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 MMS19 64210 broad.mit.edu 37 10 99219804 99219804 + Splice_Site DEL T T - TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 T - T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr10:99219804delT ENST00000438925.2 - 26 2990 c.2655delA c.(2653-2655)caa>ca p.Q885fs MMS19_ENST00000370782.2_Splice_Site_p.Q885fs|MMS19_ENST00000327238.10_Splice_Site_p.Q787fs|MMS19_ENST00000355839.6_Splice_Site_p.Q842fs|MMS19_ENST00000327277.7_3'UTR NM_022362.4 NP_071757.4 Q96T76 MMS19_HUMAN MMS19 nucleotide excision repair homolog (S. cerevisiae) 16 Colorectal(252;0.0846) ACTCCTCACCTTGGGGAGCAG 0.522000 Direct reversal of damage 0 SO:0001630 splice_region_variant ENST00000438925.2 1 0 hg19 CCDS7464.1 TCGA-IB-8127-01A-11D-2396-08 MMS19-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049706.2 1 0 0 123 458 0 71 1 1 8 165 0 71 2 0 0 0 0 0 0 1 1.000000 126 452 0 70 2 -3.714978 1 1 0 0 1 1 3 4 2.039895 1 0.350000 3.330000 0.462810 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 UNC50 25972 broad.mit.edu 37 2 99226227 99226228 + Frame_Shift_Ins INS - - A rs140953303 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 - A - - Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:99226227_99226228insA ENST00000357765.2 + 2 157_158 c.5_6insA c.(4-9)ttaccgfs p.P3fs COA5_ENST00000483527.1_5'Flank|COA5_ENST00000328709.3_5'Flank|UNC50_ENST00000409347.1_Frame_Shift_Ins_p.P20fs|UNC50_ENST00000409975.1_Frame_Shift_Ins_p.P20fs|COA5_ENST00000409997.1_5'Flank NM_014044.5 NP_054763.2 Q53HI1 UNC50_HUMAN unc-50 homolog (C. elegans) 10 AGGAAGATGTTACCGAGTACTT 0.450000 0 SO:0001589 frameshift_variant ENST00000357765.2 0 1 hg19 CCDS2035.1 TCGA-IB-8127-01A-11D-2396-08 UNC50-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252987.1 1 0 0 449 2250 0 297 0 1 0 224 0 297 2 0 0 0 0 0 0 1 1.000000 448 2230 0 297 2 -20.000000 1 1 0 0 1 2 2 4 2.240843 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ATM 472 broad.mit.edu 37 11 108199926 108199926 + Missense_Mutation SNP A A G rs121434221 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 A G A A Valid Somatic Phase_I WXS targeted Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr11:108199926A>G ENST00000452508.2 + 50 7457 c.7268A>G c.(7267-7269)gAa>gGa p.E2423G C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.E2423G Q13315 ATM_HUMAN ATM serine/threonine kinase p.E2423G(1) 448 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Caffeine(DB00201) GCCAAAGAGGAAGTAGGTCTC 0.368000 D, Mis, N, F, S T-PLL leukemia, lymphoma, medulloblastoma, glioma Genes defective in diseases associated with sensitivity to DNA damaging agents Ataxia Telangiectasia TSP Lung(14;0.12) yes Rec yes Ataxia-telangiectasia 11 11q22.3 472 ataxia telangiectasia mutated L, O 1 Substitution - Missense(1) SO:0001583 missense Familial Cancer Database AT, Louis-Bar syndrome ENST00000452508.2 1 1 hg19 CCDS31669.1 . . . . . . . . . . A 31 5.072143 0.93950 . . ENSG00000149311 ENST00000278616;ENST00000452508 T;T 0.69561 -0.41;-0.41 5.4 5.4 0.78164 PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.81034 0.4739 M 0.76002 2.32 0.80722 D 1 D 0.89917 1.0 D 0.79784 0.993 T 0.82047 -0.0651 10 0.48119 T 0.1 . 15.4276 0.75065 1.0:0.0:0.0:0.0 . 2423 Q13315 ATM_HUMAN G 2423 ENSP00000278616:E2423G;ENSP00000388058:E2423G ENSP00000278616:E2423G E + 2 0 ATM 107705136 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.332000 0.96446 2.038000 0.60285 0.528000 0.53228 GAA TCGA-IB-8127-01A-11D-2396-08 ATM-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389938.1 1 0 1 135 145 0 44 1 9.999988e-01 13 14 0 44 2 1 1 69 70 0 175 2 1 1.000000 131 144 0 44 2 -20.000000 1 1 0 0 1 0 4 4 2.045999 1 0.350000 3.330000 0.499037 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 OR10G7 390265 broad.mit.edu 37 11 123908881 123908881 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr11:123908881G>A ENST00000330487.5 - 1 836 c.828C>T c.(826-828)acC>acT p.T276T NM_001004463.1 NP_001004463.1 Q8NGN6 O10G7_HUMAN olfactory receptor, family 10, subfamily G, member 7 47 Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22) GAGTCAGCGTGGTGTAGAAAA 0.498000 0 SO:0001819 synonymous_variant ENST00000330487.5 0 1 hg19 CCDS31705.1 TCGA-IB-8127-01A-11D-2396-08 OR10G7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387271.1 0 0 0 8 453 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 0.988818 8 447 0 64 2 -3.194992 1 1 0 0 1 0 4 4 2.045999 1 0.350000 3.330000 0.499037 0.140000 5.000000e-02 1.000000 0.120000 0.245508 0.140000 0 9.000000e-02 2.400000e-01 BTBD11 121551 broad.mit.edu 37 12 108010914 108010914 + Missense_Mutation SNP G G A rs147351765 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr12:108010914G>A ENST00000280758.5 + 8 2578 c.2050G>A c.(2050-2052)Gag>Aag p.E684K BTBD11_ENST00000490090.2_Missense_Mutation_p.E684K|BTBD11_ENST00000420571.2_Missense_Mutation_p.E684K|BTBD11_ENST00000357167.4_Missense_Mutation_p.E221K|RP11-128P10.1_ENST00000548473.1_RNA NM_001018072.1 NP_001018082.1 A6QL63 BTBDB_HUMAN BTB (POZ) domain containing 11 p.E684K(2) 53 GGAGCATGGCGAGGAGAACTA 0.607000 2 Substitution - Missense(2) SO:0001583 missense ENST00000280758.5 1 1 hg19 CCDS31893.1 . . . . . . . . . . G 20.2 3.942606 0.73672 . . ENSG00000151136 ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167 T;T;T;T 0.39592 1.26;1.2;1.27;1.07 5.27 5.27 0.74061 Ankyrin repeat-containing domain (4); 0.249509 0.47455 D 0.000233 T 0.35451 0.0932 N 0.11313 0.125 0.80722 D 1 D;P;D;D 0.69078 0.99;0.618;0.98;0.997 P;B;P;P 0.48873 0.481;0.195;0.514;0.593 T 0.35871 -0.9771 10 0.49607 T 0.09 . 