1.790000 0.382347 0.990000 8.500000e-01 1.000000 1.000000 0.988070 0.990000 1 0.990000 1.000000 ACTG2 72 broad.mit.edu 37 2 74146664 74146664 + Nonsense_Mutation SNP G G T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr2:74146664G>T ENST00000409624.1 + 10 1736 c.1093G>T c.(1093-1095)Gag>Tag p.E365* ACTG2_ENST00000345517.3_Nonsense_Mutation_p.E365*|ACTG2_ENST00000409731.3_Nonsense_Mutation_p.E322* P63267 ACTH_HUMAN actin, gamma 2, smooth muscle, enteric 18 TGAGTATGATGAGGCAGGGCC 0.532000 0 SO:0001587 stop_gained ENST00000409624.1 0 1 hg19 CCDS1930.1 . . . . . . . . . . G 36 5.762352 0.96906 . . ENSG00000163017 ENST00000409731;ENST00000345517;ENST00000409624 . . . 4.8 4.8 0.61643 . 0.502454 0.17436 N 0.174289 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 . 17.1435 0.86760 0.0:0.0:1.0:0.0 . . . . X 322;365;365 . ENSP00000295137:E365X E + 1 0 ACTG2 74000172 1.000000 0.71417 1.000000 0.80357 0.950000 0.60333 9.601000 0.98297 2.651000 0.90000 0.591000 0.81541 GAG TCGA-2L-AAQL-01A-11D-A38G-08 ACTG2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328086.1 0 0 0 6 302 0 92 0 8.615652e-01 0 181 0 92 2 0 0 0 0 0 2 1 0.961260 5 292 0 91 2 0 0 0 0 92 2 -6.500245 1 0 0 0 1 1 2 3 2.100867 0 0.380000 1.790000 0.382347 0.100000 4.000000e-02 0.230000 0.100000 0.127306 0.100000 0 0.070000 0.160000 NPHP3 27031 broad.mit.edu 37 3 132415576 132415576 + Splice_Site SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr3:132415576G>A ENST00000337331.5 - 15 2256 c.2170C>T c.(2170-2172)Cgt>Tgt p.R724C NPHP3_ENST00000326682.8_Intron NM_153240.4 NP_694972.3 Q7Z494 NPHP3_HUMAN nephronophthisis 3 (adolescent) 42 ACCACTCACCGCGCGATCATT 0.458000 0 SO:0001630 splice_region_variant ENST00000337331.5 1 0 hg19 CCDS3078.1 . . . . . . . . . . G 9.374 1.071278 0.20147 . . ENSG00000113971 ENST00000337331 T 0.64085 -0.08 5.9 -3.65 0.04502 . 0.566832 0.22573 N 0.058315 T 0.30448 0.0765 N 0.02539 -0.55 0.35234 D 0.777212 B 0.02656 0.0 B 0.01281 0.0 T 0.04373 -1.0956 10 0.45353 T 0.12 -0.0351 11.0565 0.47922 0.6313:0.0:0.2772:0.0916 . 724 Q7Z494 NPHP3_HUMAN C 724 ENSP00000338766:R724C ENSP00000338766:R724C R - 1 0 NPHP3 133898266 0.000000 0.05858 0.002000 0.10522 0.043000 0.13939 -0.361000 0.07612 -0.584000 0.05913 0.650000 0.86243 CGT TCGA-2L-AAQL-01A-11D-A38G-08 NPHP3-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357020.2 1 0 1 204 860 0 352 0 0 0 0 352 2 0 0 0 0 0 2 1 1.000000 200 841 0 349 2 0 0 0 0 352 2 -20.000000 1 1 0 0 1 1 2 3 2.103567 0 0.380000 1.790000 0.382347 0.990000 8.800000e-01 1.000000 1.000000 0.981278 0.990000 1 0.940000 1.000000 TTC21A 199223 broad.mit.edu 37 3 39177931 39177931 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr3:39177931G>A ENST00000431162.2 + 23 3183 c.3049G>A c.(3049-3051)Gcc>Acc p.A1017T TTC21A_ENST00000440121.1_Missense_Mutation_p.A969T|TTC21A_ENST00000301819.6_Missense_Mutation_p.A1018T|TTC21A_ENST00000493856.1_3'UTR Q8NDW8 TT21A_HUMAN tetratricopeptide repeat domain 21A 50 CTTTGAATTGGCCAAGAAGGT 0.438000 0 SO:0001583 missense ENST00000431162.2 0 1 hg19 CCDS46800.1 . . . . . . . . . . G 13.23 2.175489 0.38413 . . ENSG00000168026 ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121 T;T;T 0.54479 0.57;0.57;0.57 4.79 2.7 0.31948 Tetratricopeptide repeat-containing (1); 0.648196 0.14838 N 0.295467 T 0.57095 0.2030 M 0.73430 2.235 0.09310 N 1 B;B;B 0.27416 0.178;0.005;0.003 B;B;B 0.33960 0.173;0.015;0.006 T 0.57370 -0.7823 10 0.66056 D 0.02 -5.5503 13.7973 0.63180 0.0:0.0:0.7115:0.2885 . 969;1018;1017 Q8NDW8-6;Q8NDW8-7;Q8NDW8 .;.;TT21A_HUMAN T 1018;1000;1017;969 ENSP00000301819:A1018T;ENSP00000398211:A1017T;ENSP00000410882:A969T ENSP00000301819:A1018T A + 1 0 TTC21A 39152935 1.000000 0.71417 0.027000 0.17364 0.857000 0.48899 1.702000 0.37836 0.990000 0.38787 0.462000 0.41574 GCC TCGA-2L-AAQL-01A-11D-A38G-08 TTC21A-021 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000377829.1 0 0 0 7 441 0 204 0 1.703103e-02 1 10 0 204 2 0 0 0 0 0 2 1 0.979332 6 433 0 201 2 0 0 0 0 204 2 -2.558218 1 1 0 0 1 0 1 1 1.703696 1 0.380000 1.790000 0.234568 0.060000 2.000000e-02 0.130000 0.070000 0.075230 0.060000 0 0.040000 0.100000 CELSR3 1951 broad.mit.edu 37 3 48696487 48696487 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr3:48696487C>T ENST00000164024.4 - 1 3861 c.3581G>A c.(3580-3582)cGc>cAc p.R1194H CELSR3_ENST00000544264.1_Missense_Mutation_p.R1194H NM_001407.2 NP_001398.2 Q9NYQ7 CELR3_HUMAN cadherin, EGF LAG seven-pass G-type receptor 3 83 AGCTGGGATGCGCCCAATAAT 0.537000 0 SO:0001583 missense ENST00000164024.4 0 1 hg19 CCDS2775.1 . . . . . . . . . . C 16.18 3.049277 0.55218 . . ENSG00000008300 ENST00000164024;ENST00000544264 T;T 0.39406 1.08;1.08 5.44 4.56 0.56223 Cadherin (1);Cadherin-like (1); . . . . T 0.59797 0.2220 M 0.82056 2.57 0.46437 D 0.999045 D;D 0.89917 1.0;0.999 D;P 0.63488 0.915;0.869 T 0.63545 -0.6613 9 0.72032 D 0.01 . 7.936 0.29931 0.0:0.7749:0.0:0.2251 . 