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 HIST1H4E 8367 broad.mit.edu 37 6 26204947 26204948 + Frame_Shift_Ins INS - - A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr6:26204947_26204948insA ENST00000360441.4 + 1 90_91 c.75_76insA c.(76-78)aacfs p.N26fs NM_003545.3 NP_003536.1 P62805 H4_HUMAN histone cluster 1, H4e 18 all_hematologic(11;0.196) TCCTGCGAGATAACATCCAGGG 0.584000 0 SO:0001589 frameshift_variant ENST00000360441.4 0 1 hg19 CCDS4593.1 TCGA-HZ-7926-01A-11D-2154-08 HIST1H4E-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040104.1 1 0 0 27 483 0 103 0 0 0 103 0 0 0 0 1 1.000000 27 481 0 102 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 2.009768 0 0.160000 1.880000 0.154589 0.650000 0.440000 0.910000 0.660000 0.671506 0.650000 0 5.400000e-01 7.900000e-01 NKAPL 222698 broad.mit.edu 37 6 28227796 28227797 + Frame_Shift_Ins INS - - T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr6:28227796_28227797insT ENST00000343684.3 + 1 699_700 c.647_648insT c.(646-651)tctgatfs p.D217fs ZKSCAN4_ENST00000423974.2_5'Flank NM_001007531.1 NP_001007532.1 Q5M9Q1 NKAPL_HUMAN NFKB activating protein-like 31 AATTCTGACTCTGATGATGATA 0.302000 0 SO:0001589 frameshift_variant ENST00000343684.3 0 1 hg19 CCDS34353.1 TCGA-HZ-7926-01A-11D-2154-08 NKAPL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040185.1 1 0 0 23 304 0 38 0 5.526389e-03 0 2 0 38 2 0 0 0 0 1 0.999999 23 301 0 38 2 0 0 0 0 0 0 -2.598650 1 1 0 0 1 0 1 1 2.009768 0 0.160000 1.880000 0.154589 0.870000 0.570000 1.000000 1.000000 0.860767 0.870000 1 7.100000e-01 1 RBM28 55131 broad.mit.edu 37 7 127963635 127963642 + Frame_Shift_Del DEL GCACGAAT GCACGAAT - TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr7:127963635_127963642delGCACGAAT ENST00000223073.2 - 13 1456_1463 c.1342_1349delATTCGTGC c.(1342-1350)attcgtgctfs p.IRA448fs RBM28_ENST00000415472.2_Frame_Shift_Del_p.IRA307fs|RBM28_ENST00000481788.1_5'Flank NM_018077.2 NP_060547.2 Q9NW13 RBM28_HUMAN RNA binding motif protein 28 21 CTTCGTCCCAGCACGAATCACTGCAGAA 0.471000 0 SO:0001589 frameshift_variant ENST00000223073.2 1 1 hg19 CCDS5801.1 TCGA-HZ-7926-01A-11D-2154-08 RBM28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349442.2 0 0 0 23 537 0 91 0 6.728583e-01 0 55 0 91 2 0 0 0 0 1 1.000000 29 539 0 90 2 0 0 0 0 0 0 -3.974658 1 1 0 0 1 2 2 4 2.126997 1 0.160000 1.880000 0.205749 0.590000 0.360000 1.000000 0.540000 0.658494 0.590000 0 4.600000e-01 1 CDKN2A 1029 broad.mit.edu 37 9 21971003 21971004 + Frame_Shift_Ins INS - - A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 - A - - Valid Somatic Phase_I WXS targeted Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr9:21971003_21971004insA ENST00000304494.5 - 2 624_625 c.354_355insT c.(352-357)gctgagfs p.E119fs CDKN2A_ENST00000530628.2_Stop_Codon_Ins|CDKN2A_ENST00000498124.1_Frame_Shift_Ins_p.E119fs|CDKN2A_ENST00000579755.1_Stop_Codon_Ins|CDKN2A_ENST00000494262.1_Frame_Shift_Ins_p.E68fs|CDKN2A_ENST00000497750.1_Frame_Shift_Ins_p.E68fs|CDKN2A_ENST00000578845.2_Frame_Shift_Ins_p.E68fs|CDKN2A_ENST00000446177.1_Frame_Shift_Ins_p.E119fs|CDKN2A_ENST00000361570.3_Stop_Codon_Ins|CDKN2A_ENST00000498628.2_Frame_Shift_Ins_p.E68fs|CDKN2A_ENST00000579122.1_Frame_Shift_Ins_p.E119fs|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Frame_Shift_Ins_p.E68fs NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.E119*(4)|p.E119Q(2)|p.0(1)|p.A118fs*10(1)|p.A118fs*27(1)|p.*174L(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) CCCAGCTCCTCAGCCAGGTCCA 0.728000 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1369 Whole gene deletion(1316)|Unknown(44)|Substitution - Nonsense(4)|Substitution - Missense(2)|Deletion - Frameshift(1)|Complex - frameshift(1)|Nonstop extension(1) SO:0001589 frameshift_variant ENST00000304494.5 0 1 hg19 CCDS6510.1 TCGA-HZ-7926-01A-11D-2154-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 24 191 0 23 1 9.999995e-01 3 197 0 23 2 1 1 67 585 0 514 2 1 1.000000 29 184 0 22 2 0 0 0 0 0 0 -10.824280 1 1 0 0 1 0 1 1 1.875499 1 0.160000 1.880000 0.086957 0.920000 0.700000 1.000000 0.990000 0.906810 0.920000 1 8.200000e-01 9.800000e-01 MYO3A 53904 broad.mit.edu 37 10 26243817 26243817 + Missense_Mutation SNP G G T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr10:26243817G>T ENST00000265944.5 + 4 349 c.183G>T c.(181-183)gaG>gaT p.E61D MYO3A_ENST00000543632.1_Missense_Mutation_p.E61D|MYO3A_ENST00000376302.1_Missense_Mutation_p.E61D|MYO3A_ENST00000376301.1_Missense_Mutation_p.E61D NM_017433.4 NP_059129.3 Q8NEV4 MYO3A_HUMAN myosin IIIA 146 TTGACGAAGAGATTGAAGCAG 0.323000 0 SO:0001583 missense ENST00000265944.5 1 1 hg19 CCDS7148.1 . . . . . . . . . . G 19.93 3.918823 0.73098 . . ENSG00000095777 ENST00000265944;ENST00000376302;ENST00000543632;ENST00000376301 T;T;T;T 0.66460 -0.21;-0.21;-0.21;-0.21 6.0 3.15 0.36227 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.67692 0.2920 N 0.20401 0.57 0.58432 D 0.999992 D;D;D;D 0.89917 0.957;0.965;1.0;0.978 P;D;D;D 0.97110 0.904;0.942;1.0;0.979 T 0.71122 -0.4684 10 0.72032 D 0.01 . 10.9035 0.47067 0.2392:0.0:0.7608:0.0 . 61;61;61;61 F5H0U9;Q0VD65;Q8NEV4;Q4G0X2 .;.;MYO3A_HUMAN;. D 61 ENSP00000265944:E61D;ENSP00000365479:E61D;ENSP00000445909:E61D;ENSP00000365478:E61D ENSP00000265944:E61D E + 3 2 MYO3A 26283823 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 2.128000 0.42045 1.558000 0.49541 0.643000 0.83706 GAG TCGA-HZ-7926-01A-11D-2154-08 MYO3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047259.1 1 0 0 43 454 0 93 0 0 0 1 0 93 2 0 0 0 0 0 2 1 1.000000 43 447 0 92 2 0 0 0 0 93 2 -12.591220 1 1 0 0 1 0 1 1 1.894654 1 0.160000 1.880000 0.086957 0.890000 0.690000 1.000000 0.980000 0.889672 0.890000 1 8.000000e-01 9.700000e-01 UBQLN3 50613 broad.mit.edu 37 11 5529285 5529285 + Missense_Mutation SNP G G T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr11:5529285G>T ENST00000311659.4 - 2 1651 c.1504C>A c.(1504-1506)Caa>Aaa p.Q502K HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_5'Flank|HBG2_ENST00000380252.1_5'Flank NM_017481.2 NP_059509.1 Q9H347 UBQL3_HUMAN ubiquilin 3 39 Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212) AGCTGTGGTTGTATCTCATCC 0.587000 Ovarian(72;684 1260 12332 41642 52180) 0 SO:0001583 missense ENST00000311659.4 1 1 hg19 CCDS7758.1 . . . . . . . . . . G 8.831 0.939872 0.18281 . . ENSG00000175520 ENST00000311659 T 0.35048 1.33 4.53 4.53 0.55603 . 0.461817 0.18254 N 0.146844 T 0.33089 0.0851 L 0.43152 1.355 0.21762 N 0.999559 B 0.15930 0.015 B 0.09377 0.004 T 0.20974 -1.0259 10 0.51188 T 0.08 . 15.1489 0.72681 0.0:0.0:1.0:0.0 . 502 Q9H347 UBQL3_HUMAN K 502 ENSP00000347997:Q502K ENSP00000347997:Q502K Q - 1 0 UBQLN3 5485861 0.387000 0.25188 0.402000 0.26371 0.171000 0.22731 2.771000 0.47670 2.499000 0.84300 0.655000 0.94253 CAA TCGA-HZ-7926-01A-11D-2154-08 UBQLN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000143348.1 1 0 0 23 370 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 0.999999 23 360 0 68 2 0 0 0 0 69 2 -20.000000 1 1 0 0 1 0 0 0 1.885132 1 0.160000 1.880000 0.096386 0.670000 0.440000 0.950000 0.660000 0.687317 0.670000 0 5.400000e-01 8.200000e-01 GIF 2694 broad.mit.edu 37 11 59596985 59596985 + Missense_Mutation SNP T T C TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr11:59596985T>C ENST00000257248.2 - 9 1273 c.1226A>G c.