18.8886 0.92389 0.0:0.0:1.0:0.0 . 684;221;684;684 A6QL63-2;E9PHS4;A6QL63;A6QL63-3 .;.;BTBDB_HUMAN;. K 684;684;684;221 ENSP00000280758:E684K;ENSP00000413889:E684K;ENSP00000447319:E684K;ENSP00000349690:E221K ENSP00000280758:E684K E + 1 0 BTBD11 106535044 1.000000 0.71417 0.975000 0.42487 0.961000 0.63080 5.294000 0.65687 2.454000 0.82982 0.655000 0.94253 GAG TCGA-IB-8127-01A-11D-2396-08 BTBD11-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318003.1 1 0 1 86 516 0 105 0 2.095123e-02 0 2 0 105 2 0 0 0 0 0 2 1 1.000000 85 509 0 103 2 -2.966679 1 1 121412 1 33 1 0 3 3 1.748988 1 0.350000 3.330000 0.435886 0.950000 7.600000e-01 1.000000 1.000000 0.936497 0.950000 1 8.500000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece 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-IB-8127-01A-11D-2396-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 48 69 0 24 1 1 46 35 0 24 2 1 1 111 246 0 420 2 1 1.000000 48 69 0 24 2 -20.000000 1 1 121404 2 44 1 2 4 6 2.345273 1 0.350000 3.330000 0.551105 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CCND2 894 broad.mit.edu 37 12 4383259 4383259 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr12:4383259G>A ENST00000261254.3 + 1 322 c.53G>A c.(52-54)cGc>cAc p.R18H RP11-264F23.3_ENST00000539135.1_RNA|RP11-264F23.4_ENST00000537370.1_RNA NM_001759.3 NP_001750.1 P30279 CCND2_HUMAN cyclin D2 17 all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206) GTGCGGGACCGCAACCTGCTC 0.667000 T IGL@ NHL,CLL Dom yes 12 12p13 894 cyclin D2 L 0 SO:0001583 missense ENST00000261254.3 0 1 hg19 CCDS8524.1 . . . . . . . . . . G 14.80 2.643155 0.47153 . . ENSG00000118971 ENST00000261254 T 0.08282 3.11 4.17 1.27 0.21489 Cyclin-like (1); 0.176202 0.51477 D 0.000085 T 0.04497 0.0123 N 0.19112 0.55 0.32574 N 0.52943 P 0.39116 0.66 B 0.30646 0.118 T 0.26155 -1.0111 10 0.72032 D 0.01 . 8.7994 0.34898 0.1271:0.4759:0.397:0.0 . 18 P30279 CCND2_HUMAN H 18 ENSP00000261254:R18H ENSP00000261254:R18H R + 2 0 CCND2 4253520 1.000000 0.71417 0.997000 0.53966 0.504000 0.33889 3.174000 0.50847 0.064000 0.16427 -0.339000 0.08088 CGC TCGA-IB-8127-01A-11D-2396-08 CCND2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398287.1 0 0 0 4 177 0 21 0 1.644763e-01 0 26 0 21 2 0 0 0 0 0 2 1 0.887322 4 174 0 20 2 -6.110801 1 1 121398 1 20 1 1 3 4 2.064882 1 0.350000 3.330000 0.485149 0.200000 5.000000e-02 1.000000 0.170000 0.340173 0.200000 0 1.100000e-01 1 HOXC10 3226 broad.mit.edu 37 12 54379388 54379388 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr12:54379388C>T ENST00000303460.4 + 1 419 c.345C>T c.(343-345)agC>agT p.S115S HOXC-AS3_ENST00000513165.1_RNA|RP11-834C11.12_ENST00000513209.1_5'Flank|HOXC-AS3_ENST00000509870.1_RNA|HOXC-AS3_ENST00000567780.1_RNA|HOXC-AS3_ENST00000514702.1_RNA NM_017409.3 NP_059105.2 Q9NYD6 HXC10_HUMAN homeobox C10 20 GCATGTACAGCGCAGAGAAGC 0.622000 0 SO:0001819 synonymous_variant ENST00000303460.4 1 1 hg19 CCDS8868.1 TCGA-IB-8127-01A-11D-2396-08 HOXC10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358952.2 1 0 1 88 337 0 62 0 4.455657e-01 0 7 0 62 2 0 0 0 0 0 2 1 1.000000 87 336 0 61 2 -20.000000 1 1 121410 1 19 1 2 3 5 2.272987 1 0.350000 3.330000 0.537119 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 LYZ 4069 broad.mit.edu 37 12 69744008 69744008 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr12:69744008G>A ENST00000261267.2 + 2 325 c.257G>A c.(256-258)gGc>gAc p.G86D LYZ_ENST00000548839.1_Missense_Mutation_p.G86D|LYZ_ENST00000549690.1_Missense_Mutation_p.G86D NM_000239.2 NP_000230.1 P61626 LYSC_HUMAN lysozyme 4 all_epithelial(5;2.98e-35)|Lung NSC(4;9.93e-33)|all_lung(4;5.66e-31)|Breast(13;2.56e-06)|Esophageal squamous(21;0.187) Epithelial(6;8.26e-19)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00503)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241) L-Aspartic Acid(DB00128) TGTAATGATGGCAAAACCCCA 0.413000 0 SO:0001583 missense ENST00000261267.2 0 1 hg19 CCDS8989.1 . . . . . . . . . . G 13.92 2.381206 0.42207 . . ENSG00000090382 ENST00000261267;ENST00000549690;ENST00000548839 T;T;T 0.76186 -1.0;-1.0;-1.0 5.94 5.94 0.96194 Lysozyme-like domain (1); 0.220360 0.46758 D 0.000261 D 0.82572 0.5066 M 0.76328 2.33 0.48288 D 0.999622 P 0.36768 0.569 P 0.53450 0.726 T 0.80830 -0.1207 9 . . . . 11.1713 0.48573 0.0826:0.0:0.9174:0.0 . 86 P61626 LYSC_HUMAN D 86 ENSP00000261267:G86D;ENSP00000449898:G86D;ENSP00000449969:G86D . G + 2 0 LYZ 68030275 1.000000 0.71417 0.999000 0.59377 0.104000 0.19210 3.368000 0.52357 2.820000 0.97059 0.650000 0.86243 GGC TCGA-IB-8127-01A-11D-2396-08 LYZ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403624.2 0 0 0 5 664 0 97 1 9.999967e-01 9 6779 0 97 2 0 0 0 0 0 2 1 0.935753 5 656 0 97 2 -2.519719 1 0 0 0 1 3 3 6 2.279019 1 0.350000 3.330000 0.537696 0.070000 1.000000e-02 1.000000 0.050000 0.289599 0.070000 0 3.000000e-02 1 ZFC3H1 196441 broad.mit.edu 37 12 72008421 72008421 + Missense_Mutation SNP T T C rs11541286 by1000genomes TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr12:72008421T>C ENST00000378743.3 - 30 5778 c.5420A>G c.(5419-5421)aAa>aGa p.K1807R NM_144982.4 NP_659419.3 O60293 ZC3H1_HUMAN zinc finger, C3H1-type containing 69 AGTAAAAAATTTGAATTCTTG 0.333000 0 SO:0001583 missense ENST00000378743.3 1 0 hg19 CCDS41813.1 76 0.0347985347985348 3 0.006097560975609756 24 0.06629834254143646 1 0.0017482517482517483 48 0.0633245382585752 T 12.11 1.840561 0.32513 0.02021 0.075571 ENSG00000133858 ENST00000378743 T 0.34072 1.38 5.35 0.0229 0.14135 . 