1194;1264 Q9NYQ7;Q5Y190 CELR3_HUMAN;. H 1194 ENSP00000164024:R1194H;ENSP00000445694:R1194H ENSP00000164024:R1194H R - 2 0 CELSR3 48671491 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 2.728000 0.47319 2.561000 0.86390 0.561000 0.74099 CGC TCGA-2L-AAQL-01A-11D-A38G-08 CELSR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257523.1 0 0 0 5 229 1 119 0 0 0 1 119 2 0 9.186729e-01 0 211 0 157 2 0 0.192128 5 224 1 119 9 0 0 0 1 119 2 -2.718182 1 1 121412 4 39 1 0 1 1 1.703696 1 0.380000 1.790000 0.234568 0.090000 3.000000e-02 0.200000 0.090000 0.106873 0.090000 0 0.050000 0.150000 DNAH1 25981 broad.mit.edu 37 3 52387151 52387151 + Missense_Mutation SNP C C G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr3:52387151C>G ENST00000420323.2 + 19 3321 c.3060C>G c.(3058-3060)ttC>ttG p.F1020L NM_015512.4 NP_056327 Q9P2D7 DYH1_HUMAN dynein, axonemal, heavy chain 1 62 TGAAGGAGTTCCAACCCTACC 0.602000 0 SO:0001583 missense ENST00000420323.2 0 1 hg19 CCDS46842.1 . . . . . . . . . . C 24.2 4.499784 0.85176 . . ENSG00000114841 ENST00000420323 T 0.58940 0.3 5.54 4.66 0.58398 . 0.000000 0.56097 D 0.000031 T 0.60907 0.2305 L 0.42632 1.34 0.51012 D 0.999902 D;P 0.76494 0.999;0.931 D;D 0.75484 0.986;0.936 T 0.57171 -0.7857 10 0.05833 T 0.94 . 10.0759 0.42360 0.0:0.8508:0.0:0.1492 . 1020;1020 C9JXH6;Q9P2D7-3 .;. L 1020 ENSP00000401514:F1020L ENSP00000401514:F1020L F + 3 2 DNAH1 52362191 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 2.810000 0.47979 2.626000 0.88956 0.650000 0.86243 TTC TCGA-2L-AAQL-01A-11D-A38G-08 DNAH1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350816.1 0 0 0 6 139 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 0.962064 4 136 0 74 2 0 0 0 0 74 2 -8.784785 1 1 0 0 1 0 1 1 1.703696 1 0.380000 1.790000 0.234568 0.180000 7.000000e-02 0.350000 0.170000 0.198464 0.180000 0 0.120000 0.270000 ANAPC4 29945 broad.mit.edu 37 4 25395511 25395511 + Nonsense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr4:25395511C>T ENST00000315368.3 + 11 1016 c.874C>T c.(874-876)Cag>Tag p.Q292* ANAPC4_ENST00000510092.1_Nonsense_Mutation_p.Q292* NM_013367.2 NP_037499.2 Q9UJX5 APC4_HUMAN anaphase promoting complex subunit 4 p.Q292*(1) 27 Breast(46;0.0503) CAAGTTTGTGCAGGTAAAGCA 0.353000 1 Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000315368.3 0 1 hg19 CCDS3434.1 . . . . . . . . . . C 39 7.341870 0.98224 . . ENSG00000053900 ENST00000315368;ENST00000510092 . . . 5.96 5.96 0.96718 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.21540 T 0.41 -20.3366 20.394 0.98981 0.0:1.0:0.0:0.0 . . . . X 292 . ENSP00000318775:Q292X Q + 1 0 ANAPC4 25004609 1.000000 0.71417 1.000000 0.80357 0.852000 0.48524 7.162000 0.77515 2.830000 0.97506 0.585000 0.79938 CAG TCGA-2L-AAQL-01A-11D-A38G-08 ANAPC4-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000214986.1 0 0 0 4 200 0 82 0 2.167323e-02 0 9 0 82 2 0 0 0 0 0 2 1 0.884062 4 194 0 81 2 0 0 0 0 82 2 -3.072895 1 1 0 0 1 0 1 1 1.917799 0 0.380000 1.790000 0.319205 0.100000 3.000000e-02 0.220000 0.090000 0.115125 0.100000 0 0.060000 0.160000 CHRNA9 55584 broad.mit.edu 37 4 40339267 40339267 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr4:40339267G>A ENST00000310169.2 + 3 390 c.251G>A c.(250-252)cGc>cAc p.R84H NM_017581.3 NP_060051.2 Q9UGM1 ACHA9_HUMAN cholinergic receptor, nicotinic, alpha 9 (neuronal) p.R84H(1) 33 Galantamine(DB00674)|Nicotine(DB00184) TTGTGGATCCGCCAAATCTGG 0.483000 Esophageal Squamous(115;1297 1602 22235 25158 43327) 1 Substitution - Missense(1) SO:0001583 missense ENST00000310169.2 0 1 hg19 CCDS3459.1 . . . . . . . . . . G 29.9 5.045322 0.93685 . . ENSG00000174343 ENST00000310169 T 0.80214 -1.35 5.83 5.83 0.93111 Neurotransmitter-gated ion-channel ligand-binding (3); 0.046822 0.85682 D 0.000000 D 0.90937 0.7151 M 0.83603 2.65 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 D 0.91105 0.4917 10 0.66056 D 0.02 . 20.1174 0.97942 0.0:0.0:1.0:0.0 . 84 Q9UGM1 ACHA9_HUMAN H 84 ENSP00000312663:R84H ENSP00000312663:R84H R + 2 0 CHRNA9 40034024 1.000000 0.71417 1.000000 0.80357 0.656000 0.38851 9.476000 0.97823 2.771000 0.95319 0.591000 0.81541 CGC TCGA-2L-AAQL-01A-11D-A38G-08 CHRNA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216822.1 0 0 0 5 150 0 59 0 0 0 0 59 2 0 0 0 0 0 2 1 0.933067 5 145 0 59 2 0 0 0 0 59 2 -3.055836 1 1 0 0 1 0 1 1 1.917799 0 0.380000 1.790000 0.319205 0.160000 6.000000e-02 0.330000 0.150000 0.180673 0.160000 0 0.100000 0.250000 SLC12A7 10723 broad.mit.edu 37 5 1074737 1074737 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr5:1074737C>A ENST00000264930.5 - 16 2060 c.2017G>T c.(2017-2019)Gcc>Tcc p.A673S NM_006598.2 NP_006589.2 Q9Y666 S12A7_HUMAN solute carrier family 12 (potassium/chloride transporter), member 7 32 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09) Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165) Potassium Chloride(DB00761) GCGTAGCGGGCGGCGTTCAGG 0.672000 0 SO:0001583 missense ENST00000264930.5 1 1 hg19 CCDS34129.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. c|c 18.40|18.40 3.616049|3.616049 0.66672|0.66672 .|. .|. ENSG00000113504|ENSG00000113504 ENST00000264930|ENST00000513223 D|. 0.98862|. -5.19|. 