(1225-1227)cAc>cGc p.H409R GIF_ENST00000541311.1_Missense_Mutation_p.H384R NM_005142.2 NP_005133.2 P27352 IF_HUMAN gastric intrinsic factor (vitamin B synthesis) 17 Cyanocobalamin(DB00115) GGCTGTGATGTGCTCGTGGTT 0.443000 NSCLC(53;1139 1245 16872 38474 42853) 0 SO:0001583 missense ENST00000257248.2 1 1 hg19 CCDS7977.1 . . . . . . . . . . T 21.7 4.182767 0.78677 . . ENSG00000134812 ENST00000257248;ENST00000541311 T;T 0.41065 1.1;1.01 6.07 6.07 0.98685 . 0.000000 0.64402 D 0.000001 T 0.52435 0.1734 L 0.50333 1.59 0.44439 D 0.997368 D 0.71674 0.998 P 0.57283 0.817 T 0.51631 -0.8681 10 0.48119 T 0.1 -27.71 13.0268 0.58819 0.0:0.0:0.0:1.0 . 409 P27352 IF_HUMAN R 409;384 ENSP00000257248:H409R;ENSP00000440427:H384R ENSP00000257248:H409R H - 2 0 GIF 59353561 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 3.670000 0.54569 2.330000 0.79161 0.477000 0.44152 CAC TCGA-HZ-7926-01A-11D-2154-08 GIF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394497.1 1 0 0 14 213 0 36 0 0 0 1 0 36 2 0 0 0 0 0 2 1 0.999761 14 210 0 36 2 0 0 0 0 36 2 -17.797300 1 1 0 0 1 0 1 1 2.014243 0 0.160000 1.880000 0.151858 0.760000 0.440000 1.000000 1.000000 0.773338 0.760000 0 5.900000e-01 9.800000e-01 CHST11 50515 broad.mit.edu 37 12 105150940 105150940 + Missense_Mutation SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr12:105150940G>A ENST00000303694.5 + 3 857 c.418G>A c.(418-420)Ggg>Agg p.G140R CHST11_ENST00000549260.1_Missense_Mutation_p.G135R NM_018413.5 NP_060883.1 Q9NPF2 CHSTB_HUMAN carbohydrate (chondroitin 4) sulfotransferase 11 18 GGTCCTGACCGGGCGGGGGAA 0.597000 0 SO:0001583 missense ENST00000303694.5 1 1 hg19 CCDS9099.1 . . . . . . . . . . G 27.5 4.834370 0.91036 . . ENSG00000171310 ENST00000549260;ENST00000303694;ENST00000549016 T;T;T 0.73789 -0.78;-0.78;-0.78 5.51 5.51 0.81932 . 0.000000 0.85682 D 0.000000 D 0.89259 0.6664 M 0.89840 3.065 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.80764 0.994;0.994 D 0.91028 0.4862 10 0.87932 D 0 -15.1321 19.4315 0.94772 0.0:0.0:1.0:0.0 . 135;140 Q9NPF2-2;Q9NPF2 .;CHSTB_HUMAN R 135;140;100 ENSP00000450004:G135R;ENSP00000305725:G140R;ENSP00000449095:G100R ENSP00000305725:G140R G + 1 0 CHST11 103675070 1.000000 0.71417 0.928000 0.36995 0.997000 0.91878 9.869000 0.99810 2.600000 0.87896 0.655000 0.94253 GGG TCGA-HZ-7926-01A-11D-2154-08 CHST11-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000405960.2 1 0 1 22 315 0 55 1 9.649329e-01 20 61 0 55 2 0 0 0 0 0 2 1 0.999999 20 310 0 55 2 0 0 0 0 55 2 -2.774760 1 1 121412 2 34 1 0 0 0 1.983561 0 0.160000 1.880000 0.142157 0.790000 0.510000 1.000000 1.000000 0.802775 0.790000 0 6.400000e-01 9.700000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HZ-7926-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 15 108 0 27 1 9.879750e-01 10 46 0 27 2 1 1 55 498 0 353 2 1 0.999901 15 107 0 27 2 1 1 1284 6745 0 27 2 -9.284926 1 1 121404 2 44 1 1 2 3 2.049554 0 0.160000 1.880000 0.169304 0.990000 0.920000 1.000000 1.000000 0.995235 0.990000 1 9.900000e-01 1 PABPC3 5042 broad.mit.edu 37 13 25671664 25671664 + Missense_Mutation SNP A A C TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr13:25671664A>C ENST00000281589.3 + 1 1365 c.1328A>C c.(1327-1329)aAt>aCt p.N443T NM_030979.2 NP_112241.2 Q9H361 PABP3_HUMAN poly(A) binding protein, cytoplasmic 3 47 Lung SC(185;0.0225)|Breast(139;0.0602) CCATTCCAAAATAAGCCCAGT 0.507000 0 SO:0001583 missense ENST00000281589.3 1 1 hg19 CCDS9311.1 . . . . . . . . . . A 3.856 -0.030769 0.07543 . . ENSG00000151846 ENST00000281589 T 0.27557 1.66 0.875 0.875 0.19130 . 0.000000 0.50627 U 0.000110 T 0.21841 0.0526 L 0.52011 1.625 0.44899 D 0.997918 B 0.02656 0.0 B 0.10450 0.005 T 0.05500 -1.0881 10 0.22706 T 0.39 . 5.8995 0.18957 1.0:0.0:0.0:0.0 . 443 Q9H361 PABP3_HUMAN T 443 ENSP00000281589:N443T ENSP00000281589:N443T N + 2 0 PABPC3 24569664 1.000000 0.71417 0.963000 0.40424 0.160000 0.22226 3.947000 0.56652 0.632000 0.30432 0.260000 0.18958 AAT TCGA-HZ-7926-01A-11D-2154-08 PABPC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044220.2 1 0 0 48 746 0 143 0 0 0 1 0 143 2 0 0 0 0 0 2 1 1.000000 47 645 0 143 2 0 0 0 0 143 2 -20.000000 1 1 0 0 1 0 1 1 1.876293 1 0.160000 1.880000 0.086957 0.680000 0.510000 0.880000 0.690000 0.697811 0.680000 0 5.900000e-01 7.900000e-01 FLT3 2322 broad.mit.edu 37 13 28622533 28622533 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr13:28622533C>T ENST00000241453.7 - 9 1165 c.1084G>A c.(1084-1086)Gac>Aac p.D362N FLT3_ENST00000380982.4_Missense_Mutation_p.D362N|FLT3_ENST00000537084.1_Missense_Mutation_p.D362N NM_004119.2 NP_004110.2 P36888 FLT3_HUMAN fms-related tyrosine kinase 3 12390 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0156)|Ovarian(182;0.0392) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268) TCATATTGGTCAATTTCATAA 0.323000 Mis, O AML, ALL Dom yes 13 13q12 2322 fms-related tyrosine kinase 3 L 0 SO:0001583 missense ENST00000241453.7 1 1 hg19 CCDS31953.1 . . . . . . . . . . C 15.65 2.896911 0.52121 . . ENSG00000122025 ENST00000241453;ENST00000380982;ENST00000537084 T;T;T 0.76060 -0.92;-0.99;-0.7 5.45 5.45 0.79879 Immunoglobulin-like fold (1); 0.263771 0.32901 N 0.005511 T 0.69931 0.3166 L 0.27053 0.805 0.34801 D 0.736766 D;D 0.58620 0.966;0.983 P;P 0.51742 0.678;0.58 T 0.69412 -0.5152 10 0.10111 T 0.7 . 17.4634 0.87626 0.0:1.0:0.0:0.0 . 362;362 P36888-2;P36888 .;FLT3_HUMAN N 362 ENSP00000241453:D362N;ENSP00000370369:D362N;ENSP00000438139:D362N ENSP00000241453:D362N D - 1 0 FLT3 27520533 1.000000 0.71417 1.000000 0.80357 0.735000 0.41995 3.429000 0.52800 2.572000 0.86782 0.462000 0.41574 GAC TCGA-HZ-7926-01A-11D-2154-08 FLT3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000044319.2 1 0 1 32 214 0 55 0 8.976144e-02 0 4 0 55 2 0 0 0 0 0 2 1 1.000000 31 212 0 55 2 0 0 0 0 55 2 -20.000000 1 1 121412 2 31 1 0 1 1 1.876293 1 0.160000 1.880000 0.086957 0.950000 0.780000 1.000000 0.990000 0.939454 0.950000 1 8.800000e-01 9.900000e-01 ATL1 51062 broad.mit.edu 37 14 51094836 51094836 + Nonsense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr14:51094836C>T ENST00000358385.6 + 12 1448 c.1207C>T c.(1207-1209)Cga>Tga p.R403* ATL1_ENST00000354525.4_Nonsense_Mutation_p.R403*|ATL1_ENST00000357032.3_Nonsense_Mutation_p.R403*|ATL1_ENST00000441560.2_Nonsense_Mutation_p.R403* NM_015915.4 NP_056999.2 Q8WXF7 ATLA1_HUMAN atlastin GTPase 1 18 GAAGCTATTCCGAGGGGTGAA 0.443000 0 SO:0001587 stop_gained ENST00000358385.6 0 1 hg19 CCDS9700.1 . . . . . . . . . . C 40 8.204160 0.98704 . . ENSG00000198513 ENST00000441560;ENST00000358385;ENST00000357032;ENST00000354525 . . . 5.91 5.91 0.95273 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.12430 T 0.62 -6.6736 19.2865 0.94077 0.0:1.0:0.0:0.0 . . . . X 403 . ENSP00000346522:R403X R + 1 2 ATL1 50164586 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 4.936000 0.63506 2.802000 0.96397 0.655000 0.94253 CGA TCGA-HZ-7926-01A-11D-2154-08 ATL1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000276884.2 1 0 0 21 319 0 71 0 7.427205e-01 1 41 0 71 2 0 0 0 0 0 2 1 0.999997 19 315 0 71 2 0 0 0 0 71 2 -2.598117 1 1 0 0 1 0 1 1 2.000627 0 0.160000 1.880000 0.151858 0.760000 0.490000 1.000000 1.000000 0.774580 0.760000 0 6.100000e-01 9.400000e-01 KCNK13 56659 broad.mit.edu 37 14 90650874 90650874 + Nonsense_Mutation SNP G G T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr14:90650874G>T ENST00000282146.4 + 2 1195 c.754G>T c.(754-756)Gag>Tag p.E252* NM_022054.2 NP_071337.2 Q9HB14 KCNKD_HUMAN potassium channel, subfamily K, member 13 25 all_cancers(154;0.186) CGCCCACTATGAGAGCCAAGG 0.493000 0 SO:0001587 stop_gained ENST00000282146.4 0 1 hg19 CCDS9889.1 . . . . . . . . . . G 32 5.158982 0.94686 . . ENSG00000152315 ENST00000282146 . . . 5.42 2.49 0.30216 . 