0.161807 0.53938 N 0.000047 T 0.00998 0.0033 L 0.27053 0.805 0.80722 D 1 B 0.15141 0.012 B 0.12156 0.007 T 0.08310 -1.0728 10 0.48119 T 0.1 . 5.3631 0.16099 0.1189:0.2036:0.0:0.6775 rs11541286;rs52822945;rs59889096;rs11541286 1807 O60293 ZC3H1_HUMAN R 1807 ENSP00000368017:K1807R ENSP00000368017:K1807R K - 2 0 ZFC3H1 70294688 1.000000 0.71417 0.993000 0.49108 0.997000 0.91878 0.659000 0.24994 -0.238000 0.09724 0.455000 0.32223 AAA TCGA-IB-8127-01A-11D-2396-08 ZFC3H1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404751.1 0 0 1 240 837 0 126 1 1 36 61 0 126 2 0 0 0 0 0 2 1 1.000000 238 828 2 125 36 -0.878318 0 1 120786 8088 74 1 3 3 6 2.279019 1 0.350000 3.330000 0.537696 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CLEC2D 29121 broad.mit.edu 37 12 9840545 9840545 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr12:9840545G>A ENST00000290855.6 + 3 242 c.220G>A c.(220-222)Gca>Aca p.A74T CLEC2D_ENST00000543300.1_Missense_Mutation_p.A74T|CLEC2D_ENST00000261340.7_Missense_Mutation_p.A74T|CLEC2D_ENST00000545918.1_Missense_Mutation_p.A37T|CLEC2D_ENST00000261339.6_Missense_Mutation_p.A37T NM_013269.5 NP_037401.1 Q9UHP7 CLC2D_HUMAN C-type lectin domain family 2, member D 9 TCTTCAAGCTGCATGCCCAGA 0.328000 0 SO:0001583 missense ENST00000290855.6 0 1 hg19 CCDS8602.1 . . . . . . . . . . G 10.14 1.268812 0.23136 . . ENSG00000069493 ENST00000479410;ENST00000261340;ENST00000290855;ENST00000545918;ENST00000543300;ENST00000261339;ENST00000466035;ENST00000430909;ENST00000544322;ENST00000460309 T;T;T;T;T;T;T;T;T;T 0.63096 -0.02;0.96;0.96;-0.02;-0.02;0.96;0.96;-0.02;-0.02;0.96 3.17 2.01 0.26516 C-type lectin-like (1); 0.215967 0.20083 U 0.099615 T 0.46619 0.1402 N 0.22421 0.69 0.09310 N 1 B;B;B 0.31790 0.104;0.112;0.34 B;B;B 0.40009 0.316;0.05;0.316 T 0.32903 -0.9889 9 . . . -6.2397 5.3342 0.15949 0.2405:0.0:0.7595:0.0 . 74;74;74 Q9UHP7-5;Q9UHP7;Q9UHP7-3 .;CLC2D_HUMAN;. T 32;74;74;37;74;37;31;53;48;17 ENSP00000442252:A32T;ENSP00000261340:A74T;ENSP00000290855:A74T;ENSP00000444818:A37T;ENSP00000443065:A74T;ENSP00000261339:A37T;ENSP00000446028:A31T;ENSP00000413045:A53T;ENSP00000437861:A48T;ENSP00000443177:A17T . A + 1 0 CLEC2D 9731812 0.000000 0.05858 0.002000 0.10522 0.063000 0.16089 -1.111000 0.03303 0.390000 0.25115 0.430000 0.28490 GCA TCGA-IB-8127-01A-11D-2396-08 CLEC2D-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000335424.2 0 0 0 7 595 0 114 0 1.113916e-01 0 41 0 114 2 0 0 0 0 0 2 1 0.979506 7 585 0 112 2 -2.257911 0 1 0 0 1 1 3 4 2.022611 1 0.350000 3.330000 0.486572 0.090000 3.000000e-02 1.000000 0.080000 0.253313 0.090000 0 5.000000e-02 1 PCDH9 5101 broad.mit.edu 37 13 66879140 66879140 + Nonsense_Mutation SNP C C A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr13:66879140C>A ENST00000377865.2 - 4 3495 c.3361G>T c.(3361-3363)Gga>Tga p.G1121* PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000328454.5_Nonsense_Mutation_p.G1087*|PCDH9_ENST00000456367.1_Nonsense_Mutation_p.G1087*|PCDH9_ENST00000544246.1_Nonsense_Mutation_p.G1121* Q9HC56 PCDH9_HUMAN protocadherin 9 103 Hepatocellular(98;0.0906)|Breast(118;0.107) TCAGCTAATCCTCGGGGACCC 0.428000 0 SO:0001587 stop_gained ENST00000377865.2 0 1 hg19 CCDS9444.1 . . . . . . . . . . C 41 8.954328 0.99016 . . ENSG00000184226 ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454 . . . 6.07 6.07 0.98685 . 0.000000 0.48286 D 0.000197 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.66056 D 0.02 . 20.6439 0.99570 0.0:1.0:0.0:0.0 . . . . X 1121;1121;1087;1087 . ENSP00000332060:G1087X G - 1 0 PCDH9 65777141 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.463000 0.80869 2.890000 0.99128 0.650000 0.86243 GGA TCGA-IB-8127-01A-11D-2396-08 PCDH9-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000276387.1 1 0 1 45 189 0 50 0 3.865408e-02 0 2 0 50 2 0 0 0 0 0 2 1 1.000000 45 186 0 50 2 -3.547497 1 1 0 0 1 0 2 2 1.665391 1 0.350000 3.330000 0.350000 0.990000 8.200000e-01 1.000000 1.000000 0.980959 0.990000 1 9.500000e-01 1 KIAA0586 9786 broad.mit.edu 37 14 58927860 58927860 + Missense_Mutation SNP G G T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr14:58927860G>T ENST00000556134.1 + 15 2270 c.1996G>T c.(1996-1998)Gta>Tta p.V666L KIAA0586_ENST00000261244.5_Missense_Mutation_p.V605L|KIAA0586_ENST00000354386.6_Missense_Mutation_p.V734L|KIAA0586_ENST00000423743.3_Missense_Mutation_p.V637L|KIAA0586_ENST00000538571.2_3'UTR NM_001244190.1|NM_001244193.1 NP_001231119.1|NP_001231122.1 Q9BVV6 TALD3_HUMAN KIAA0586 34 GAGACCAAAAGTAATAGAACG 0.323000 0 SO:0001583 missense ENST00000556134.1 1 1 hg19 CCDS58321.1 . . . . . . . . . . G 15.90 2.970319 0.53614 . . ENSG00000100578 ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000546216 T;T;T;T 0.54479 0.57;0.57;0.57;0.57 5.8 3.93 0.45458 . 0.098661 0.44483 N 0.000456 T 0.52289 0.1725 L 0.36672 1.1 0.36033 D 0.839523 B;B;D;P;B;B 0.56521 0.197;0.197;0.976;0.879;0.197;0.197 B;B;P;B;B;B 0.52424 0.062;0.062;0.698;0.36;0.062;0.062 T 0.62826 -0.6772 10 0.72032 D 0.01 . 11.1811 0.48629 0.0656:0.2395:0.6949:0.0 . 