4.11|4.11 4.11|4.11 0.48088|0.48088 Amino acid permease domain (1);|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.84097|0.84097 0.5397|0.5397 M|M 0.92459|0.92459 3.31|3.31 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.91635|. 0.999|. D|D 0.88363|0.88363 0.2989|0.2989 10|5 0.87932|. D|. 0|. .|. 14.1738|14.1738 0.65527|0.65527 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 673|. Q9Y666|. S12A7_HUMAN|. S|L 673|30 ENSP00000264930:A673S|. ENSP00000264930:A673S|. A|R -|- 1|2 0|0 SLC12A7|SLC12A7 1127737|1127737 1.000000|1.000000 0.71417|0.71417 0.979000|0.979000 0.43373|0.43373 0.045000|0.045000 0.14185|0.14185 6.881000|6.881000 0.75584|0.75584 1.996000|1.996000 0.58369|0.58369 0.313000|0.313000 0.20887|0.20887 GCC|CGC TCGA-2L-AAQL-01A-11D-A38G-08 SLC12A7-001 KNOWN non_canonical_TEC|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366446.2 1 0 1 38 166 0 83 1 9.980570e-01 9 36 0 83 2 0 0 0 0 0 2 1 1.000000 38 159 0 81 2 0 0 0 0 83 2 -3.144754 1 1 0 0 1 0 1 1 1.909116 0 0.380000 1.790000 0.317782 0.880000 6.500000e-01 1.000000 1.000000 0.879766 0.880000 1 0.760000 1.000000 DDX46 9879 broad.mit.edu 37 5 134130654 134130654 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr5:134130654G>A ENST00000354283.4 + 14 1876 c.1741G>A c.(1741-1743)Gta>Ata p.V581I DDX46_ENST00000509178.1_3'UTR|DDX46_ENST00000452510.2_Missense_Mutation_p.V581I Q7L014 DDX46_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 46 30 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) ACCTATTGAAGTACAAGTTGG 0.468000 Colon(13;391 453 4901 21675 24897) 0 SO:0001583 missense ENST00000354283.4 1 1 hg19 CCDS34240.1 . . . . . . . . . . G 12.22 1.872519 0.33069 . . ENSG00000145833 ENST00000452510;ENST00000354283 D;D 0.92149 -2.98;-2.98 5.42 5.42 0.78866 DEAD-like helicase (2); 0.000000 0.85682 D 0.000000 T 0.81673 0.4872 N 0.04335 -0.225 0.80722 D 1 B 0.12630 0.006 B 0.16289 0.015 T 0.77138 -0.2698 10 0.02654 T 1 -15.5181 19.5998 0.95557 0.0:0.0:1.0:0.0 . 581 Q7L014 DDX46_HUMAN I 581 ENSP00000416534:V581I;ENSP00000346236:V581I ENSP00000346236:V581I V + 1 0 DDX46 134158553 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.887000 0.87295 2.717000 0.92951 0.655000 0.94253 GTA TCGA-2L-AAQL-01A-11D-A38G-08 DDX46-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371584.1 1 0 1 147 487 0 311 1 9.128506e-01 7 9 0 311 2 0 0 0 0 0 2 1 1.000000 145 470 0 309 2 0 0 0 0 311 2 -20.000000 1 1 0 0 1 0 1 1 1.923135 0 0.380000 1.790000 0.324839 0.990000 9.600000e-01 1.000000 1.000000 0.997887 0.990000 1 0.990000 1.000000 PCDHA1 56147 broad.mit.edu 37 5 140167336 140167336 + Silent SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr5:140167336C>T ENST00000504120.2 + 1 1461 c.1461C>T c.(1459-1461)aaC>aaT p.N487N PCDHA1_ENST00000378133.3_Silent_p.N487N|PCDHA1_ENST00000394633.3_Silent_p.N487N NM_018900.2 NP_061723.1 Q9Y5I3 PCDA1_HUMAN protocadherin alpha 1 p.N487K(2) 70 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CGCAGGAGAACGCGCTGGTGT 0.657000 2 Substitution - Missense(2) SO:0001819 synonymous_variant ENST00000504120.2 1 1 hg19 CCDS54913.1 TCGA-2L-AAQL-01A-11D-A38G-08 PCDHA1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000389127.1 1 0 1 112 403 1 184 0 0 0 1 184 2 0 0 0 0 0 2 1 1.000000 106 363 1 174 11 0 0 0 1 184 2 -20.000000 1 1 0 0 1 0 1 1 1.912484 0 0.380000 1.790000 0.322034 0.990000 8.700000e-01 1.000000 1.000000 0.984339 0.990000 1 0.950000 1.000000 FBXL7 23194 broad.mit.edu 37 5 15928366 15928366 + Silent SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr5:15928366C>T ENST00000504595.1 + 3 976 c.495C>T c.(493-495)aaC>aaT p.N165N FBXL7_ENST00000329673.7_Silent_p.N153N|FBXL7_ENST00000510662.1_Silent_p.N118N NM_001278317.1|NM_012304.3 NP_001265246.1|NP_036436.1 Q9UJT9 FBXL7_HUMAN F-box and leucine-rich repeat protein 7 60 AGACCATCAACGTGGACCGCG 0.667000 0 SO:0001819 synonymous_variant ENST00000504595.1 1 1 hg19 CCDS54833.1 TCGA-2L-AAQL-01A-11D-A38G-08 FBXL7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366117.1 1 0 1 19 75 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.999995 19 73 0 41 2 0 0 0 0 42 2 -20.000000 1 1 0 0 1 0 1 1 1.909116 0 0.380000 1.790000 0.317782 0.950000 6.100000e-01 1.000000 1.000000 0.908901 0.950000 1 0.770000 1.000000 ADAMTS2 9509 broad.mit.edu 37 5 178541162 178541162 + Silent SNP G G A rs79606317 TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr5:178541162G>A ENST00000251582.7 - 22 3443 c.3342C>T c.(3340-3342)aaC>aaT p.N1114N NM_014244.4 NP_055059.2 O95450 ATS2_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 2 p.N1114N(1) 72 all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326) all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) CGTCAATGTCGTTGTGCTTCC 0.587000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000251582.7 1 1 hg19 CCDS4444.1 TCGA-2L-AAQL-01A-11D-A38G-08 ADAMTS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253507.1 1 0 0 13 248 0 89 0 8.056376e-01 0 60 0 89 2 0 0 0 0 0 2 1 0.999525 13 244 0 87 2 0 0 0 0 89 2 -4.772792 1 1 121412 30 48 1 0 1 1 1.912484 0 0.380000 1.790000 0.322034 0.240000 1.300000e-01 0.390000 0.240000 0.254155 0.240000 0 0.180000 0.320000 LIN28B 389421 broad.mit.edu 37 6 105474175 105474175 + Missense_Mutation SNP C C A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr6:105474175C>A ENST00000345080.4 + 3 404 c.201C>A c.