0.955768 0.08571 N 0.926120 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.11794 T 0.64 . 8.8689 0.35303 0.1376:0.1231:0.7393:0.0 . . . . X 252 . ENSP00000282146:E252X E + 1 0 KCNK13 89720627 0.999000 0.42202 0.003000 0.11579 0.127000 0.20565 4.148000 0.58085 0.655000 0.30866 -0.137000 0.14449 GAG TCGA-HZ-7926-01A-11D-2154-08 KCNK13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411251.1 1 0 0 31 472 0 67 0 1.184349e-02 0 3 0 67 2 0 0 0 0 0 2 1 1.000000 30 465 0 66 2 0 0 0 0 67 2 -20.000000 1 1 0 0 1 0 1 1 2.015903 0 0.160000 1.880000 0.155949 0.760000 0.530000 1.000000 1.000000 0.775898 0.760000 0 6.400000e-01 9.100000e-01 CSK 1445 broad.mit.edu 37 15 75091650 75091650 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr15:75091650C>T ENST00000220003.9 + 5 1009 c.280C>T c.(280-282)Cgg>Tgg p.R94W CSK_ENST00000567571.1_Missense_Mutation_p.R94W|CSK_ENST00000309470.9_Missense_Mutation_p.R94W|CSK_ENST00000439220.2_Missense_Mutation_p.R94W NM_004383.2 NP_004374.1 P41240 CSK_HUMAN c-src tyrosine kinase 3 GCAGGCTGAGCGGCTTCTGTA 0.637000 0 SO:0001583 missense ENST00000220003.9 1 1 hg19 CCDS10269.1 . . . . . . . . . . C 21.0 4.086457 0.76642 . . ENSG00000103653 ENST00000220003;ENST00000439220;ENST00000309470 D;D;D 0.89875 -2.58;-2.58;-2.58 4.63 2.6 0.31112 SH2 motif (5); 0.068217 0.64402 D 0.000020 D 0.93148 0.7818 M 0.85373 2.75 0.80722 D 1 D 0.69078 0.997 P 0.58928 0.848 D 0.93959 0.7239 10 0.87932 D 0 -21.5651 13.0337 0.58859 0.3937:0.6063:0.0:0.0 . 94 P41240 CSK_HUMAN W 94 ENSP00000220003:R94W;ENSP00000414764:R94W;ENSP00000438808:R94W ENSP00000220003:R94W R + 1 2 CSK 72878703 1.000000 0.71417 1.000000 0.80357 0.808000 0.45660 1.164000 0.31810 1.148000 0.42385 -0.500000 0.04577 CGG TCGA-HZ-7926-01A-11D-2154-08 CSK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286398.2 1 0 0 15 238 0 37 1 9.996585e-01 10 207 0 37 2 0 0 0 0 0 2 1 0.999863 15 232 0 36 2 0 0 0 0 37 2 -17.928910 1 1 0 0 1 0 2 2 1.918771 0 0.160000 1.880000 0.160000 0.750000 0.440000 1.000000 1.000000 0.758259 0.750000 0 5.800000e-01 9.600000e-01 TSC2 7249 broad.mit.edu 37 16 2137908 2137908 + Silent SNP C C T rs45467993 TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr16:2137908C>T ENST00000219476.3 + 39 5664 c.5034C>T c.(5032-5034)taC>taT p.Y1678Y TSC2_ENST00000353929.4_Silent_p.Y1635Y|MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000439673.2_Silent_p.Y1575Y|TSC2_ENST00000401874.2_Silent_p.Y1611Y|TSC2_ENST00000350773.4_Silent_p.Y1655Y|TSC2_ENST00000382538.6_Silent_p.Y1563Y|TSC2_ENST00000568454.1_Silent_p.Y1622Y NM_000548.3 NP_000539.2 P49815 TSC2_HUMAN tuberous sclerosis 2 56 Hepatocellular(780;0.0202) CGCTGGACTACGAGTGCAACC 0.642000 D, Mis, N, F, S hamartoma, renal cell Tuberous Sclerosis yes Rec Tuberous sclerosis 2 16 16p13.3 7249 tuberous sclerosis 2 gene E, O 0 GRCh37 CM054870 TSC2 M rs45467993 SO:0001819 synonymous_variant Familial Cancer Database TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease ENST00000219476.3 1 1 hg19 CCDS10458.1 TCGA-HZ-7926-01A-11D-2154-08 TSC2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250657.2 1 0 0 11 229 0 54 1 9.701751e-01 12 115 0 54 2 0 0 0 0 0 2 1 0.998332 10 227 0 53 2 0 0 0 0 54 2 -13.034440 1 1 121206 4 37 1 1 2 3 2.020720 0 0.160000 1.880000 0.163347 0.590000 0.310000 1.000000 0.560000 0.622124 0.590000 0 4.300000e-01 8.100000e-01 ZNF75A 7627 broad.mit.edu 37 16 3367798 3367798 + Missense_Mutation SNP A A G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr16:3367798A>G ENST00000574298.1 + 6 1293 c.820A>G c.(820-822)Act>Gct p.T274A ZNF75A_ENST00000498240.2_3'UTR NM_153028.2 NP_694573.1 Q96N20 ZN75A_HUMAN zinc finger protein 75a 12 GCAGCCATATACTTGTAGCAT 0.463000 0 SO:0001583 missense ENST00000574298.1 1 1 hg19 CCDS10501.1 . . . . . . . . . . A 3.920 -0.018269 0.07681 . . ENSG00000162086 ENST00000293995 . . . 4.46 -2.76 0.05896 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 1.109970 0.06937 N 0.812053 T 0.16385 0.0394 N 0.04297 -0.235 0.09310 N 1 B 0.06786 0.001 B 0.11329 0.006 T 0.25847 -1.0120 9 0.51188 T 0.08 . 6.3677 0.21463 0.2835:0.0:0.0837:0.6328 . 274 Q96N20 ZN75A_HUMAN A 274 . ENSP00000293995:T274A T + 1 0 ZNF75A 3307799 0.000000 0.05858 0.000000 0.03702 0.771000 0.43674 -2.209000 0.01228 -0.674000 0.05253 0.455000 0.32223 ACT TCGA-HZ-7926-01A-11D-2154-08 ZNF75A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251506.2 1 0 1 27 495 0 92 1 6.519972e-01 8 34 0 92 2 0 0 0 0 0 2 1 1.000000 27 488 0 92 2 0 0 0 0 92 2 -20.000000 1 1 0 0 1 1 2 3 2.020720 0 0.160000 1.880000 0.163347 0.650000 0.440000 1.000000 0.640000 0.676459 0.650000 0 5.400000e-01 8.000000e-01 MED1 5469 broad.mit.edu 37 17 37565585 37565585 + Missense_Mutation SNP T T G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr17:37565585T>G ENST00000300651.6 - 17 3112 c.2889A>C c.(2887-2889)ttA>ttC p.L963F MED1_ENST00000394287.3_Intron NM_004774.3 NP_004765.2 O95243 MBD4_HUMAN mediator complex subunit 1 59 Ovarian(249;1.78e-06)|Lung SC(565;0.0262) Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146) TTTCTTTCCCTAAGTCCCCAG 0.483000 HNSCC(31;0.082) Pancreas(21;279 768 2492 4877 24026) 0 SO:0001583 missense ENST00000300651.6 1 1 hg19 CCDS11336.1 . . . . . . . . . . T 12.45 1.941018 0.34283 . . ENSG00000125686 ENST00000300651 T 0.33865 1.39 5.65 3.4 0.38934 . . . . . T 0.16685 0.0401 N 0.12182 0.205 0.53688 D 0.999973 B 0.06786 0.001 B 0.06405 0.002 T 0.05971 -1.0853 9 0.09590 T 0.72 -0.6855 7.2644 0.26222 0.0:0.2903:0.0:0.7097 . 963 Q15648 MED1_HUMAN F 963 ENSP00000300651:L963F ENSP00000300651:L963F L - 3 2 MED1 34819111 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 0.767000 0.26575 1.165000 0.42670 0.533000 0.62120 TTA TCGA-HZ-7926-01A-11D-2154-08 MED1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256943.3 1 0 0 11 216 0 53 1 7.047300e-01 4 45 0 53 2 0 0 0 0 0 2 1 0.998249 11 211 0 53 2 0 0 0 0 53 2 -4.324474 1 1 0 0 1 1 2 3 2.020617 0 0.160000 1.880000 0.163347 0.630000 0.330000 1.000000 1.000000 0.653078 0.630000 0 4.600000e-01 8.500000e-01 TRMT1 55621 broad.mit.edu 37 19 13227177 13227177 + Missense_Mutation SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr19:13227177G>A ENST00000592062.1 - 3 607 c.37C>T c.(37-39)Cgc>Tgc p.R13C TRMT1_ENST00000592892.1_5'UTR|TRMT1_ENST00000357720.4_Missense_Mutation_p.R13C|NACC1_ENST00000292431.4_5'Flank|TRMT1_ENST00000437766.1_Missense_Mutation_p.R13C|TRMT1_ENST00000221504.8_Missense_Mutation_p.R13C Q9NXH9 TRM1_HUMAN tRNA methyltransferase 1 homolog (S. cerevisiae) 14 OV - Ovarian serous cystadenocarcinoma(19;6.08e-22) CGGGCGGAGCGGAAAGTGAGG 0.657000 0 SO:0001583 missense ENST00000592062.1 1 1 hg19 CCDS12293.1 . . . . . . . . . . G 13.97 2.396554 0.42512 . . ENSG00000104907 ENST00000357720;ENST00000437766;ENST00000221504 . . . 5.28 3.15 0.36227 . 0.180442 0.31772 N 0.007085 T 0.34366 0.0895 L 0.27053 0.805 0.19300 N 0.999976 D;D 0.71674 0.998;0.997 P;P 0.53861 0.736;0.548 T 0.10064 -1.0646 9 0.72032 D 0.01 -15.9499 8.3666 0.32391 0.1833:0.0:0.8167:0.0 . 13;13 Q9NXH9-2;Q9NXH9 .;TRM1_HUMAN C 13 . ENSP00000221504:R13C R - 1 0 TRMT1 13088177 0.973000 0.33851 0.106000 0.21319 0.003000 0.03518 2.511000 0.45476 0.728000 0.32382 -0.140000 0.14226 CGC TCGA-HZ-7926-01A-11D-2154-08 TRMT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452780.2 1 0 0 17 339 0 58 0 6.507543e-01 0 45 0 58 2 0 0 0 0 0 2 1 0.999961 17 331 0 58 2 0 0 0 0 58 2 -18.077450 1 1 0 0 1 0 1 1 2.016097 0 0.160000 1.880000 0.155949 0.590000 0.360000 0.890000 0.580000 0.615449 0.590000 0 4.700000e-01 7.500000e-01 CABP5 56344 broad.mit.edu 37 19 48537514 48537514 + Missense_Mutation SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr19:48537514G>A ENST00000293255.2 - 5 584 c.454C>T c.