541;541;734;605;666;637 F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20 .;.;.;.;K0586_HUMAN;. L 734;666;637;605;541 ENSP00000346359:V734L;ENSP00000452351:V666L;ENSP00000399427:V637L;ENSP00000261244:V605L ENSP00000261244:V605L V + 1 0 KIAA0586 57997613 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 0.740000 0.26188 0.751000 0.32900 0.650000 0.86243 GTA TCGA-IB-8127-01A-11D-2396-08 KIAA0586-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000411887.1 1 0 1 31 108 0 16 1 9.888295e-01 9 19 0 16 2 0 0 0 0 0 2 1 1.000000 30 107 0 16 2 -20.000000 1 1 0 0 1 2 2 4 2.164920 1 0.350000 3.330000 0.513473 0.990000 9.900000e-01 1.000000 1.000000 0.999934 0.990000 1 9.900000e-01 1 NRXN3 9369 broad.mit.edu 37 14 80328016 80328016 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr14:80328016G>A ENST00000557594.1 + 6 2576 c.1623G>A c.(1621-1623)acG>acA p.T541T NRXN3_ENST00000281127.7_Silent_p.T336T|NRXN3_ENST00000554719.1_Silent_p.T965T|NRXN3_ENST00000335750.5_Silent_p.T965T|NRXN3_ENST00000428277.2_Silent_p.T363T|NRXN3_ENST00000556003.1_3'UTR NM_001272020.1 NP_001258949.1 Q9HDB5 NRX3B_HUMAN neurexin 3 p.T965T(1)|p.T363T(1) 104 Renal(4;0.00876) CAAACCCCACGGAGCCGGGAA 0.597000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000557594.1 1 1 hg19 TCGA-IB-8127-01A-11D-2396-08 NRXN3-004 NOVEL basic protein_coding protein_coding OTTHUMT00000413790.1 1 0 1 41 310 0 52 0 3.977462e-02 0 3 0 52 2 0 0 0 0 0 2 1 1.000000 41 309 0 51 2 -3.221893 1 1 121412 1 34 1 2 2 4 2.164920 1 0.350000 3.330000 0.513473 0.900000 6.500000e-01 1.000000 1.000000 0.889592 0.900000 1 7.700000e-01 1 CYP19A1 1588 broad.mit.edu 37 15 51504611 51504611 + Missense_Mutation SNP T T C TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr15:51504611T>C ENST00000396402.1 - 9 1322 c.1169A>G c.(1168-1170)aAg>aGg p.K390R CYP19A1_ENST00000559878.1_Missense_Mutation_p.K390R|CYP19A1_ENST00000396404.4_Missense_Mutation_p.K390R|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000260433.2_Missense_Mutation_p.K390R NM_000103.3 NP_000094.2 P11511 CP19A_HUMAN cytochrome P450, family 19, subfamily A, polypeptide 1 33 Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072) GTTTGTCCCCTTTTTCACTGG 0.413000 Melanoma(142;1016 1807 39614 48966 51721) 0 SO:0001583 missense ENST00000396402.1 0 1 hg19 CCDS10139.1 . . . . . . . . . . T 15.74 2.922211 0.52653 . . ENSG00000137869 ENST00000396402;ENST00000260433;ENST00000396404 T;T;T 0.73575 -0.76;-0.76;-0.76 6.06 2.13 0.27403 . 0.084915 0.85682 N 0.000000 T 0.69691 0.3139 L 0.58354 1.805 0.46279 D 0.998961 B 0.15141 0.012 B 0.27262 0.078 T 0.66152 -0.5995 10 0.52906 T 0.07 -23.6398 10.5475 0.45068 0.0:0.2114:0.0:0.7886 . 390 P11511 CP19A_HUMAN R 390 ENSP00000379683:K390R;ENSP00000260433:K390R;ENSP00000379685:K390R ENSP00000260433:K390R K - 2 0 CYP19A1 49291903 1.000000 0.71417 1.000000 0.80357 0.919000 0.55068 3.131000 0.50515 0.541000 0.28827 0.533000 0.62120 AAG TCGA-IB-8127-01A-11D-2396-08 CYP19A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254669.1 0 0 0 5 806 1 119 0 0 0 1 119 2 0 0 0 0 0 2 0 0.000600 6 794 1 116 22 -1.939015 0 1 0 0 1 1 2 3 1.928734 1 0.350000 3.330000 0.446809 0.040000 0 0.100000 0.030000 0.048321 0.040000 0 1.000000e-02 7.000000e-02 CPPED1 55313 broad.mit.edu 37 16 12875142 12875142 + Missense_Mutation SNP C C A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr16:12875142C>A ENST00000381774.4 - 2 429 c.189G>T c.(187-189)caG>caT p.Q63H CPPED1_ENST00000433677.2_Missense_Mutation_p.Q63H|CPPED1_ENST00000261660.4_Missense_Mutation_p.Q63H NM_018340.2 NP_060810.2 Q9BRF8 CPPED_HUMAN calcineurin-like phosphoesterase domain containing 1 18 GACGGATCTCCTGTTCCCATT 0.567000 0 SO:0001583 missense ENST00000381774.4 1 1 hg19 CCDS42120.1 . . . . . . . . . . C 14.67 2.603337 0.46423 . . ENSG00000103381 ENST00000381774;ENST00000433677;ENST00000261660 T;T;T 0.03358 3.96;4.02;3.96 5.25 4.29 0.51040 . 0.231983 0.42964 D 0.000630 T 0.08268 0.0206 L 0.56769 1.78 0.43885 D 0.996505 P;B 0.40875 0.731;0.01 P;B 0.47528 0.549;0.026 T 0.01814 -1.1268 10 0.62326 D 0.03 -22.7053 10.8774 0.46919 0.0:0.9093:0.0:0.0907 . 63;63 Q9BRF8-2;Q9BRF8 .;CPPED_HUMAN H 63 ENSP00000371193:Q63H;ENSP00000411127:Q63H;ENSP00000261660:Q63H ENSP00000261660:Q63H Q - 3 2 CPPED1 12782643 1.000000 0.71417 0.999000 0.59377 0.801000 0.45260 2.390000 0.44416 2.450000 0.82876 0.563000 0.77884 CAG TCGA-IB-8127-01A-11D-2396-08 CPPED1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395795.2 1 0 1 71 185 0 49 0 1 0 110 0 49 2 0 0 0 0 0 2 1 1.000000 68 182 0 49 2 -5.914900 1 1 0 0 1 3 3 6 2.254030 1 0.350000 3.330000 0.533046 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 C16orf62 57020 broad.mit.edu 37 16 19621689 19621689 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr16:19621689G>A ENST00000251143.5 + 12 987 c.975G>A c.(973-975)ggG>ggA p.G325G C16orf62_ENST00000448695.1_Silent_p.G175G|C16orf62_ENST00000543152.1_Silent_p.G74G|C16orf62_ENST00000438132.3_Silent_p.G414G|C16orf62_ENST00000417362.2_Silent_p.G325G|C16orf62_ENST00000542263.1_Silent_p.G414G Q7Z3J2 CP062_HUMAN chromosome 16 open reading frame 62 36 TGATCAGAGGGATCGGAGACC 0.572000 0 SO:0001819 synonymous_variant ENST00000251143.5 1 1 hg19 TCGA-IB-8127-01A-11D-2396-08 C16orf62-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 1 65 172 0 36 1 1 51 91 0 36 2 0 0 0 0 0 2 1 1.000000 64 167 0 36 2 -20.000000 1 1 0 0 1 2 2 4 2.223094 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ERBB2 2064 broad.mit.edu 37 17 37881332 37881332 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr17:37881332G>A ENST00000269571.5 + 21 2683 c.2524G>A c.