(199-201)agC>agA p.S67R NM_001004317.3 NP_001004317.1 Q6ZN17 LN28B_HUMAN lin-28 homolog B (C. elegans) 12 all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204) CTTTACAGAGCAAACTATTCA 0.338000 0 SO:0001583 missense ENST00000345080.4 1 1 hg19 CCDS34504.1 . . . . . . . . . . C 19.21 3.783141 0.70222 . . ENSG00000187772 ENST00000345080 . . . 5.92 5.05 0.67936 Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1); 0.074367 0.85682 D 0.000000 T 0.61160 0.2325 L 0.49640 1.575 0.80722 D 1 D;D 0.76494 0.991;0.999 P;D 0.66497 0.818;0.944 T 0.65302 -0.6201 9 0.52906 T 0.07 -13.7426 14.9456 0.71029 0.0:0.9318:0.0:0.0682 . 44;67 A7E2T3;Q6ZN17 .;LN28B_HUMAN R 67 . ENSP00000344401:S67R S + 3 2 LIN28B 105580868 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.128000 0.50492 1.499000 0.48617 0.650000 0.86243 AGC TCGA-2L-AAQL-01A-11D-A38G-08 LIN28B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041646.2 1 0 1 77 351 0 132 0 0 0 0 132 2 0 0 0 0 0 2 1 1.000000 76 344 0 132 2 0 0 0 0 132 2 -20.000000 1 1 121384 1 35 1 0 1 1 1.892103 1 0.380000 1.790000 0.319205 0.850000 6.900000e-01 1.000000 1.000000 0.862233 0.850000 1 0.770000 0.950000 PKHD1 5314 broad.mit.edu 37 6 51944795 51944795 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr6:51944795G>A ENST00000371117.3 - 5 568 c.293C>T c.(292-294)tCt>tTt p.S98F PKHD1_ENST00000340994.4_Missense_Mutation_p.S98F NM_138694.3 NP_619639.3 P08F94 PKHD1_HUMAN polycystic kidney and hepatic disease 1 (autosomal recessive) 304 Lung NSC(77;0.0605) ATGTGCTTCAGACAGCACAGA 0.473000 0 SO:0001583 missense ENST00000371117.3 1 1 hg19 CCDS4935.1 . . . . . . . . . . G 13.80 2.345983 0.41599 . . ENSG00000170927 ENST00000371117;ENST00000340994;ENST00000393616 D;D 0.88124 -2.13;-2.34 5.31 3.41 0.39046 . 0.768295 0.12007 N 0.508240 T 0.74951 0.3784 L 0.46157 1.445 0.09310 N 1 P;P 0.45474 0.859;0.779 B;B 0.40444 0.329;0.177 T 0.67452 -0.5667 10 0.62326 D 0.03 . 9.7386 0.40404 0.0:0.1492:0.6976:0.1532 . 98;98 P08F94-2;P08F94 .;PKHD1_HUMAN F 98 ENSP00000360158:S98F;ENSP00000341097:S98F ENSP00000341097:S98F S - 2 0 PKHD1 52052754 0.010000 0.17322 0.008000 0.14137 0.776000 0.43924 1.556000 0.36288 2.631000 0.89168 0.655000 0.94253 TCT TCGA-2L-AAQL-01A-11D-A38G-08 PKHD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000040893.1 1 0 0 90 296 0 155 0 0 0 1 0 155 2 0 0 0 0 0 2 1 1.000000 89 293 0 155 2 0 0 0 0 155 2 -20.000000 1 1 0 0 1 0 1 1 1.935087 0 0.380000 1.790000 0.319205 0.990000 9.100000e-01 1.000000 1.000000 0.994192 0.990000 1 0.990000 1.000000 GRM8 2918 broad.mit.edu 37 7 126173853 126173853 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:126173853G>A ENST00000339582.2 - 9 2391 c.1583C>T c.(1582-1584)aCg>aTg p.T528M GRM8_ENST00000358373.3_Missense_Mutation_p.T528M|GRM8_ENST00000444921.2_Missense_Mutation_p.T528M|GRM8_ENST00000480995.1_Intron O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 125 Prostate(267;0.186) CCCTTTCACCGTTTTCTTCCT 0.542000 HNSCC(24;0.065) 0 SO:0001583 missense ENST00000339582.2 1 1 hg19 CCDS5794.1 . . . . . . . . . . G 1.717 -0.497514 0.04291 . . ENSG00000179603 ENST00000339582;ENST00000444921;ENST00000358373 D;D;D 0.89617 -2.54;-2.54;-2.54 5.8 4.92 0.64577 GPCR, family 3, nine cysteines domain (1); 0.100013 0.64402 D 0.000001 T 0.74261 0.3693 N 0.03999 -0.3 0.80722 D 1 B;B 0.16166 0.013;0.016 B;B 0.22880 0.002;0.042 T 0.69075 -0.5241 10 0.02654 T 1 . 14.0626 0.64808 0.0721:0.0:0.9279:0.0 . 528;528 O00222-2;O00222 .;GRM8_HUMAN M 528 ENSP00000344173:T528M;ENSP00000409790:T528M;ENSP00000351142:T528M ENSP00000344173:T528M T - 2 0 GRM8 125961089 0.754000 0.28360 0.709000 0.30452 0.984000 0.73092 1.180000 0.32005 1.468000 0.48064 0.643000 0.83706 ACG TCGA-2L-AAQL-01A-11D-A38G-08 GRM8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059209.4 1 0 1 55 365 0 154 0 0 0 0 154 2 0 0 0 0 0 2 1 1.000000 54 363 0 154 2 0 0 0 0 154 2 -2.920908 1 1 121412 4 38 1 1 2 3 2.121637 0 0.380000 1.790000 0.386988 0.700000 5.300000e-01 1.000000 0.690000 0.717619 0.700000 0 0.610000 0.810000 FLNC 2318 broad.mit.edu 37 7 128495282 128495282 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:128495282G>A ENST00000325888.8 + 43 7426 c.7165G>A c.(7165-7167)Gat>Aat p.D2389N RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.D2356N NM_001458.4 NP_001449.3 Q14315 FLNC_HUMAN filamin C, gamma 128 CAAGTTCAATGATGAGCACAT 0.622000 0 SO:0001583 missense ENST00000325888.8 1 0 hg19 CCDS43644.1 . . . . . . . . . . G 16.66 3.184039 0.57800 . . ENSG00000128591 ENST00000325888;ENST00000346177 D;D 0.92249 -3.0;-3.0 5.29 5.29 0.74685 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.053142 0.64402 D 0.000001 D 0.90007 0.6880 L 0.46567 1.45 0.48452 D 0.999652 B;B 0.21071 0.008;0.051 B;B 0.24394 0.013;0.053 D 0.86013 0.1502 10 0.33940 T 0.23 . 