(454-456)Cgg>Tgg p.R152W NM_019855.4 NP_062829.1 Q9NP86 CABP5_HUMAN calcium binding protein 5 11 all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203) TCAGCCTCCCGGACAACCTCA 0.617000 0 SO:0001583 missense ENST00000293255.2 1 1 hg19 CCDS12709.1 . . . . . . . . . . G 21.8 4.197685 0.79015 . . ENSG00000105507 ENST00000293255 T 0.73469 -0.75 5.01 5.01 0.66863 EF-hand-like domain (1); 0.424187 0.24642 N 0.036784 D 0.82393 0.5027 M 0.79926 2.475 0.42202 D 0.991774 D 0.54207 0.965 P 0.51777 0.679 D 0.85894 0.1430 10 0.87932 D 0 -0.4457 16.1949 0.82021 0.0:0.0:1.0:0.0 . 152 Q9NP86 CABP5_HUMAN W 152 ENSP00000293255:R152W ENSP00000293255:R152W R - 1 2 CABP5 53229326 0.002000 0.14202 0.723000 0.30687 0.981000 0.71138 0.819000 0.27308 2.509000 0.84616 0.561000 0.74099 CGG TCGA-HZ-7926-01A-11D-2154-08 CABP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465212.1 1 0 1 26 214 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1.000000 24 209 0 46 2 0 0 0 0 46 2 -3.318835 1 1 121410 1 33 1 0 1 1 2.010911 0 0.160000 1.880000 0.154589 0.990000 0.900000 1.000000 1.000000 0.994568 0.990000 1 9.900000e-01 1 ZSCAN1 284312 broad.mit.edu 37 19 58549468 58549468 + Silent SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr19:58549468C>T ENST00000282326.1 + 3 511 c.264C>T c.(262-264)ggC>ggT p.G88G ZSCAN1_ENST00000391700.1_Silent_p.G88G|ZSCAN1_ENST00000601162.1_Silent_p.G88G NM_182572.3 NP_872378.3 Q8NBB4 ZSCA1_HUMAN zinc finger and SCAN domain containing 1 48 Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157) AGTTCCTGGGCGCGCTGCCCA 0.697000 0 SO:0001819 synonymous_variant ENST00000282326.1 1 1 hg19 CCDS12969.1 TCGA-HZ-7926-01A-11D-2154-08 ZSCAN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466427.1 1 0 0 9 116 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.994366 9 114 0 29 2 0 0 0 0 30 2 -13.570830 1 1 120990 2 30 1 1 2 3 2.047905 0 0.160000 1.880000 0.171271 0.980000 0.470000 1.000000 1.000000 0.880941 0.980000 1 6.900000e-01 1 CLEC4M 10332 broad.mit.edu 37 19 7833838 7833838 + Silent SNP C C A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr19:7833838C>A ENST00000327325.5 + 7 1282 c.1164C>A c.(1162-1164)atC>atA p.I388I CLEC4M_ENST00000597522.1_3'UTR|CLEC4M_ENST00000248228.4_Silent_p.I366I|CLEC4M_ENST00000595496.1_Silent_p.I252I|CLEC4M_ENST00000596363.1_3'UTR|CLEC4M_ENST00000596707.1_Silent_p.I321I|CLEC4M_ENST00000357361.2_3'UTR|CLEC4M_ENST00000359059.5_Silent_p.I321I|CLEC4M_ENST00000334806.5_Silent_p.I337I|CLEC4M_ENST00000394122.2_Silent_p.I376I NM_001144909.1|NM_014257.4 NP_001138381.1|NP_055072.3 Q9H2X3 CLC4M_HUMAN C-type lectin domain family 4, member M 26 ATTACTGGATCTGCAAAAAGC 0.498000 0 SO:0001819 synonymous_variant ENST00000327325.5 1 1 hg19 CCDS12187.1 TCGA-HZ-7926-01A-11D-2154-08 CLEC4M-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000461161.1 1 0 0 24 387 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1.000000 24 380 0 68 2 0 0 0 0 68 2 -20.000000 1 1 0 0 1 0 1 1 2.012408 0 0.160000 1.880000 0.153226 0.720000 0.470000 1.000000 1.000000 0.737314 0.720000 0 5.900000e-01 8.800000e-01 MUC1 4582 broad.mit.edu 37 1 155160807 155160807 + Silent SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:155160807G>A ENST00000368395.1 - 3 791 c.720C>T c.(718-720)agC>agT p.S240S RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000462215.1_5'UTR|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000342482.4_Intron|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000368398.3_Intron NM_001204285.1|NM_001204286.1 NP_001191214.1|NP_001191215.1 P15941 MUC1_HUMAN mucin 1, cell surface associated 10 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) GAGGTACCGTGCTATGGTGAG 0.507000 T IGH@ B-NHL Dom yes 1 1q21 4582 mucin 1, transmembrane L 0 SO:0001819 synonymous_variant ENST00000368395.1 1 1 hg19 CCDS55640.1 TCGA-HZ-7926-01A-11D-2154-08 MUC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000086735.1 1 0 0 34 236 0 45 1 1 624 5067 0 45 2 0 0 0 0 0 2 1 1.000000 33 232 0 45 2 0 0 0 0 45 2 -15.324850 1 1 0 0 1 1 2 3 2.111113 1 0.160000 1.880000 0.181606 0.990000 0.990000 1.000000 1.000000 0.999867 0.990000 1 9.900000e-01 1 OR10K1 391109 broad.mit.edu 37 1 158435756 158435756 + Silent SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:158435756C>T ENST00000289451.2 + 1 485 c.405C>T c.(403-405)ctC>ctT p.L135L NM_001004473.1 NP_001004473.1 Q8NGX5 O10K1_HUMAN olfactory receptor, family 10, subfamily K, member 1 27 all_hematologic(112;0.0378) ACTCAGTGCTCATGGGACATG 0.547000 0 SO:0001819 synonymous_variant ENST00000289451.2 1 1 hg19 CCDS30897.1 TCGA-HZ-7926-01A-11D-2154-08 OR10K1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046367.1 1 0 1 97 758 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 1.000000 94 724 0 124 2 0 0 0 0 131 2 -3.318794 1 1 0 0 1 1 2 3 2.111113 1 0.160000 1.880000 0.181606 0.990000 0.990000 1.000000 1.000000 0.999997 0.990000 1 9.900000e-01 1 DDR2 4921 broad.mit.edu 37 1 162688902 162688902 + Missense_Mutation SNP A A G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:162688902A>G ENST00000367922.3 + 4 487 c.49A>G c.(49-51)Atc>Gtc p.I17V DDR2_ENST00000367921.3_Missense_Mutation_p.I17V NM_001014796.1 NP_001014796.1 Q16832 DDR2_HUMAN discoidin domain receptor tyrosine kinase 2 7 all_hematologic(112;0.115) BRCA - Breast invasive adenocarcinoma(70;0.113) Regorafenib(DB08896) GCTGCTGCCTATCTTGAGTTC 0.438000 NSCLC(161;314 2006 8283 19651 23192) 0 SO:0001583 missense ENST00000367922.3 1 1 hg19 CCDS1241.1 . . . . . . . . . . A 2.456 -0.325175 0.05350 . . ENSG00000162733 ENST00000446985;ENST00000415555;ENST00000542391;ENST00000367922;ENST00000367921 D;D;D;D 0.97642 -4.2;-4.47;-1.68;-1.68 4.25 -2.92 0.05615 . 0.491466 0.19764 N 0.106619 T 0.82226 0.4991 N 0.25647 0.755 0.26350 N 0.977213 B 0.06786 0.001 B 0.04013 0.001 T 0.68622 -0.5360 9 0.19590 T 0.45 . 2.942 0.05834 0.3119:0.45:0.0921:0.146 . 17 Q16832 DDR2_HUMAN V 17 ENSP00000400309:I17V;ENSP00000391310:I17V;ENSP00000356899:I17V;ENSP00000356898:I17V ENSP00000356898:I17V I + 1 0 DDR2 160955526 0.076000 0.21285 0.303000 0.25071 0.931000 0.56810 -0.197000 0.09518 -0.682000 0.05197 -0.605000 0.04089 ATC TCGA-HZ-7926-01A-11D-2154-08 DDR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083213.2 1 0 1 48 393 0 82 0 7.319722e-01 0 23 0 82 2 0 0 0 0 0 2 1 1.000000 48 387 0 81 2 0 0 0 0 82 2 -20.000000 1 1 0 0 1 1 2 3 2.111113 1 0.160000 1.880000 0.181606 0.990000 0.990000 1.000000 1.000000 0.999591 0.990000 1 9.900000e-01 1 NBPF1 55672 broad.mit.edu 37 1 16918794 16918794 + Translation_Start_Site SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:16918794G>A ENST00000430580.2 - 0 712 NM_017940.3 NP_060410.2 Q3BBV0 NBPF1_HUMAN neuroblastoma breakpoint family, member 1 TGTGGCCAGCGTGCCAGGTAA 0.502000 0 ENST00000430580.2 0 1 hg19 TCGA-HZ-7926-01A-11D-2154-08 NBPF1-005 NOVEL upstream_uORF|basic|appris_principal protein_coding protein_coding OTTHUMT00000106436.3 0 0 0 7 69 0 10 1 8.157118e-01 2 31 0 10 2 0 0 0 0 0 2 1 0.964224 6 56 0 10 2 0 0 0 0 10 2 -2.356422 0 1 0 0 1 0.160000 1.880000 0 0 MIA3 375056 broad.mit.edu 37 1 222835427 222835427 + Nonsense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:222835427C>T ENST00000344922.5 + 25 5168 c.5143C>T c.