(2524-2526)Gta>Ata p.V842I ERBB2_ENST00000541774.1_Missense_Mutation_p.V827I|ERBB2_ENST00000584450.1_Missense_Mutation_p.V842I|ERBB2_ENST00000445658.2_Missense_Mutation_p.V566I|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584601.1_Missense_Mutation_p.V812I|ERBB2_ENST00000406381.2_Missense_Mutation_p.V812I|ERBB2_ENST00000540147.1_Missense_Mutation_p.V812I P04626 ERBB2_HUMAN v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 p.V842I(6) 247 all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) Ovarian(249;0.0547)|Colorectal(1115;0.234) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171) ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072) TGTGCGGCTCGTACACAGGGA 0.597000 1 A, Mis, O breast, ovarian, other tumour types, NSCLC, gastric TCGA GBM(5;<1E-08) Dom yes 17 17q21.1 2064 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) E 6 Substitution - Missense(6) SO:0001583 missense ENST00000269571.5 1 1 hg19 CCDS32642.1 . . . . . . . . . . G 16.87 3.241303 0.58995 . . ENSG00000141736 ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147 D;D;D;D;D 0.83163 -1.69;-1.69;-1.69;-1.69;-1.69 5.09 5.09 0.68999 Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); . . . . D 0.85106 0.5621 N 0.21142 0.635 0.80722 D 1 D;D;D 0.76494 0.997;0.979;0.999 D;P;D 0.64506 0.92;0.559;0.926 D 0.87344 0.2333 9 0.87932 D 0 . 18.2846 0.90110 0.0:0.0:1.0:0.0 . 566;827;842 B4DTR1;P04626-4;P04626 .;.;ERBB2_HUMAN I 812;827;566;842;812 ENSP00000385185:V812I;ENSP00000446466:V827I;ENSP00000404047:V566I;ENSP00000269571:V842I;ENSP00000443562:V812I ENSP00000269571:V842I V + 1 0 ERBB2 35134858 1.000000 0.71417 0.919000 0.36401 0.900000 0.52787 9.657000 0.98554 2.651000 0.90000 0.563000 0.77884 GTA TCGA-IB-8127-01A-11D-2396-08 ERBB2-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445621.2 1 0 1 79 342 0 60 1 1 109 303 0 60 2 0 0 0 0 0 2 1 1.000000 78 333 0 60 2 -3.159312 1 1 0 0 1 1 3 4 2.017476 1 0.350000 3.330000 0.458108 0.990000 9.900000e-01 1.000000 1.000000 0.999740 0.990000 1 9.900000e-01 1 SPNS3 201305 broad.mit.edu 37 17 4348390 4348390 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr17:4348390G>A ENST00000355530.2 + 3 609 c.329G>A c.(328-330)cGc>cAc p.R110H SPNS3_ENST00000333476.2_Intron|SPNS3_ENST00000576069.1_Intron NM_182538.4 NP_872344.3 Q6ZMD2 SPNS3_HUMAN spinster homolog 3 (Drosophila) 28 CGACATAGCCGCAAGGCTACC 0.612000 0 SO:0001583 missense ENST00000355530.2 0 1 hg19 CCDS11045.1 . . . . . . . . . . G 17.99 3.522058 0.64747 . . ENSG00000182557 ENST00000355530 T 0.67345 -0.26 4.51 4.51 0.55191 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.000000 0.85682 D 0.000000 D 0.85427 0.5694 M 0.92169 3.28 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.89136 0.3513 10 0.87932 D 0 -27.825 15.5243 0.75890 0.0:0.0:1.0:0.0 . 110 Q6ZMD2 SPNS3_HUMAN H 110 ENSP00000347721:R110H ENSP00000347721:R110H R + 2 0 SPNS3 4295139 1.000000 0.71417 1.000000 0.80357 0.036000 0.12997 9.349000 0.97066 2.446000 0.82766 0.561000 0.74099 CGC TCGA-IB-8127-01A-11D-2396-08 SPNS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438793.1 0 0 0 7 769 0 181 0 6.988969e-04 0 4 0 181 2 0 0 0 0 0 2 1 0.979822 7 760 0 180 2 -1.819676 0 1 121412 4 45 1 0 2 2 1.683566 1 0.350000 3.330000 0.350000 0.050000 1.000000e-02 0.100000 0.060000 0.058657 0.050000 0 3.000000e-02 8.000000e-02 RNF43 54894 broad.mit.edu 37 17 56437563 56437563 + Missense_Mutation SNP T T C TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr17:56437563T>C ENST00000584437.1 - 7 2854 c.899A>G c.(898-900)gAc>gGc p.D300G RNF43_ENST00000407977.2_Missense_Mutation_p.D300G|RNF43_ENST00000583753.1_Missense_Mutation_p.D259G|RNF43_ENST00000500597.2_Missense_Mutation_p.D259G|RNF43_ENST00000581868.1_Missense_Mutation_p.D173G|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.D300G|RNF43_ENST00000577625.1_Missense_Mutation_p.D173G Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) TAACCAGGGGTCCACACAGTT 0.532000 0 SO:0001583 missense ENST00000584437.1 1 1 hg19 CCDS11607.1 . . . . . . . . . . T 29.8 5.038923 0.93630 . . ENSG00000108375 ENST00000407977;ENST00000500597 T;T 0.61274 0.12;0.12 5.09 5.09 0.68999 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1); 0.110516 0.64402 D 0.000014 T 0.73900 0.3646 M 0.77103 2.36 0.58432 D 0.999998 P;D;D 0.60575 0.913;0.988;0.982 P;P;P 0.62740 0.767;0.906;0.762 T 0.78319 -0.2250 10 0.87932 D 0 -12.8846 14.0453 0.64702 0.0:0.0:0.0:1.0 . 259;300;300 Q68DV7-2;Q68DV7-4;Q68DV7 .;.;RNF43_HUMAN G 300;259 ENSP00000385328:D300G;ENSP00000441969:D259G ENSP00000385328:D300G D - 2 0 RNF43 53792562 1.000000 0.71417 1.000000 0.80357 0.946000 0.59487 7.649000 0.83500 1.925000 0.55765 0.454000 0.30748 GAC TCGA-IB-8127-01A-11D-2396-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 152 348 1 100 1 9.999987e-01 62 1 1 100 4 1 1 104 215 1 511 4 1 1.000000 151 343 1 100 17 -20.000000 1 1 0 0 1 0 2 2 1.688006 1 0.350000 3.330000 0.350000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TNFSF12 8742 broad.mit.edu 37 17 7460597 7460597 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr17:7460597G>A ENST00000293825.6 + 7 943 c.680G>A c.(679-681)cGc>cAc p.R227H TNFSF13_ENST00000483039.1_5'Flank|TNFSF13_ENST00000380535.4_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000338784.4_5'Flank|TNFSF13_ENST00000349228.4_5'Flank|TNFSF12_ENST00000462811.1_3'UTR|TNFSF13_ENST00000396545.