18.9397 0.92600 0.0:0.0:1.0:0.0 . 2356;2389 Q14315-2;Q14315 .;FLNC_HUMAN N 2389;2356 ENSP00000327145:D2389N;ENSP00000344002:D2356N ENSP00000327145:D2389N D + 1 0 FLNC 128282518 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 4.797000 0.62503 2.470000 0.83445 0.462000 0.41574 GAT TCGA-2L-AAQL-01A-11D-A38G-08 FLNC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059948.3 1 0 0 62 417 0 169 0 3.834085e-01 0 10 0 169 2 0 0 0 0 0 2 1 1.000000 62 409 0 168 2 0 0 0 0 169 2 -19.999990 1 1 0 0 1 1 2 3 2.121637 0 0.380000 1.790000 0.386988 0.690000 5.300000e-01 1.000000 0.680000 0.709231 0.690000 0 0.610000 0.790000 KEL 3792 broad.mit.edu 37 7 142655036 142655036 + Missense_Mutation SNP T T G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:142655036T>G ENST00000355265.2 - 6 1024 c.550A>C c.(550-552)Aaa>Caa p.K184Q KEL_ENST00000479768.2_5'UTR NM_000420.2 NP_000411.1 P23276 KELL_HUMAN Kell blood group, metallo-endopeptidase 60 Melanoma(164;0.059) GAAGTCCATTTACCAGAGATG 0.517000 0 SO:0001583 missense ENST00000355265.2 1 1 hg19 CCDS34766.1 . . . . . . . . . . T 8.336 0.827505 0.16749 . . ENSG00000197993 ENST00000355265;ENST00000467543 T;T 0.73363 -0.74;-0.74 5.8 3.26 0.37387 Peptidase M13 (1); 0.316302 0.26719 N 0.022860 T 0.49677 0.1571 N 0.14661 0.345 0.09310 N 1 B 0.32010 0.351 B 0.29663 0.105 T 0.30416 -0.9979 10 0.16896 T 0.51 -4.6538 5.6937 0.17843 0.0:0.0867:0.1694:0.744 . 184 P23276 KELL_HUMAN Q 184;165 ENSP00000347409:K184Q;ENSP00000420011:K165Q ENSP00000347409:K184Q K - 1 0 KEL 142365158 0.003000 0.15002 0.096000 0.21009 0.846000 0.48090 0.398000 0.20899 0.992000 0.38840 0.528000 0.53228 AAA TCGA-2L-AAQL-01A-11D-A38G-08 KEL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347671.2 1 0 1 38 165 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 36 160 0 68 2 0 0 0 0 70 2 -20.000000 1 1 0 0 1 1 2 3 2.121637 0 0.380000 1.790000 0.386988 0.990000 7.300000e-01 1.000000 1.000000 0.947411 0.990000 1 0.860000 1.000000 DNAH11 8701 broad.mit.edu 37 7 21640427 21640427 + Missense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:21640427G>A ENST00000409508.3 + 16 3165 c.3134G>A c.(3133-3135)cGa>cAa p.R1045Q DNAH11_ENST00000328843.6_Missense_Mutation_p.R1045Q NM_001277115.1 NP_001264044.1 Q96DT5 DYH11_HUMAN dynein, axonemal, heavy chain 11 230 GTGGATGATCGAGCTGAGTTT 0.448000 Kartagener syndrome 0 SO:0001583 missense Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000409508.3 1 1 hg19 . . . . . . . . . . G 19.10 3.762115 0.69763 . . ENSG00000105877 ENST00000328843 T 0.23348 1.91 5.23 5.23 0.72850 . 0.280795 0.30639 N 0.009182 T 0.35537 0.0935 . . . 0.46317 D 0.998987 D 0.76494 0.999 P 0.55615 0.78 T 0.02320 -1.1177 9 0.23891 T 0.37 . 13.1616 0.59547 0.0791:0.0:0.9209:0.0 . 1045 Q96DT5 DYH11_HUMAN Q 1045 ENSP00000330671:R1045Q ENSP00000330671:R1045Q R + 2 0 DNAH11 21606952 1.000000 0.71417 0.965000 0.40720 0.921000 0.55340 4.241000 0.58707 2.452000 0.82932 0.551000 0.68910 CGA TCGA-2L-AAQL-01A-11D-A38G-08 DNAH11-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000326582.6 0 0 1 136 769 0 321 0 0 0 0 321 2 0 0 0 0 0 2 1 1.000000 133 756 0 318 2 0 0 0 0 321 2 -20.000000 1 1 120870 3 38 1 1 2 3 2.120206 0 0.380000 1.790000 0.385835 0.790000 6.700000e-01 1.000000 0.800000 0.808651 0.790000 0 0.730000 0.870000 HECW1 23072 broad.mit.edu 37 7 43351452 43351452 + Nonsense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:43351452C>T ENST00000395891.2 + 4 723 c.118C>T c.(118-120)Cga>Tga p.R40* HECW1_ENST00000453890.1_Nonsense_Mutation_p.R40* NM_015052.3 NP_055867.3 Q76N89 HECW1_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 125 GGAGCCGCTCCGATACAGCTA 0.617000 0 SO:0001587 stop_gained ENST00000395891.2 0 1 hg19 CCDS5469.2 . . . . . . . . . . C 27.5 4.838602 0.91117 . . ENSG00000002746 ENST00000395891;ENST00000453890;ENST00000265522 . . . 5.96 5.05 0.67936 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 14.103 0.65070 0.3056:0.6944:0.0:0.0 . . . . X 40;40;39 . ENSP00000265522:R39X R + 1 2 HECW1 43317977 0.992000 0.36948 0.995000 0.50966 0.246000 0.25737 2.924000 0.48876 2.813000 0.96785 0.655000 0.94253 CGA TCGA-2L-AAQL-01A-11D-A38G-08 HECW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250893.2 1 0 1 55 243 0 100 0 0 0 0 100 2 0 0 0 0 0 2 1 1.000000 55 234 0 97 2 0 0 0 0 100 2 -3.016166 1 1 0 0 1 1 2 3 2.120206 0 0.380000 1.790000 0.385835 0.980000 7.600000e-01 1.000000 1.000000 0.947448 0.980000 1 0.860000 1.000000 STYXL1 51657 broad.mit.edu 37 7 75634627 75634627 + Silent SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:75634627C>T ENST00000248600.1 - 6 891 c.549G>A c.