(5143-5145)Cga>Tga p.R1715* RP11-378J18.8_ENST00000608771.1_RNA|MIA3_ENST00000340535.7_Nonsense_Mutation_p.R593*|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Nonsense_Mutation_p.R1715* NM_198551.2 NP_940953.2 Q5JRA6 MIA3_HUMAN melanoma inhibitory activity family, member 3 80 ACCTCATCCTCGATGGTCAGC 0.443000 0 SO:0001587 stop_gained ENST00000344922.5 0 1 hg19 CCDS41470.1 . . . . . . . . . . C 42 9.607272 0.99217 . . ENSG00000154305 ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471 . . . 5.14 1.59 0.23543 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 13.457 0.61204 0.5192:0.4808:0.0:0.0 . . . . X 1715;1715;1656;593;593 . ENSP00000284471:R593X R + 1 2 MIA3 220902050 0.006000 0.16342 0.004000 0.12327 0.130000 0.20726 0.825000 0.27393 0.624000 0.30286 -0.181000 0.13052 CGA TCGA-HZ-7926-01A-11D-2154-08 MIA3-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000091489.4 1 0 1 43 310 0 63 1 9.999948e-01 5 128 0 63 2 0 0 0 0 0 2 1 1.000000 43 308 0 62 2 0 0 0 0 63 2 -3.017792 1 1 0 0 1 1 2 3 2.072648 0 0.160000 1.880000 0.173879 0.990000 0.990000 1.000000 1.000000 0.999903 0.990000 1 9.900000e-01 1 NLRP3 114548 broad.mit.edu 37 1 247592989 247592989 + Silent SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:247592989G>A ENST00000336119.3 + 4 3005 c.2259G>A c.(2257-2259)ctG>ctA p.L753L NLRP3_ENST00000391827.2_Intron|NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000391828.3_Silent_p.L753L|NLRP3_ENST00000366496.2_Silent_p.L753L|NLRP3_ENST00000366497.2_Silent_p.L753L NM_001127462.2|NM_001243133.1|NM_004895.4 NP_001120934.1|NP_001230062.1|NP_004886.3 Q96P20 NALP3_HUMAN NLR family, pyrin domain containing 3 142 all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.0172) OV - Ovarian serous cystadenocarcinoma(106;0.0141) ACAATTCTCTGGGGGACCCAG 0.527000 0 SO:0001819 synonymous_variant ENST00000336119.3 1 1 hg19 CCDS1632.1 TCGA-HZ-7926-01A-11D-2154-08 NLRP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097740.1 1 0 0 22 386 0 65 0 2.896669e-02 0 5 0 65 2 0 0 0 0 0 2 1 0.999999 22 383 0 65 2 0 0 0 0 65 2 -2.804967 1 1 0 0 1 1 2 3 2.072648 0 0.160000 1.880000 0.173879 0.720000 0.450000 1.000000 1.000000 0.749587 0.720000 0 5.700000e-01 1 CCDC18 343099 broad.mit.edu 37 1 93672842 93672842 + Nonsense_Mutation SNP G G T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr1:93672842G>T ENST00000343253.7 + 9 1598 c.1096G>T c.(1096-1098)Gaa>Taa p.E366* CCDC18_ENST00000401026.3_Nonsense_Mutation_p.E366*|CCDC18_ENST00000557479.1_Nonsense_Mutation_p.E484*|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000338949.4_Nonsense_Mutation_p.E165* Q5T9S5 CCD18_HUMAN coiled-coil domain containing 18 42 all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203) TGAAAACCGAGAATTAAAGGT 0.333000 0 SO:0001587 stop_gained ENST00000343253.7 0 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 37|37 5.984821|5.984821 0.97173|0.97173 .|. .|. ENSG00000122483|ENSG00000122483 ENST00000370276|ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267 .|. .|. .|. 5.83|5.83 5.83|5.83 0.93111|0.93111 .|. 0.164121|0.164121 0.52532|0.52532 D|D 0.000077|0.000077 T|. 0.59783|. 0.2219|. .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. T|. 0.53085|. -0.8488|. 5|. .|0.22109 .|T .|0.4 .|. 18.2995|18.2995 0.90158|0.90158 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|. .|. .|. D|X 419|366;366;484;165;86 .|. .|ENSP00000344380:E165X E|E +|+ 3|1 2|0 CCDC18|CCDC18 93445430|93445430 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.993000|0.993000 0.82548|0.82548 4.263000|4.263000 0.58853|0.58853 2.763000|2.763000 0.94921|0.94921 0.555000|0.555000 0.69702|0.69702 GAG|GAA TCGA-HZ-7926-01A-11D-2154-08 CCDC18-008 PUTATIVE basic|appris_principal|exp_conf protein_coding protein_coding OTTHUMT00000382327.1 1 0 0 14 235 0 41 0 2.062390e-02 0 3 0 41 2 0 0 0 0 0 2 1 0.999745 14 230 0 41 2 0 0 0 0 41 2 -17.022350 1 1 0 0 1 0 0 0 1.903721 0 0.160000 1.880000 0.105622 0.650000 0.380000 1.000000 1.000000 0.673774 0.650000 0 5.000000e-01 8.400000e-01 FOXS1 2307 broad.mit.edu 37 20 30432695 30432695 + Silent SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr20:30432695C>T ENST00000375978.3 - 1 725 c.651G>A c.(649-651)gcG>gcA p.A217A NM_004118.3 NP_004109.1 O43638 FOXS1_HUMAN forkhead box S1 9 GAAAGCCAAACGCTGGGCATG 0.617000 0 SO:0001819 synonymous_variant ENST00000375978.3 1 1 hg19 CCDS13192.1 TCGA-HZ-7926-01A-11D-2154-08 FOXS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078560.2 1 0 1 34 267 0 48 1 9.605592e-01 8 36 0 48 2 0 0 0 0 0 2 1 1.000000 33 263 0 47 2 0 0 0 0 48 2 -20.000000 1 1 0 0 1 1 2 3 2.027936 0 0.160000 1.880000 0.164678 0.990000 0.990000 1.000000 1.000000 0.998743 0.990000 1 9.900000e-01 1 MATN4 8785 broad.mit.edu 37 20 43926857 43926857 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr20:43926857C>T ENST00000372754.1 - 7 1510 c.1502G>A c.(1501-1503)cGc>cAc p.R501H MATN4_ENST00000537548.1_Missense_Mutation_p.R460H|MATN4_ENST00000353917.5_Missense_Mutation_p.R378H|MATN4_ENST00000372751.4_Missense_Mutation_p.R311H|MATN4_ENST00000372756.1_Missense_Mutation_p.R460H|MATN4_ENST00000342716.4_Missense_Mutation_p.R460H|MATN4_ENST00000360607.6_Missense_Mutation_p.R419H O95460 MATN4_HUMAN matrilin 4 27 Myeloproliferative disorder(115;0.0122) ATCCTGGGAGCGGCCATCCGT 0.672000 0 SO:0001583 missense ENST00000372754.1 1 1 hg19 . . . . . . . . . . C 33 5.239741 0.95240 . . ENSG00000124159 ENST00000372753;ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751 D;D;D;D;D;D;D;D 0.83673 -1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75 5.46 5.46 0.80206 . 0.000000 0.44902 D 0.000411 D 0.92456 0.7605 M 0.86343 2.81 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.97;0.999 D 0.93464 0.6813 10 0.87932 D 0 . 18.3439 0.90314 0.0:1.0:0.0:0.0 . 378;419;460 A6NNA4;O95460-4;O95460-2 .;.;. H 311;501;460;378;419;460;460;501;311 ENSP00000361839:R311H;ENSP00000361840:R501H;ENSP00000361842:R460H;ENSP00000243983:R378H;ENSP00000353819:R419H;ENSP00000343164:R460H;ENSP00000440328:R460H;ENSP00000361837:R311H ENSP00000255132:R501H R - 2 0 MATN4 43360271 1.000000 0.71417 1.000000 0.80357 0.960000 0.62799 7.759000 0.85235 2.559000 0.86315 0.644000 0.83932 CGC TCGA-HZ-7926-01A-11D-2154-08 MATN4-002 KNOWN non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000080335.1 1 0 0 32 381 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 32 375 0 72 2 0 0 0 0 73 2 -9.181191 1 1 0 0 1 1 2 3 2.027936 0 0.160000 1.880000 0.164678 0.980000 0.680000 1.000000 1.000000 0.931718 0.980000 1 8.200000e-01 1 MAP2 4133 broad.mit.edu 37 2 210559008 210559008 + Missense_Mutation SNP C C T rs146432517 TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr2:210559008C>T ENST00000360351.4 + 7 2620 c.2114C>T c.(2113-2115)cCg>cTg p.P705L MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.P701L|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron NM_002374.3 NP_002365.3 P11137 MTAP2_HUMAN microtubule-associated protein 2 p.P705L(1) 124 Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202) Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229) ATCAATTTGCCGATGTCTTGC 0.438000 Pancreas(27;423 979 28787 29963) 1 Substitution - Missense(1) SO:0001583 missense ENST00000360351.4 1 1 hg19 CCDS2384.1 . . . . . . . . . . C 22.8 4.342024 0.81911 0.0 1.16E-4 ENSG00000078018 ENST00000360351;ENST00000447185 T;T 0.28666 1.6;1.6 6.06 6.06 0.98353 MAP2/Tau projection (1); 0.000000 0.64402 D 0.000006 T 0.55832 0.1945 L 0.59436 1.845 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.76071 0.977;0.987 T 0.52682 -0.8543 10 0.87932 D 0 -13.3508 20.6244 0.99512 0.0:1.0:0.0:0.0 . 