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank NM_003809.2 NP_003800.1 O43508 TNF12_HUMAN tumor necrosis factor (ligand) superfamily, member 12 11 Prostate(122;0.157) CTGCGGATCCGCACCCTCCCC 0.677000 0 SO:0001583 missense ENST00000293825.6 0 1 hg19 CCDS11109.1 . . . . . . . . . . G 21.8 4.203583 0.79127 . . ENSG00000239697 ENST00000293825 D 0.94417 -3.42 4.76 2.58 0.30949 Tumour necrosis factor (3);Tumour necrosis factor-like (2); . . . . D 0.94679 0.8284 L 0.36672 1.1 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 D 0.93286 0.6664 9 0.41790 T 0.15 . 12.3257 0.55009 0.0:0.0:0.695:0.305 . 227 O43508 TNF12_HUMAN H 227 ENSP00000293825:R227H ENSP00000293825:R227H R + 2 0 TNFSF12 7401321 1.000000 0.71417 1.000000 0.80357 0.852000 0.48524 2.653000 0.46691 1.127000 0.42034 0.561000 0.74099 CGC TCGA-IB-8127-01A-11D-2396-08 TNFSF12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000226951.2 0 0 0 6 359 0 74 0 9.190987e-01 0 270 0 74 2 0 0 0 0 0 2 1 0.962825 6 351 0 73 2 -2.716136 1 1 121396 3 34 1 0 2 2 1.675089 1 0.350000 3.330000 0.350000 0.090000 3.000000e-02 0.190000 0.100000 0.108424 0.090000 0 6.000000e-02 1.500000e-01 TP53 7157 broad.mit.edu 37 17 7577121 7577121 + Missense_Mutation SNP G G A rs121913343 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr17:7577121G>A ENST00000269305.4 - 8 1006 c.817C>T c.(817-819)Cgt>Tgt p.R273C TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCACAAACACGCACCTCAAAG 0.542000 R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID) 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 533 Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2) GRCh37 CM010471|CM010473|CM951233 TP53 M rs121913343 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 17.48 3.400216 0.62177 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.92 3.95 0.45737 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99851 0.9931 M 0.90759 3.145 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.998;0.998;0.999;0.996 D 0.96877 0.9643 10 0.87932 D 0 -11.9995 11.2235 0.48869 0.0895:0.0:0.9105:0.0 . 273;273;273;273 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. C 273;273;273;273;273;262;141 ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C ENSP00000269305:R273C R - 1 0 TP53 7517846 1.000000 0.71417 0.066000 0.19879 0.723000 0.41478 4.540000 0.60664 1.299000 0.44798 0.462000 0.41574 CGT TCGA-IB-8127-01A-11D-2396-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 38 88 0 34 1 1 65 50 0 34 2 1 1 206 391 0 1139 2 1 1.000000 38 84 0 34 2 -20.000000 1 1 121412 1 37 1 0 2 2 1.675089 1 0.350000 3.330000 0.350000 0.990000 9.900000e-01 1.000000 1.000000 0.999987 0.990000 1 9.900000e-01 1 ZNF521 25925 broad.mit.edu 37 18 22805518 22805518 + Silent SNP G G A rs28689581 byFrequency TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr18:22805518G>A ENST00000361524.3 - 4 2512 c.2364C>T c.(2362-2364)tgC>tgT p.C788C ZNF521_ENST00000538137.2_Silent_p.C788C|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.C568C NM_015461.2 NP_056276.1 Q96K83 ZN521_HUMAN zinc finger protein 521 149 all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991) AGGACTCACCGCAGAAAATGC 0.493000 T PAX5 ALL Dom yes 18 18q11.2 25925 zinc finger protein 521 L 0 SO:0001819 synonymous_variant ENST00000361524.3 1 0 hg19 CCDS32806.1 TCGA-IB-8127-01A-11D-2396-08 ZNF521-001 KNOWN overlapping_uORF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446781.2 1 0 1 83 566 0 84 0 9.655219e-01 0 39 0 84 2 0 0 0 0 0 2 1 1.000000 83 558 0 84 2 -2.879460 1 1 121412 527 60 1 0.350000 3.330000 0 0 ATP1A3 478 broad.mit.edu 37 19 42480634 42480634 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr19:42480634G>A ENST00000302102.5 - 15 2178 c.2028C>T c.(2026-2028)acC>acT p.T676T ATP1A3_ENST00000602133.1_Silent_p.T646T|ATP1A3_ENST00000545399.1_Silent_p.T689T|ATP1A3_ENST00000543770.1_Silent_p.T687T NM_152296.4 NP_689509.1 P13637 AT1A3_HUMAN ATPase, Na+/K+ transporting, alpha 3 polypeptide 52 AGACGATCTCGGTGTGATTCT 0.622000 0 SO:0001819 synonymous_variant ENST00000302102.5 1 1 hg19 CCDS12594.1 TCGA-IB-8127-01A-11D-2396-08 ATP1A3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000268107.1 1 0 1 118 316 0 71 0 0 1 0 0 71 2 0 0 0 0 0 2 1 1.000000 117 313 0 70 2 -7.009313 1 1 121412 1 29 1 3 3 6 2.271022 1 0.350000 3.330000 0.535382 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ZNRF4 148066 broad.mit.edu 37 19 5456673 5456673 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr19:5456673C>T ENST00000222033.4 + 1 1248 c.1171C>T c.(1171-1173)Cgc>Tgc p.R391C NM_181710.3 NP_859061.3 Q8WWF5 ZNRF4_HUMAN zinc and ring finger 4 16 AGTCCAGCTACGCTCCCGGAG 0.657000 0 SO:0001583 missense ENST00000222033.4 1 1 hg19 CCDS42475.1 . . . . . . . . . . C 13.35 2.211845 0.39102 . . ENSG00000105428 ENST00000222033 T 0.05319 3.46 3.47 3.47 0.39725 . 0.172241 0.34435 U 0.003970 T 0.13713 0.0332 L 0.32530 0.975 0.40657 D 0.982097 D 0.89917 1.0 D 0.75020 0.985 T 0.02477 -1.1153 10 0.62326 D 0.03 -27.0721 11.1698 0.48565 0.0:1.0:0.0:0.0 . 391 Q8WWF5 ZNRF4_HUMAN C 391 ENSP00000222033:R391C ENSP00000222033:R391C R + 1 0 ZNRF4 5407673 0.977000 0.34250 1.000000 0.80357 0.045000 0.14185 1.309000 0.33539 1.891000 0.54761 0.561000 0.74099 CGC TCGA-IB-8127-01A-11D-2396-08 ZNRF4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450924.1 1 0 1 56 293 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 56 287 0 71 2 -20.000000 1 1 120884 1 29 1 1 2 3 1.970622 1 0.350000 3.330000 0.446809 0.990000 8.300000e-01 1.000000 1.000000 0.980593 0.990000 1 9.400000e-01 1 VWA1 64856 broad.mit.edu 37 1 1374492 1374492 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:1374492G>A ENST00000476993.1 + 3 741 c.663G>A c.