(547-549)aaG>aaA p.K183K STYXL1_ENST00000359697.3_Silent_p.K183K|STYXL1_ENST00000431581.1_Silent_p.K183K|STYXL1_ENST00000360591.3_3'UTR|STYXL1_ENST00000340062.5_Silent_p.K87K|STYXL1_ENST00000451157.1_Silent_p.K183K NM_016086.2 NP_057170.1 Q9Y6J8 STYL1_HUMAN serine/threonine/tyrosine interacting-like 1 10 TTTTCAAGTCCTTCTGAATCT 0.398000 0 SO:0001819 synonymous_variant ENST00000248600.1 1 1 hg19 CCDS5580.1 TCGA-2L-AAQL-01A-11D-A38G-08 STYXL1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344825.1 1 0 0 55 300 0 144 1 1 33 133 0 144 2 0 0 0 0 0 2 1 1.000000 55 298 0 144 2 0 0 0 0 144 2 -2.848931 1 0 0 0 1 1 2 3 2.119452 0 0.380000 1.790000 0.385835 0.820000 6.300000e-01 1.000000 1.000000 0.833725 0.820000 0 0.720000 0.950000 PTPN12 5782 broad.mit.edu 37 7 77212936 77212936 + Missense_Mutation SNP T T G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr7:77212936T>G ENST00000248594.6 + 4 622 c.350T>G c.(349-351)tTt>tGt p.F117C PTPN12_ENST00000435495.2_Intron|PTPN12_ENST00000415482.2_5'UTR NM_002835.3 NP_002826.3 Q05209 PTN12_HUMAN protein tyrosine phosphatase, non-receptor type 12 39 GTAATAGATTTTTGGAGGATG 0.299000 0 SO:0001583 missense ENST00000248594.6 1 1 hg19 CCDS5592.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 18.31|18.31 3.594923|3.594923 0.66219|0.66219 .|. .|. ENSG00000127947|ENSG00000127947 ENST00000248594|ENST00000522115 T|. 0.39997|. 1.05|. 5.65|5.65 5.65|5.65 0.86999|0.86999 Protein-tyrosine phosphatase, receptor/non-receptor type (4);|. 0.051905|0.051905 0.85682|0.85682 D|D 0.000000|0.000000 D|D 0.89339|0.89339 0.6687|0.6687 H|H 0.99626|0.99626 4.665|4.665 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.91635|. 0.999|. D|D 0.92460|0.92460 0.5977|0.5977 10|7 0.87932|0.87932 D|D 0|0 .|. 10.7297|10.7297 0.46089|0.46089 0.1422:0.0:0.0:0.8578|0.1422:0.0:0.0:0.8578 .|. 117|. Q05209|. PTN12_HUMAN|. C|V 117|80 ENSP00000248594:F117C|. ENSP00000248594:F117C|ENSP00000430726:F80V F|F +|+ 2|1 0|0 PTPN12|PTPN12 77050872|77050872 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.998000|0.998000 0.95712|0.95712 4.753000|4.753000 0.62183|0.62183 2.140000|2.140000 0.66376|0.66376 0.482000|0.482000 0.46254|0.46254 TTT|TTT TCGA-2L-AAQL-01A-11D-A38G-08 PTPN12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253183.3 1 0 1 58 278 0 116 1 2.827759e-01 2 4 0 116 2 0 0 0 0 0 2 1 1.000000 56 270 0 115 2 0 0 0 0 116 2 -20.000000 1 1 0 0 1 1 2 3 2.119452 0 0.380000 1.790000 0.385835 0.920000 7.100000e-01 1.000000 1.000000 0.910397 0.920000 1 0.810000 1.000000 NEIL2 252969 broad.mit.edu 37 8 11637109 11637109 + Silent SNP C C G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr8:11637109C>G ENST00000284503.6 + 3 740 c.141C>G c.(139-141)gtC>gtG p.V47V NEIL2_ENST00000436750.3_Silent_p.V47V|NEIL2_ENST00000403422.3_5'UTR|NEIL2_ENST00000528323.1_Intron|NEIL2_ENST00000455213.2_Silent_p.V47V NM_145043.2 NP_659480.1 Q969S2 NEIL2_HUMAN nei endonuclease VIII-like 2 (E. coli) 10 all_epithelial(15;0.103) STAD - Stomach adenocarcinoma(15;0.00225) TTTTCTAGGTCCATGGAAAGA 0.468000 Base excision repair (BER), DNA glycosylases 0 SO:0001819 synonymous_variant ENST00000284503.6 1 1 hg19 CCDS5984.1 TCGA-2L-AAQL-01A-11D-A38G-08 NEIL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207583.3 1 0 1 136 438 0 249 0 1.428475e-01 1 2 0 249 2 0 0 0 0 0 2 1 1.000000 135 430 0 249 2 0 0 0 0 249 2 -20.000000 1 1 0 0 1 0 2 2 1.952558 1 0.380000 1.790000 0.380000 0.990000 9.900000e-01 1.000000 1.000000 0.999940 0.990000 1 0.990000 1.000000 LGI3 203190 broad.mit.edu 37 8 22006465 22006465 + Silent SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr8:22006465C>T ENST00000306317.2 - 8 1144 c.855G>A c.(853-855)ccG>ccA p.P285P LGI3_ENST00000424267.2_Silent_p.P261P NM_139278.2 NP_644807.1 Q8N145 LGI3_HUMAN leucine-rich repeat LGI family, member 3 17 CCACCACCATCGGCTTGCAGT 0.637000 0 SO:0001819 synonymous_variant ENST00000306317.2 1 1 hg19 CCDS6025.1 TCGA-2L-AAQL-01A-11D-A38G-08 LGI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254482.1 1 0 1 41 82 0 47 0 1.146667e-01 0 2 0 47 2 0 0 0 0 0 2 1 1.000000 40 81 0 46 2 0 0 0 0 47 2 -6.901602 1 1 121408 29 41 1 0 2 2 1.910041 1 0.380000 1.790000 0.380000 0.990000 9.900000e-01 1.000000 1.000000 0.999997 0.990000 1 0.990000 1.000000 ATP6V1H 51606 broad.mit.edu 37 8 54684564 54684564 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr8:54684564C>T ENST00000359530.2 - 10 1297 c.1034G>A c.(1033-1035)aGt>aAt p.S345N ATP6V1H_ENST00000520188.1_Missense_Mutation_p.S305N|ATP6V1H_ENST00000523899.1_5'Flank|ATP6V1H_ENST00000355221.3_Missense_Mutation_p.S327N|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.S345N NM_015941.3 NP_057025.2 Q9UI12 VATH_HUMAN ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H 18 all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181) OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359) GTCCTGGACACTCTCTCCAAG 0.373000 0 SO:0001583 missense ENST00000359530.2 1 1 hg19 CCDS6153.1 . . . . . . . . . . C 19.48 3.835276 0.71373 . . ENSG00000047249 ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774 . . . 5.31 5.31 0.75309 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.58264 0.2110 L 0.46567 1.45 0.80722 D 1 P;P 0.40360 0.68;0.714 P;B 0.44946 0.465;0.414 T 0.50800 -0.8785 9 0.15952 T 0.53 -20.9211 19.3551 0.94408 0.0:1.0:0.0:0.0 . 