701;705 P11137-3;P11137 .;MAP2_HUMAN L 705;701 ENSP00000353508:P705L;ENSP00000392164:P701L ENSP00000353508:P705L P + 2 0 MAP2 210267253 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.238000 0.78173 2.879000 0.98667 0.650000 0.86243 CCG TCGA-HZ-7926-01A-11D-2154-08 MAP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256521.2 1 0 1 117 930 0 164 0 0 0 0 164 2 0 0 0 0 0 2 1 1.000000 116 909 0 163 2 0 0 0 0 164 2 -2.966611 1 1 0 0 1 1 2 3 2.102214 1 0.160000 1.880000 0.179688 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 ERBB4 2066 broad.mit.edu 37 2 212589903 212589903 + Silent SNP A A G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr2:212589903A>G ENST00000342788.4 - 6 949 c.639T>C c.(637-639)tgT>tgC p.C213C ERBB4_ENST00000484474.1_5'UTR|ERBB4_ENST00000402597.1_Silent_p.C213C|ERBB4_ENST00000436443.1_Silent_p.C213C NM_005235.2 NP_005226.1 Q15303 ERBB4_HUMAN v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4 179 Renal(323;0.06)|Lung NSC(271;0.197) Afatinib(DB08916) ATTGTTCTGCACACACCGTCC 0.507000 TSP Lung(8;0.080) 0 SO:0001819 synonymous_variant ENST00000342788.4 1 1 hg19 CCDS2394.1 . . . . . . . . . . A 11.01 1.513447 0.27123 . . ENSG00000178568 ENST00000260943 . . . 5.73 3.36 0.38483 . . . . . T 0.57873 0.2083 . . . 0.80722 D 1 . . . . . . T 0.53365 -0.8449 4 . . . . 8.2245 0.31560 0.7842:0.0:0.2158:0.0 . . . . A 213 . . V - 2 0 ERBB4 212298148 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 1.777000 0.38604 0.983000 0.38602 0.528000 0.53228 GTG TCGA-HZ-7926-01A-11D-2154-08 ERBB4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000256597.1 1 0 0 14 403 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 0.999743 14 398 0 55 2 0 0 0 0 55 2 -13.822640 1 1 0 0 1 1 2 3 2.102214 1 0.160000 1.880000 0.179688 0.470000 0.250000 1.000000 0.420000 0.563728 0.470000 0 3.400000e-01 1 OBSL1 23363 broad.mit.edu 37 2 220420834 220420834 + Missense_Mutation SNP C C T rs138086602 by1000genomes TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr2:220420834C>T ENST00000404537.1 - 14 4573 c.4517G>A c.(4516-4518)cGc>cAc p.R1506H OBSL1_ENST00000265318.4_Missense_Mutation_p.A1373T|OBSL1_ENST00000603926.1_Missense_Mutation_p.R1506H|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000265317.5_Missense_Mutation_p.R405H|OBSL1_ENST00000373876.1_Missense_Mutation_p.R1414H NM_015311.2 NP_056126.1 O75147 OBSL1_HUMAN obscurin-like 1 p.R1506H(1) Renal(207;0.0376) GATGAAGAGGCGGTGGATGTG 0.697000 1 Substitution - Missense(1) SO:0001583 missense ENST00000404537.1 1 1 hg19 CCDS46520.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 24.0|24.0 4.478052|4.478052 0.84747|0.84747 .|. .|. ENSG00000124006|ENSG00000124006 ENST00000265318;ENST00000456147|ENST00000404537;ENST00000373876;ENST00000265317 T|T;T;T 0.57273|0.67865 0.41|-0.29;-0.29;-0.29 4.49|4.49 4.49|4.49 0.54785|0.54785 .|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); .|. .|. .|. .|. T|T 0.73458|0.73458 0.3589|0.3589 L|L 0.39147|0.39147 1.195|1.195 0.22940|0.22940 N|N 0.998532|0.998532 .|D;D;D;D .|0.89917 .|1.0;0.999;1.0;0.999 .|D;D;D;D .|0.74674 .|0.964;0.977;0.982;0.984 T|T 0.62642|0.62642 -0.6811|-0.6811 7|9 0.06099|0.45353 T|T 0.92|0.12 .|. 11.9214|11.9214 0.52793|0.52793 0.0:0.6679:0.3321:0.0|0.0:0.6679:0.3321:0.0 .|. .|313;1507;1506;405 .|B7Z5P5;A4KVA4;O75147;E7ER99 .|.;.;OBSL1_HUMAN;. T|H 1373;408|1506;1414;405 ENSP00000265318:A1373T|ENSP00000385636:R1506H;ENSP00000362983:R1414H;ENSP00000265317:R405H ENSP00000265318:A1373T|ENSP00000265317:R405H A|R -|- 1|2 0|0 OBSL1|OBSL1 220129078|220129078 0.998000|0.998000 0.40836|0.40836 1.000000|1.000000 0.80357|0.80357 0.943000|0.943000 0.58893|0.58893 2.024000|2.024000 0.41049|0.41049 2.327000|2.327000 0.79052|0.79052 0.491000|0.491000 0.48974|0.48974 GCC|CGC TCGA-HZ-7926-01A-11D-2154-08 OBSL1-014 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322012.1 1 0 1 22 186 0 35 1 9.375234e-01 7 34 0 35 2 0 0 0 0 0 2 1 0.999999 19 182 0 35 2 0 0 0 0 35 2 -2.578509 1 1 121020 3 34 1 1 2 3 2.102214 1 0.160000 1.880000 0.179688 0.990000 0.900000 1.000000 1.000000 0.994524 0.990000 1 9.900000e-01 1 UGP2 7360 broad.mit.edu 37 2 64117306 64117306 + Missense_Mutation SNP A A G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr2:64117306A>G ENST00000337130.5 + 9 1882 c.1406A>G c.(1405-1407)aAt>aGt p.N469S UGP2_ENST00000394417.2_Missense_Mutation_p.N458S|UGP2_ENST00000467648.2_Missense_Mutation_p.N458S|UGP2_ENST00000445915.2_Missense_Mutation_p.N478S NM_006759.3 NP_006750.3 Q16851 UGPA_HUMAN UDP-glucose pyrophosphorylase 2 18 TTTGGAAAAAATGTTTCATTA 0.289000 0 SO:0001583 missense ENST00000337130.5 1 1 hg19 CCDS1875.1 . . . . . . . . . . A 17.57 3.421711 0.62622 . . ENSG00000169764 ENST00000394417;ENST00000467648;ENST00000337130;ENST00000445915 T;T;T;T 0.20463 2.07;2.07;2.07;2.07 5.82 5.82 0.92795 . 0.129339 0.64402 D 0.000001 T 0.22205 0.0535 L 0.45051 1.395 0.80722 D 1 P;P 0.42337 0.776;0.494 B;B 0.39935 0.314;0.314 T 0.01152 -1.1435 10 0.45353 T 0.12 -6.9138 16.1814 0.81903 1.0:0.0:0.0:0.0 . 478;469 E7EUC7;Q16851 .;UGPA_HUMAN S 458;458;469;478 ENSP00000377939:N458S;ENSP00000420793:N458S;ENSP00000338703:N469S;ENSP00000411803:N478S ENSP00000338703:N469S N + 2 0 UGP2 63970810 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 9.339000 0.96797 2.234000 0.73211 0.533000 0.62120 AAT TCGA-HZ-7926-01A-11D-2154-08 UGP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251688.1 1 0 1 29 255 0 25 1 1 79 398 0 25 2 0 0 0 0 0 2 1 1.000000 28 253 0 24 2 0 0 0 0 25 2 -20.000000 1 1 121374 3 32 1 2 2 4 2.129790 1 0.160000 1.880000 0.206949 0.990000 0.950000 1.000000 1.000000 0.997101 0.990000 1 9.900000e-01 1 PAIP2B 400961 broad.mit.edu 37 2 71417026 71417026 + Silent SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr2:71417026C>T ENST00000244221.8 - 3 430 c.264G>A c.(262-264)caG>caA p.Q88Q NM_020459.1 NP_065192.1 Q9ULR5 PAI2B_HUMAN poly(A) binding protein interacting protein 2B 2 CATTTAACTGCTGTTGCAACT 0.453000 0 SO:0001819 synonymous_variant ENST00000244221.8 0 1 hg19 CCDS46322.1 TCGA-HZ-7926-01A-11D-2154-08 PAIP2B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330547.2 0 0 0 4 41 0 11 0 4.295810e-01 0 14 0 11 2 0 0 0 0 0 2 0 0.870158 0 41 0 11 2 0 0 0 0 11 2 -9.351660 1 0 0 0 1 2 2 4 2.129790 1 0.160000 1.880000 0.206949 0.990000 0.470000 1.000000 1.000000 0.934796 0.990000 1 8.300000e-01 1 IP6K2 51447 broad.mit.edu 37 3 48726088 48726088 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr3:48726088C>T ENST00000328631.5 - 6 1122 c.899G>A c.(898-900)cGc>cAc p.R300H NCKIPSD_ENST00000416649.2_5'Flank|NCKIPSD_ENST00000294129.2_5'Flank|NCKIPSD_ENST00000341520.4_5'Flank NM_001005909.2|NM_016291.3 NP_001005909.1|NP_057375.2 Q9UHH9 IP6K2_HUMAN inositol hexakisphosphate kinase 2 15 GAGTTCACGGCGCAGGTACCG 0.567000 0 SO:0001583 missense ENST00000328631.5 1 1 hg19 CCDS2777.1 . . . . . . . . . . C 27.8 4.867840 0.91587 . . ENSG00000068745 ENST00000328631 T 0.19105 2.17 5.75 4.88 0.63580 . 0.000000 0.85682 D 0.000000 T 0.52125 0.1715 M 0.87900 2.915 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.61657 -0.7018 10 0.72032 D 0.01 -3.6578 14.8375 0.70194 0.0:0.9314:0.0:0.0686 . 300 Q9UHH9 IP6K2_HUMAN H 300 ENSP00000331103:R300H ENSP00000331103:R300H R - 2 0 IP6K2 48701092 1.000000 0.71417 0.998000 0.56505 0.990000 0.78478 7.818000 0.86416 1.451000 0.47736 0.655000 0.94253 CGC TCGA-HZ-7926-01A-11D-2154-08 IP6K2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257521.2 1 0 1 20 393 0 61 1 9.952526e-01 17 151 0 61 2 0 0 0 0 0 2 1 0.999994 19 384 0 60 2 0 0 0 0 61 2 -19.879780 1 1 0 0 1 0 0 0 1.981432 0 0.160000 1.880000 0.140753 0.590000 0.370000 0.860000 0.580000 0.609012 0.590000 0 4.700000e-01 7.300000e-01 MTTP 4547 broad.mit.edu 37 4 100512445 100512445 + Silent SNP G G C TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr4:100512445G>C ENST00000265517.5 + 5 758 c.555G>C c.