(661-663)acG>acA p.T221T VWA1_ENST00000338660.5_3'UTR|VWA1_ENST00000404702.3_Silent_p.T9T NM_022834.4 NP_073745.2 Q6PCB0 VWA1_HUMAN von Willebrand factor A domain containing 1 8 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) TCCATGCCACGGAGATCACGT 0.711000 0 SO:0001819 synonymous_variant ENST00000476993.1 1 1 hg19 CCDS27.1 TCGA-IB-8127-01A-11D-2396-08 VWA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008291.1 1 0 1 13 120 0 24 1 1 57 330 0 24 2 0 0 0 0 0 2 1 0.999583 13 118 0 24 2 -19.419930 1 1 120026 3 30 1 2 2 4 1.868805 1 0.350000 3.330000 0.438445 0.730000 3.900000e-01 1.000000 1.000000 0.753450 0.730000 0 5.300000e-01 1 ACP6 51205 broad.mit.edu 37 1 147131792 147131792 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:147131792G>A ENST00000369238.6 - 2 765 c.318C>T c.(316-318)taC>taT p.Y106Y ACP6_ENST00000392988.2_Silent_p.Y106Y NM_016361.3 NP_057445.4 Q9NPH0 PPA6_HUMAN acid phosphatase 6, lysophosphatidic 16 all_hematologic(923;0.0276) ATTGAGAGTCGTAAGGAGAAT 0.507000 0 SO:0001819 synonymous_variant ENST00000369238.6 1 1 hg19 CCDS928.1 TCGA-IB-8127-01A-11D-2396-08 ACP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039420.2 1 0 0 100 286 0 59 1 1 19 58 0 59 2 0 0 0 0 0 2 1 1.000000 99 283 0 59 2 -20.000000 1 1 121412 4 37 1 3 3 6 2.255618 1 0.350000 3.330000 0.533046 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PSMB4 5692 broad.mit.edu 37 1 151372491 151372491 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:151372491G>A ENST00000290541.6 + 2 229 c.175G>A c.(175-177)Gtt>Att p.V59I NM_002796.2 NP_002787.2 P28070 PSB4_HUMAN proteasome (prosome, macropain) subunit, beta type, 4 14 Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) AGTCCTCGGCGTTAAGTTCGA 0.592000 0 SO:0001583 missense ENST00000290541.6 0 1 hg19 CCDS996.1 . . . . . . . . . . G 9.747 1.166446 0.21621 . . ENSG00000159377 ENST00000290541 T 0.28255 1.62 5.34 4.42 0.53409 Proteasome, beta-type subunit, conserved site (1); 0.057731 0.64402 D 0.000001 T 0.04543 0.0124 N 0.03903 -0.33 0.58432 D 0.999996 B;B 0.09022 0.001;0.002 B;B 0.17098 0.012;0.017 T 0.26815 -1.0092 10 0.02654 T 1 -15.3311 14.7134 0.69249 0.0:0.146:0.854:0.0 . 59;59 B4DFL3;P28070 .;PSB4_HUMAN I 59 ENSP00000290541:V59I ENSP00000290541:V59I V + 1 0 PSMB4 149639115 1.000000 0.71417 0.712000 0.30502 0.997000 0.91878 4.476000 0.60216 1.232000 0.43678 0.561000 0.74099 GTT TCGA-IB-8127-01A-11D-2396-08 PSMB4-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034885.1 0 0 0 7 815 0 136 0 9.980575e-01 0 1420 0 136 2 0 0 0 0 0 2 1 0.979769 7 805 0 131 2 -2.483483 0 1 0 0 1 2 2 4 2.214488 1 0.350000 3.330000 0.518519 0.060000 1.000000e-02 0.140000 0.080000 0.074091 0.060000 0 3.000000e-02 1.000000e-01 FLG 2312 broad.mit.edu 37 1 152280068 152280068 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:152280068C>T ENST00000368799.1 - 3 7329 c.7294G>A c.(7294-7296)Ggg>Agg p.G2432R FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GTGCTGGTCCCGGTCCGTCCA 0.592000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . C 10.22 1.291031 0.23564 . . ENSG00000143631 ENST00000368799 T 0.01705 4.68 4.37 -6.56 0.01848 . . . . . T 0.00300 0.0009 N 0.21448 0.665 0.09310 N 1 B 0.27013 0.166 B 0.16289 0.015 T 0.47935 -0.9078 9 0.14656 T 0.56 . 1.9786 0.03421 0.1118:0.2438:0.3309:0.3135 . 2432 P20930 FILA_HUMAN R 2432 ENSP00000357789:G2432R ENSP00000357789:G2432R G - 1 0 FLG 150546692 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -1.200000 0.03029 -1.351000 0.02197 -2.865000 0.00100 GGG TCGA-IB-8127-01A-11D-2396-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 0 0 1 643 1774 1 343 0 0 0 1 1 343 2 0 0 0 0 0 2 1 1.000000 639 1759 1 340 23 -17.278260 1 1 121412 4 44 1 2 2 4 2.214488 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 MUC1 4582 broad.mit.edu 37 1 155161799 155161799 + Missense_Mutation SNP T T G TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:155161799T>G ENST00000368395.1 - 2 405 c.334A>C c.(334-336)Acc>Ccc p.T112P 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_Intron|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) GCTGGCGGGGTGGTGGAGCCC 0.711000 T IGH@ B-NHL Dom yes 1 1q21 4582 mucin 1, transmembrane L 0 SO:0001583 missense ENST00000368395.1 0 1 hg19 CCDS55640.1 . . . . . . . . . . T 8.249 0.808546 0.16467 . . ENSG00000185499 ENST00000368395;ENST00000425082 T 0.20200 2.09 2.73 0.35 0.16037 . 2.188600 0.02617 N 0.102742 T 0.11024 0.0269 N 0.14661 0.345 0.09310 N 0.999999 D 0.65815 0.995 D 0.68483 0.958 T 0.17684 -1.0361 10 0.39692 T 0.17 . 3.1844 0.06596 0.0:0.2782:0.2183:0.5034 . 112 P15941 MUC1_HUMAN P 112 ENSP00000357380:T112P ENSP00000357380:T112P T - 1 0 MUC1 153428423 0.000000 0.05858 0.001000 0.08648 0.003000 0.03518 -0.417000 0.07088 0.027000 0.15297 -1.038000 0.02383 ACC TCGA-IB-8127-01A-11D-2396-08 MUC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000086735.1 0 0 0 28 82 1 23 1 9.999948e-01 69 550 1 23 60 0 0 0 0 0 2 1 0.986001 27 78 1 22 15 -2.663877 1 1 120668 181 36 1 2 2 4 2.214488 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 0.999991 0.990000 1 9.900000e-01 1 HMCN1 83872 broad.mit.edu 37 1 185902879 185902879 + Missense_Mutation SNP A A G rs143393655 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:185902879A>G ENST00000271588.4 + 11 1980 c.1751A>G c.(1750-1752)aAc>aGc p.N584S HMCN1_ENST00000367492.2_Missense_Mutation_p.N584S NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 GTGAAATTCAACGATGCTGGA 0.463000 0 SO:0001583 missense ENST00000271588.4 1 1 hg19 CCDS30956.