327;345 Q9UI12-2;Q9UI12 .;VATH_HUMAN N 327;305;345;345 . ENSP00000347359:S327N S - 2 0 ATP6V1H 54847117 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.776000 0.85560 2.639000 0.89480 0.609000 0.83330 AGT TCGA-2L-AAQL-01A-11D-A38G-08 ATP6V1H-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377865.1 1 0 1 127 315 0 182 1 1 58 82 0 182 2 0 0 0 0 0 2 1 1.000000 125 303 0 180 2 0 0 0 0 182 2 -20.000000 1 1 0 0 1 0 2 2 1.910041 1 0.380000 1.790000 0.380000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 DMRT2 10655 broad.mit.edu 37 9 1056510 1056510 + Missense_Mutation SNP A A G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr9:1056510A>G ENST00000358146.2 + 3 923 c.923A>G c.(922-924)gAt>gGt p.D308G DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Missense_Mutation_p.D308G|DMRT2_ENST00000302441.6_Missense_Mutation_p.D308G|DMRT2_ENST00000382255.3_3'UTR Q9Y5R5 DMRT2_HUMAN doublesex and mab-3 related transcription factor 2 4 all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09) ACCTGCCTTGATTTAACCATG 0.458000 0 SO:0001583 missense ENST00000358146.2 1 1 hg19 CCDS6444.1 . . . . . . . . . . A 19.06 3.753973 0.69648 . . ENSG00000173253 ENST00000382251;ENST00000302441;ENST00000358146 T;T;T 0.34275 1.37;1.37;1.37 5.62 5.62 0.85841 . 0.289079 0.38663 N 0.001609 T 0.57755 0.2075 M 0.64404 1.975 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.74674 0.965;0.984 T 0.61108 -0.7129 10 0.87932 D 0 -21.4324 15.5071 0.75748 1.0:0.0:0.0:0.0 . 308;152 Q9Y5R5;Q5HYK2 DMRT2_HUMAN;. G 308 ENSP00000371686:D308G;ENSP00000305785:D308G;ENSP00000350865:D308G ENSP00000305785:D308G D + 2 0 DMRT2 1046510 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 8.730000 0.91510 2.153000 0.67306 0.528000 0.53228 GAT TCGA-2L-AAQL-01A-11D-A38G-08 DMRT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051492.1 1 0 1 51 245 0 113 0 0 1 0 0 113 2 0 0 0 0 0 2 1 1.000000 51 239 0 112 2 0 0 0 0 113 2 -20.000000 1 1 0 0 1 0 1 1 1.689498 1 0.380000 1.790000 0.234568 0.720000 5.500000e-01 0.910000 0.730000 0.734629 0.720000 0 0.630000 0.820000 COL5A1 1289 broad.mit.edu 37 9 137593107 137593107 + Silent SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr9:137593107C>T ENST00000371817.3 + 4 996 c.582C>T c.(580-582)agC>agT p.S194S COL5A1_ENST00000464187.1_3'UTR NM_000093.3|NM_001278074.1 NP_000084.3|NP_001265003.1 P20908 CO5A1_HUMAN collagen, type V, alpha 1 115 Myeloproliferative disorder(178;0.0341) TCGACCGCAGCGACCACCCCA 0.522000 0 SO:0001819 synonymous_variant ENST00000371817.3 1 1 hg19 CCDS6982.1 TCGA-2L-AAQL-01A-11D-A38G-08 COL5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054954.2 1 0 1 38 147 0 64 0 8.123676e-01 0 14 0 64 2 0 0 0 0 0 2 1 1.000000 36 144 0 63 2 0 0 0 0 64 2 -3.541542 1 1 121364 3 32 1 1 2 3 2.113077 0 0.380000 1.790000 0.385835 0.990000 8.000000e-01 1.000000 1.000000 0.977072 0.990000 1 0.940000 1.000000 PLAA 9373 broad.mit.edu 37 9 26919394 26919394 + Missense_Mutation SNP A A G TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr9:26919394A>G ENST00000397292.3 - 9 1748 c.1331T>C c.(1330-1332)cTg>cCg p.L444P PLAA_ENST00000520641.1_5'UTR|PLAA_ENST00000520884.1_Missense_Mutation_p.L444P NM_001031689.2 NP_001026859.1 Q9Y263 PLAP_HUMAN phospholipase A2-activating protein 17 all_neural(3;3.53e-10)|Glioma(3;2.71e-09) TACTTGATCCAGAAACATAGG 0.353000 Melanoma(175;2670 2735 14091 35526) 0 SO:0001583 missense ENST00000397292.3 1 1 hg19 CCDS35000.1 . . . . . . . . . . A 21.9 4.212242 0.79240 . . ENSG00000137055 ENST00000397292;ENST00000520884 T;T 0.61627 0.09;0.23 5.53 5.53 0.82687 PLAA family ubiquitin binding, PFU (2); 0.000000 0.85682 D 0.000000 T 0.81108 0.4754 M 0.91140 3.18 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.85613 0.1259 10 0.72032 D 0.01 -5.71 15.6677 0.77242 1.0:0.0:0.0:0.0 . 444;444 E5RIM3;Q9Y263 .;PLAP_HUMAN P 444 ENSP00000380460:L444P;ENSP00000429372:L444P ENSP00000380460:L444P L - 2 0 PLAA 26909394 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.059000 0.76684 2.092000 0.63282 0.482000 0.46254 CTG TCGA-2L-AAQL-01A-11D-A38G-08 PLAA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051958.2 0 0 0 16 590 0 270 0 5.877833e-02 0 14 0 270 2 0 0 0 0 0 2 1 0.999920 16 576 0 267 2 0 0 0 0 270 2 -3.411513 1 1 0 0 1 0 1 1 1.703823 1 0.380000 1.790000 0.238142 0.110000 6.000000e-02 0.180000 0.110000 0.119129 0.110000 0 0.080000 0.150000 GLIS3 169792 broad.mit.edu 37 9 4118378 4118378 + Missense_Mutation SNP C C T TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chr9:4118378C>T ENST00000324333.10 - 3 828 c.635G>A c.(634-636)gGc>gAc p.G212D GLIS3_ENST00000381971.3_Missense_Mutation_p.G367D NM_152629.3 NP_689842.3 Q8NEA6 GLIS3_HUMAN GLIS family zinc finger 3 26 Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148) CTTCTGGCTGCCGGGCACCGG 0.736000 0 SO:0001583 missense ENST00000324333.10 1 1 hg19 CCDS6451.1 . . . . . . . . . . C 4.448 0.083027 0.08533 . . ENSG00000107249 ENST00000324333;ENST00000381971 T;T 0.10573 2.87;2.86 5.63 4.73 0.59995 . 0.314417 0.25622 N 0.029409 T 0.06005 0.0156 N 0.19112 0.55 0.09310 N 1 B;B 0.17667 0.023;0.006 B;B 0.18561 0.022;0.01 T 0.40117 -0.9580 10 0.15066 T 0.55 . 5.5169 0.16912 0.0:0.6111:0.1599:0.229 . 