(553-555)gtG>gtC p.V185V MTTP_ENST00000511045.1_Silent_p.V212V|MTTP_ENST00000457717.1_Silent_p.V185V P55157 MTP_HUMAN microsomal triglyceride transfer protein 57 Hesperetin(DB01094)|Lomitapide(DB08827) AAGACAAAGTGATCAAAATTA 0.403000 0 SO:0001819 synonymous_variant ENST00000265517.5 1 1 hg19 CCDS3651.1 TCGA-HZ-7926-01A-11D-2154-08 MTTP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253662.3 1 0 1 47 391 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 1.000000 46 386 0 63 2 0 0 0 0 63 2 -3.318794 1 1 0 0 1 1 2 3 2.025198 0 0.160000 1.880000 0.164678 0.990000 0.990000 1.000000 1.000000 0.998994 0.990000 1 9.900000e-01 1 ATP8A1 10396 broad.mit.edu 37 4 42627669 42627669 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr4:42627669C>T ENST00000381668.5 - 3 457 c.226G>A c.(226-228)Gct>Act p.A76T ATP8A1_ENST00000264449.10_Missense_Mutation_p.A76T|ATP8A1_ENST00000510289.1_3'UTR NM_006095.2 NP_006086.1 Q9Y2Q0 AT8A1_HUMAN ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 51 Phosphatidylserine(DB00144) GAATTAGCAGCTCTTCTGAAC 0.353000 0 SO:0001583 missense ENST00000381668.5 1 1 hg19 CCDS3466.1 . . . . . . . . . . C 18.53 3.644594 0.67358 . . ENSG00000124406 ENST00000381668;ENST00000264449 T;T 0.54479 0.57;0.57 5.8 5.8 0.92144 ATPase, P-type, cytoplasmic transduction domain A (1); 0.000000 0.85682 D 0.000000 T 0.66137 0.2759 L 0.39467 1.215 0.80722 D 1 D;B;B 0.63880 0.993;0.35;0.209 D;B;B 0.68192 0.956;0.299;0.097 T 0.61377 -0.7075 10 0.41790 T 0.15 . 20.418 0.99029 0.0:1.0:0.0:0.0 . 76;76;76 B4DII6;Q32M35;Q9Y2Q0 .;.;AT8A1_HUMAN T 76 ENSP00000371084:A76T;ENSP00000264449:A76T ENSP00000264449:A76T A - 1 0 ATP8A1 42322426 1.000000 0.71417 1.000000 0.80357 0.500000 0.33767 7.370000 0.79589 2.902000 0.99343 0.650000 0.86243 GCT TCGA-HZ-7926-01A-11D-2154-08 ATP8A1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000216861.2 1 0 0 21 270 0 42 0 3.154213e-02 0 4 0 42 2 0 0 0 0 0 2 1 0.999998 21 267 0 42 2 0 0 0 0 42 2 -20.000000 1 1 0 0 1 1 2 3 2.025198 0 0.160000 1.880000 0.164678 0.920000 0.580000 1.000000 1.000000 0.887851 0.920000 1 7.400000e-01 1 HELQ 113510 broad.mit.edu 37 4 84353360 84353360 + Silent SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr4:84353360C>T ENST00000295488.3 - 10 2271 c.2109G>A c.(2107-2109)caG>caA p.Q703Q HELQ_ENST00000510985.1_Silent_p.Q636Q NM_133636.2 NP_598375 Q8TDG4 HELQ_HUMAN helicase, POLQ-like 38 TGCCAATCATCTGTTTATATT 0.358000 Other identified genes with known or suspected DNA repair function 0 SO:0001819 synonymous_variant ENST00000295488.3 1 1 hg19 CCDS3603.1 TCGA-HZ-7926-01A-11D-2154-08 HELQ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252810.1 1 0 0 18 298 0 66 0 3.360513e-01 1 19 0 66 2 0 0 0 0 0 2 1 0.999982 18 294 0 66 2 0 0 0 0 66 2 -3.317573 1 1 0 0 1 1 2 3 2.025198 0 0.160000 1.880000 0.164678 0.730000 0.440000 1.000000 1.000000 0.748025 0.730000 0 5.700000e-01 9.400000e-01 SLCO4C1 353189 broad.mit.edu 37 5 101576431 101576431 + Nonsense_Mutation SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr5:101576431G>A ENST00000310954.6 - 11 2153 c.1867C>T c.(1867-1869)Cga>Tga p.R623* NM_180991.4 NP_851322.3 solute carrier organic anion transporter family, member 4C1 50 all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486) CCTAATAATCGAAGGACCATA 0.323000 0 SO:0001587 stop_gained ENST00000310954.6 0 1 hg19 CCDS34205.1 . . . . . . . . . . G 40 8.187990 0.98696 0.0 1.16E-4 ENSG00000173930 ENST00000310954 . . . 5.96 5.96 0.96718 . 0.000000 0.53938 D 0.000057 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 18.9858 0.92769 0.0:0.0:1.0:0.0 . . . . X 623 . ENSP00000309741:R623X R - 1 2 SLCO4C1 101604330 1.000000 0.71417 0.998000 0.56505 0.488000 0.33401 4.086000 0.57664 2.832000 0.97577 0.655000 0.94253 CGA TCGA-HZ-7926-01A-11D-2154-08 SLCO4C1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370332.1 0 0 1 84 588 0 118 0 8.910057e-01 0 29 0 118 2 0 0 0 0 0 2 1 1.000000 82 576 0 116 2 0 0 0 0 118 2 -20.000000 1 1 121404 6 43 1 0 1 1 2.007109 0 0.160000 1.880000 0.153908 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 SLCO6A1 133482 broad.mit.edu 37 5 101834438 101834438 + Silent SNP T T G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr5:101834438T>G ENST00000506729.1 - 1 282 c.111A>C c.(109-111)ggA>ggC p.G37G SLCO6A1_ENST00000379807.3_Silent_p.G37G|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000379810.1_Silent_p.G37G|SLCO6A1_ENST00000514551.1_5'Flank|SLCO6A1_ENST00000513675.1_Silent_p.G37G|SLCO6A1_ENST00000389019.3_Silent_p.G37G Q86UG4 SO6A1_HUMAN solute carrier organic anion transporter family, member 6A1 60 all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323) ACTTCGGGGTTCCCTTGGCCC 0.602000 0 SO:0001819 synonymous_variant ENST00000506729.1 1 1 hg19 CCDS34206.1 TCGA-HZ-7926-01A-11D-2154-08 SLCO6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370335.1 1 0 1 125 1012 0 178 0 0 0 0 178 2 0 0 0 0 0 2 1 1.000000 122 1000 0 175 2 0 0 0 0 178 2 -20.000000 1 1 0 0 1 0 1 1 2.007109 0 0.160000 1.880000 0.153908 0.990000 0.990000 1.000000 1.000000 0.999994 0.990000 1 9.900000e-01 1 PCDHB3 56132 broad.mit.edu 37 5 140482066 140482066 + Silent SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr5:140482066G>A ENST00000231130.2 + 1 1833 c.1833G>A c.(1831-1833)gaG>gaA p.E611E AC005754.7_ENST00000607216.1_RNA NM_018937.2 NP_061760.1 Q9Y5E6 PCDB3_HUMAN protocadherin beta 3 p.E611D(1) 72 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) AGGCCACGGAGCCCGGGCTGT 0.706000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000231130.2 1 1 hg19 CCDS4245.1 TCGA-HZ-7926-01A-11D-2154-08 PCDHB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251817.2 0 0 0 26 566 0 106 0 0 0 0 106 2 0 0 0 0 0 2 1 0.999978 14 350 0 149 2 0 0 0 0 106 2 -4.954673 1 0 117574 4 35 1 0 1 1 2.007109 0 0.160000 1.880000 0.153908 0.540000 0.360000 0.760000 0.540000 0.558853 0.540000 0 4.400000e-01 6.600000e-01 CDH10 1008 broad.mit.edu 37 5 24535262 24535262 + Missense_Mutation SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr5:24535262G>A ENST00000264463.4 - 5 1280 c.773C>T c.(772-774)aCg>aTg p.T258M NM_006727.3 NP_006718.2 Q9Y6N8 CAD10_HUMAN cadherin 10, type 2 (T2-cadherin) 185 ATCTGTCAGCGTGATGTTCAC 0.483000 HNSCC(23;0.051) 0 SO:0001583 missense ENST00000264463.4 1 1 hg19 CCDS3892.1 . . . . . . . . . . G 17.16 3.319154 0.60524 . . ENSG00000040731 ENST00000264463 T 0.03004 4.08 5.67 5.67 0.87782 Cadherin (5);Cadherin conserved site (1);Cadherin-like (1); 0.000000 0.85682 D 0.000000 T 0.14917 0.0360 L 0.52011 1.625 0.46478 D 0.99906 D 0.89917 1.0 D 0.71184 0.972 T 0.00062 -1.2157 10 0.66056 D 0.02 . 18.738 0.91763 0.0:0.0:1.0:0.0 . 258 Q9Y6N8 CAD10_HUMAN M 258 ENSP00000264463:T258M ENSP00000264463:T258M T - 2 0 CDH10 24571019 1.000000 0.71417 0.996000 0.52242 0.246000 0.25737 7.884000 0.87274 2.674000 0.91012 0.591000 0.81541 ACG TCGA-HZ-7926-01A-11D-2154-08 CDH10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207345.2 1 0 0 17 307 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 0.999965 17 303 0 53 2 0 0 0 0 54 2 -3.317686 1 1 121406 1 36 1 0 1 1 2.007109 0 0.160000 1.880000 0.153908 0.650000 0.390000 0.980000 1.000000 0.671584 0.650000 0 5.100000e-01 8.200000e-01 DDX4 54514 broad.mit.edu 37 5 55059848 55059848 + Nonsense_Mutation SNP C C G TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr5:55059848C>G ENST00000505374.1 + 6 382 c.290C>G c.