367;212 Q8NEA6-2;Q8NEA6 .;GLIS3_HUMAN D 212;367 ENSP00000325494:G212D;ENSP00000371398:G367D ENSP00000325494:G212D G - 2 0 GLIS3 4108378 0.000000 0.05858 0.016000 0.15963 0.060000 0.15804 0.091000 0.15046 1.372000 0.46190 0.655000 0.94253 GGC TCGA-2L-AAQL-01A-11D-A38G-08 GLIS3-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000051559.1 1 0 0 20 44 0 22 0 0 0 1 0 22 2 0 0 0 0 0 2 1 0.999999 20 44 0 22 2 0 0 0 0 22 2 -20.000000 1 1 0 0 1 0 1 1 1.689498 1 0.380000 1.790000 0.234568 0.920000 7.000000e-01 1.000000 0.990000 0.909478 0.920000 1 0.820000 0.980000 ACTRT1 139741 broad.mit.edu 37 X 127185417 127185417 + Nonsense_Mutation SNP G G A TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chrX:127185417G>A ENST00000371124.3 - 1 965 c.769C>T c.(769-771)Caa>Taa p.Q257* NM_138289.3 NP_612146.1 Q8TDG2 ACTT1_HUMAN actin-related protein T1 34 TCGGGCACTTGGTACAGCTCA 0.542000 0 SO:0001587 stop_gained ENST00000371124.3 0 1 hg19 CCDS14611.1 . . . . . . . . . . G 15.36 2.811660 0.50527 . . ENSG00000123165 ENST00000371124 . . . 3.58 0.589 0.17452 . 0.537891 0.16370 N 0.217347 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 . 9.9033 0.41362 0.0:0.0:0.4788:0.5212 . . . . X 257 . ENSP00000360165:Q257X Q - 1 0 ACTRT1 127013098 1.000000 0.71417 0.001000 0.08648 0.023000 0.10783 1.058000 0.30504 0.001000 0.14605 0.600000 0.82982 CAA TCGA-2L-AAQL-01A-11D-A38G-08 ACTRT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058192.1 0 0 0 6 419 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 0.962845 6 410 0 133 2 0 0 0 0 133 2 -2.606201 1 1 0 0 1 0 1 1 0.380000 1.790000 0.380000 0.030000 1.000000e-02 0.080000 0.040000 0.042971 0.030000 0 0.020000 0.060000 BCORL1 63035 broad.mit.edu 37 X 129185988 129185988 + Missense_Mutation SNP G G A rs143047034 TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chrX:129185988G>A ENST00000218147.7 + 12 5047 c.4850G>A c.(4849-4851)cGc>cAc p.R1617H BCORL1_ENST00000359304.2_Missense_Mutation_p.R1487H|BCORL1_ENST00000303743.5_Missense_Mutation_p.R1691H|BCORL1_ENST00000540052.1_Missense_Mutation_p.R1617H Q5H9F3 BCORL_HUMAN BCL6 corepressor-like 1 75 TCAGTGTCCCGCGGGTAAGTG 0.527000 0 SO:0001583 missense ENST00000218147.7 1 1 hg19 CCDS14616.1 . . . . . . . . . . G 11.97 1.798032 0.31777 . . ENSG00000085185 ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822 T;T;T;T;T 0.40476 1.03;1.32;1.04;1.03;1.37 5.53 2.58 0.30949 . 0.759301 0.10829 N 0.629586 T 0.36220 0.0959 L 0.47716 1.5 0.32970 D 0.522206 B;B 0.24651 0.108;0.023 B;B 0.18871 0.023;0.006 T 0.42310 -0.9459 10 0.66056 D 0.02 -3.2989 9.7559 0.40502 0.2547:0.0:0.7453:0.0 . 1691;1617 Q5H9F3-3;Q5H9F3 .;BCORL_HUMAN H 1617;1691;1487;1617;1291 ENSP00000218147:R1617H;ENSP00000307541:R1691H;ENSP00000352253:R1487H;ENSP00000437775:R1617H;ENSP00000399483:R1291H ENSP00000218147:R1617H R + 2 0 BCORL1 129013669 0.988000 0.35896 0.628000 0.29241 0.404000 0.30871 2.792000 0.47837 0.420000 0.25954 0.513000 0.50165 CGC TCGA-2L-AAQL-01A-11D-A38G-08 BCORL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058223.1 1 0 1 61 234 0 95 1 8.454529e-01 3 12 0 95 2 1 1 46 212 0 107 2 1 1.000000 61 223 0 94 2 0 0 0 0 95 2 -3.757349 1 1 121322 3 38 1 0 1 1 0.380000 1.790000 0.380000 0.530000 4.200000e-01 0.660000 0.540000 0.546326 0.530000 0 0.470000 0.610000 CNKSR2 22866 broad.mit.edu 37 X 21627423 21627423 + Missense_Mutation SNP T T C TCGA-2L-AAQL-01A-11D-A38G-08 TCGA-2L-AAQL-11A-11D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx ac8948c6-17c3-4cc4-b432-8f66595f2769 8145a789-a66e-4b2d-ae0e-2784364aff45 g.chrX:21627423T>C ENST00000379510.3 + 20 2416 c.2380T>C c.(2380-2382)Ttc>Ctc p.F794L CNKSR2_ENST00000543067.1_Missense_Mutation_p.F745L|CNKSR2_ENST00000279451.4_Missense_Mutation_p.F794L|CNKSR2_ENST00000425654.2_Missense_Mutation_p.F764L NM_014927.3 NP_055742.2 Q8WXI2 CNKR2_HUMAN connector enhancer of kinase suppressor of Ras 2 61 GGATTCTGTCTTCTCTGACTC 0.567000 0 SO:0001583 missense ENST00000379510.3 0 1 hg19 CCDS14198.1 . . . . . . . . . . T 11.23 1.577480 0.28180 . . ENSG00000149970 ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510 T;T;T;T 0.17691 2.52;2.26;2.27;2.55 5.51 5.51 0.81932 . 0.161421 0.56097 D 0.000028 T 0.17619 0.0423 L 0.60455 1.87 0.47037 D 0.999295 B;B;B;B 0.18610 0.0;0.0;0.008;0.029 B;B;B;B 0.16289 0.002;0.001;0.015;0.008 T 0.06006 -1.0851 10 0.08599 T 0.76 -27.16 14.6111 0.68517 0.0:0.0:0.0:1.0 . 764;745;386;794 B7ZLJ1;B4DGR4;B3KPN2;Q8WXI2 .;.;.;CNKR2_HUMAN L 764;745;794;794 ENSP00000397906:F764L;ENSP00000444633:F745L;ENSP00000279451:F794L;ENSP00000368824:F794L ENSP00000279451:F794L F + 1 0 CNKSR2 21537344 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 4.187000 0.58344 1.831000 0.53308 0.417000 0.27973 TTC TCGA-2L-AAQL-01A-11D-A38G-08 CNKSR2-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056019.1 0 0 0 5 202 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 0.935072 5 198 0 84 2 0 0 0 0 85 2 -6.828703 1 0 0 0 1 0 1 1 0.380000 1.790000 0.380000 0.060000 2.000000e-02 0.140000 0.060000 0.074947 0.060000 0 0.040000 0.100000