(289-291)tCa>tGa p.S97* DDX4_ENST00000514278.2_Nonsense_Mutation_p.S97*|DDX4_ENST00000508580.1_3'UTR|DDX4_ENST00000353507.5_Nonsense_Mutation_p.S97*|SLC38A9_ENST00000504880.1_Intron|DDX4_ENST00000511853.1_5'Flank|DDX4_ENST00000354991.5_Nonsense_Mutation_p.S97* NM_024415.2 NP_077726.1 Q9NQI0 DDX4_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 24 Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223) ATAGGTTTTTCAAACAGCAGG 0.318000 0 SO:0001587 stop_gained ENST00000505374.1 0 1 hg19 CCDS3969.1 . . . . . . . . . . C 35 5.473344 0.96274 . . ENSG00000152670 ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000515709;ENST00000506848;ENST00000514679;ENST00000354991;ENST00000511491 . . . 4.82 2.93 0.34026 . 1.124900 0.06856 N 0.798125 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.11485 T 0.65 -22.8246 5.4174 0.16382 0.0:0.7133:0.0:0.2867 . . . . X 97;97;97;97;71;97;97;97;97 . ENSP00000334167:S97X S + 2 0 DDX4 55095605 1.000000 0.71417 1.000000 0.80357 0.971000 0.66376 1.097000 0.30988 0.534000 0.28695 0.591000 0.81541 TCA TCGA-HZ-7926-01A-11D-2154-08 DDX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214147.2 0 0 0 14 372 0 48 0 0 0 0 48 2 0 0 0 1 0 0 2 1 0.999743 14 367 0 48 2 0 0 0 0 48 2 -3.339229 1 1 0 0 1 0 1 1 2.007109 0 0.160000 1.880000 0.153908 0.450000 0.260000 0.710000 0.440000 0.472941 0.450000 0 3.400000e-01 5.900000e-01 VCAN 1462 broad.mit.edu 37 5 82835841 82835841 + Missense_Mutation SNP G G A TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr5:82835841G>A ENST00000265077.3 + 8 7584 c.7019G>A c.(7018-7020)gGa>gAa p.G2340E VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.G1353E|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron NM_004385.4 NP_004376.2 P13611 CSPG2_HUMAN versican 190 Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142) Hyaluronan(DB08818) AGTGACACTGGAGCAGAAGGA 0.468000 0 SO:0001583 missense ENST00000265077.3 1 1 hg19 CCDS4060.1 . . . . . . . . . . G 4.418 0.077349 0.08485 . . ENSG00000038427 ENST00000265077;ENST00000343200 T;T 0.13089 2.62;2.62 6.07 2.27 0.28462 . 0.514767 0.19096 N 0.122838 T 0.12050 0.0293 L 0.38175 1.15 0.09310 N 1 P;B 0.40515 0.719;0.1 B;B 0.44085 0.44;0.036 T 0.16748 -1.0392 10 0.24483 T 0.36 . 7.4303 0.27124 0.1416:0.2539:0.6045:0.0 . 1353;2340 P13611-2;P13611 .;CSPG2_HUMAN E 2340;1353 ENSP00000265077:G2340E;ENSP00000340062:G1353E ENSP00000265077:G2340E G + 2 0 VCAN 82871597 0.033000 0.19621 0.000000 0.03702 0.040000 0.13550 0.946000 0.29069 0.445000 0.26639 0.650000 0.86243 GGA TCGA-HZ-7926-01A-11D-2154-08 VCAN-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000254092.3 1 0 0 48 376 0 73 1 1 53 236 0 73 2 0 0 0 0 0 2 1 1.000000 49 371 0 72 2 0 0 0 0 73 2 -20.000000 1 1 0 0 1 0 1 1 2.007109 0 0.160000 1.880000 0.153908 0.990000 0.990000 1.000000 1.000000 0.999521 0.990000 1 9.900000e-01 1 PRDM13 59336 broad.mit.edu 37 6 100061823 100061823 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr6:100061823C>T ENST00000369215.4 + 4 1617 c.1312C>T c.(1312-1314)Ccc>Tcc p.P438S NM_021620.3 NP_067633.2 Q9H4Q3 PRD13_HUMAN PR domain containing 13 17 all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186) CGCGCTGCCGCCCCTCGACCC 0.731000 0 SO:0001583 missense ENST00000369215.4 1 1 hg19 CCDS43487.1 . . . . . . . . . . C 10.02 1.237088 0.22711 . . ENSG00000112238 ENST00000369215;ENST00000369214 T;T 0.05717 3.4;3.4 3.59 0.61 0.17580 . 0.394677 0.18533 N 0.138435 T 0.01730 0.0055 L 0.29908 0.895 0.32681 N 0.515456 B 0.20052 0.041 B 0.21917 0.037 T 0.44298 -0.9337 10 0.22109 T 0.4 -3.4988 13.5999 0.62013 0.0:0.6342:0.3658:0.0 . 438 Q9H4Q3 PRD13_HUMAN S 438;448 ENSP00000358217:P438S;ENSP00000358216:P448S ENSP00000358216:P448S P + 1 0 PRDM13 100168544 0.056000 0.20664 0.437000 0.26809 0.095000 0.18619 1.172000 0.31908 -0.104000 0.12154 0.561000 0.74099 CCC TCGA-HZ-7926-01A-11D-2154-08 PRDM13-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041619.2 1 0 0 13 155 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999551 13 152 0 31 2 0 0 0 0 32 2 -18.208850 1 1 0 0 1 0 0 0 1.963456 0 0.160000 1.880000 0.132231 0.920000 0.530000 1.000000 1.000000 0.878961 0.920000 1 7.100000e-01 1 CUL9 23113 broad.mit.edu 37 6 43155033 43155033 + Silent SNP G G A rs148427416 TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr6:43155033G>A ENST00000252050.4 + 6 1521 c.1437G>A c.(1435-1437)ccG>ccA p.P479P CUL9_ENST00000354495.3_Intron|CUL9_ENST00000372647.2_Silent_p.P479P NM_015089.2 NP_055904.1 Q8IWT3 CUL9_HUMAN cullin 9 92 ACCCTTTGCCGTACCTCCAGC 0.532000 0 SO:0001819 synonymous_variant ENST00000252050.4 1 1 hg19 CCDS4890.1 TCGA-HZ-7926-01A-11D-2154-08 CUL9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040582.2 1 0 0 41 687 0 132 0 1.300348e-01 0 11 0 132 2 0 0 0 0 0 2 1 1.000000 41 678 0 131 2 0 0 0 0 132 2 -6.279674 1 1 121412 2 30 1 0 0 0 1.963456 0 0.160000 1.880000 0.132231 0.670000 0.490000 0.890000 0.670000 0.689762 0.670000 0 5.800000e-01 7.900000e-01 ASTN2 23245 broad.mit.edu 37 9 119903693 119903693 + Silent SNP G G A rs115011238 byFrequency TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chr9:119903693G>A ENST00000313400.4 - 4 1180 c.1080C>T c.(1078-1080)cgC>cgT p.R360R ASTN2_ENST00000361209.2_Intron|ASTN2_ENST00000373996.3_Silent_p.R360R|ASTN2_ENST00000361477.3_Intron O75129 ASTN2_HUMAN astrotactin 2 102 GCGTGTTAGCGCGGAAACTCT 0.587000 0 SO:0001819 synonymous_variant ENST00000313400.4 1 1 hg19 TCGA-HZ-7926-01A-11D-2154-08 ASTN2-201 KNOWN basic protein_coding protein_coding 0 0 0 19 260 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 0.999991 19 255 0 69 2 0 0 0 0 69 2 -12.608130 1 1 121408 41 48 1 0 1 1 2.012137 0 0.160000 1.880000 0.155270 0.840000 0.530000 1.000000 1.000000 0.839046 0.840000 0 6.700000e-01 1 SHROOM2 357 broad.mit.edu 37 X 9907312 9907312 + Missense_Mutation SNP C C T TCGA-HZ-7926-01A-11D-2154-08 TCGA-HZ-7926-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 52a320eb-4f2e-435f-911d-75790f855b96 65e65329-48f3-452a-aa5c-f9c26692b9f4 g.chrX:9907312C>T ENST00000380913.3 + 8 4307 c.4217C>T c.(4216-4218)gCg>gTg p.A1406V SHROOM2_ENST00000418909.2_Missense_Mutation_p.A241V NM_001649.2 NP_001640.1 Q13796 SHRM2_HUMAN shroom family member 2 57 Hepatocellular(5;0.000888) GCCCCCAAGGCGGAGCTGCTG 0.597000 0 SO:0001583 missense ENST00000380913.3 0 1 hg19 CCDS14135.1 . . . . . . . . . . C 21.6 4.166693 0.78339 . . ENSG00000146950 ENST00000380913;ENST00000418909;ENST00000452575;ENST00000540923 T;T;T 0.37235 1.21;1.21;1.21 5.44 5.44 0.79542 Apx/shroom, ASD2 (2); 0.058670 0.64402 N 0.000002 T 0.39733 0.1089 L 0.52206 1.635 0.58432 D 0.999999 B;B 0.33755 0.424;0.194 B;B 0.35727 0.209;0.041 T 0.35500 -0.9786 10 0.72032 D 0.01 -12.7128 18.4668 0.90758 0.0:1.0:0.0:0.0 . 241;1406 Q68DU3;Q13796 .;SHRM2_HUMAN V 1406;241;241;241 ENSP00000370299:A1406V;ENSP00000415229:A241V;ENSP00000406724:A241V ENSP00000370299:A1406V A + 2 0 SHROOM2 9867312 1.000000 0.71417 0.928000 0.36995 0.789000 0.44602 7.339000 0.79282 2.301000 0.77427 0.596000 0.82720 GCG TCGA-HZ-7926-01A-11D-2154-08 SHROOM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055721.1 1 0 1 9 59 0 14 1 5.540650e-01 5 8 0 14 2 0 0 0 0 0 2 1 0.994946 9 58 0 14 2 0 0 0 0 14 2 -16.075190 1 1 0 0 1 0 1 1 0.160000 1.880000 0.160000 0.740000 0.390000 0.980000 0.780000 0.733505 0.740000 0 5.500000e-01 9.000000e-01