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 A 0.109 -1.141427 0.01728 0.0 1.16E-4 ENSG00000143341 ENST00000271588;ENST00000367492 T;T 0.23950 1.88;1.88 5.67 -3.39 0.04868 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.763207 0.13136 N 0.411053 T 0.04679 0.0127 N 0.00783 -1.19 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.38972 -0.9636 10 0.07990 T 0.79 . 2.6597 0.05023 0.2194:0.4469:0.1585:0.1752 . 584 Q96RW7 HMCN1_HUMAN S 584 ENSP00000271588:N584S;ENSP00000356462:N584S ENSP00000271588:N584S N + 2 0 HMCN1 184169502 0.000000 0.05858 0.001000 0.08648 0.545000 0.35147 -0.230000 0.09083 -0.188000 0.10499 -0.242000 0.12053 AAC TCGA-IB-8127-01A-11D-2396-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 1 0 1 174 511 0 110 0 3.763574e-01 0 5 0 110 2 0 0 0 0 0 2 1 1.000000 172 509 0 110 2 -20.000000 1 1 121412 7 43 1 2 2 4 2.214488 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 GABRD 2563 broad.mit.edu 37 1 1961126 1961126 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:1961126C>T ENST00000378585.4 + 8 1067 c.984C>T c.(982-984)taC>taT p.Y328Y NM_000815.4 NP_000806.2 O14764 GBRD_HUMAN gamma-aminobutyric acid (GABA) A receptor, delta 20 all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) TGGTGGAGTACGCCTTTGCTC 0.612000 0 SO:0001819 synonymous_variant ENST00000378585.4 1 1 hg19 CCDS36.1 TCGA-IB-8127-01A-11D-2396-08 GABRD-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000098493.1 1 0 1 32 251 0 64 0 3.250425e-01 0 10 0 64 2 0 0 0 0 0 2 1 1.000000 32 247 0 64 2 -20.000000 1 0 121348 1 32 1 2 3 5 1.844463 1 0.350000 3.330000 0.428069 0.770000 5.200000e-01 1.000000 0.730000 0.793561 0.770000 0 6.300000e-01 1 EPHA8 2046 broad.mit.edu 37 1 22925390 22925390 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:22925390C>T ENST00000166244.3 + 13 2310 c.2238C>T c.(2236-2238)gcC>gcT p.A746A NM_020526.3 NP_065387.1 P29322 EPHA8_HUMAN EPH receptor A8 61 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) GAGTGGGTGCCGGCATGCGCT 0.627000 0 SO:0001819 synonymous_variant ENST00000166244.3 1 1 hg19 CCDS225.1 TCGA-IB-8127-01A-11D-2396-08 EPHA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008085.1 1 0 1 20 119 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.999997 20 117 0 34 2 -3.342141 1 1 121364 13 40 1 1 2 3 1.835520 1 0.350000 3.330000 0.415468 0.990000 6.100000e-01 1.000000 1.000000 0.912953 0.990000 1 7.700000e-01 1 SERINC2 347735 broad.mit.edu 37 1 31899619 31899619 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr1:31899619C>T ENST00000373709.3 + 6 879 c.729C>T c.(727-729)aaC>aaT p.N243N SERINC2_ENST00000536384.1_Silent_p.N247N|SERINC2_ENST00000536859.1_Silent_p.N247N|SERINC2_ENST00000373710.1_Silent_p.N252N|SERINC2_ENST00000491976.1_3'UTR NM_178865.4 NP_849196.2 Q96SA4 SERC2_HUMAN serine incorporator 2 12 Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123) TCAGCCTCAACCTCACCTTCT 0.622000 0 SO:0001819 synonymous_variant ENST00000373709.3 1 1 hg19 CCDS30662.1 TCGA-IB-8127-01A-11D-2396-08 SERINC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000010680.1 1 0 0 193 968 0 199 1 1 525 864 0 199 2 0 0 0 0 0 2 1 1.000000 190 959 0 197 2 -20.000000 1 1 0 0 1 1 2 3 1.835520 1 0.350000 3.330000 0.415468 0.990000 9.200000e-01 1.000000 1.000000 0.994084 0.990000 1 9.900000e-01 1 C20orf112 0 broad.mit.edu 37 20 31043974 31043974 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr20:31043974C>T ENST00000359676.5 - 3 476 c.334G>A c.(334-336)Ggt>Agt p.G112S RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR NM_001256798.1|NM_080616.4 NP_001243727.1|NP_542183.2 Q96MY1 NOL4L_HUMAN 15 CCGTCGGCACCGCAGCCATCC 0.652000 0 SO:0001583 missense ENST00000359676.5 1 1 hg19 CCDS13202.1 . . . . . . . . . . C 3.429 -0.116427 0.06881 . . ENSG00000197183 ENST00000359676;ENST00000397984 . . . 4.98 -0.0961 0.13638 . 0.486110 0.19807 N 0.105638 T 0.15478 0.0373 N 0.02011 -0.69 0.80722 D 1 B 0.11235 0.004 B 0.08055 0.003 T 0.14699 -1.0463 9 0.08599 T 0.76 -3.2168 7.111 0.25390 0.0:0.312:0.0:0.688 . 112 Q96MY1 CT112_HUMAN S 112 . ENSP00000352704:G112S G - 1 0 C20orf112 30507635 0.003000 0.15002 0.036000 0.18154 0.019000 0.09904 -0.563000 0.05943 0.071000 0.16664 -0.367000 0.07326 GGT TCGA-IB-8127-01A-11D-2396-08 C20orf112-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000078628.2 1 0 1 214 589 0 117 1 9.999928e-01 20 29 0 117 2 0 0 0 0 0 2 1 1.000000 212 585 0 114 2 -8.496379 1 1 121324 1 35 1 2 2 4 2.202238 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 KCNB1 3745 broad.mit.edu 37 20 48098546 48098546 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr20:48098546G>A ENST00000371741.4 - 1 638 c.472C>T c.(472-474)Cgg>Tgg p.R158W NM_004975.2 NP_004966.1 Q14721 KCNB1_HUMAN potassium voltage-gated channel, Shab-related subfamily, member 1 53 BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166) Dalfampridine(DB06637) TCGCCTTCCCGCTCCCGTAGG 0.582000 0 SO:0001583 missense ENST00000371741.4 0 1 hg19 CCDS13418.1 . . . . . . . . . . G 15.24 2.774548 0.49786 . . ENSG00000158445 ENST00000371741;ENST00000538812 D 0.96685 -4.09 5.15 4.19 0.49359 . 0.000000 0.85682 D 0.000000 D 0.97309 0.9120 M 0.67397 2.05 0.58432 D 0.999999 D 0.76494 0.999 D 0.68621 0.959 D 0.97675 1.0169 10 0.87932 D 0 . 12.9275 0.58268 0.0:0.0:0.652:0.348 . 158 Q14721 KCNB1_HUMAN W 158;113 ENSP00000360806:R158W ENSP00000360806:R158W R - 1 2 KCNB1 47531953 1.000000 0.71417 1.000000 0.80357 0.636000 0.38137 2.892000 0.48625 1.380000 0.46344 -0.311000 0.09066 CGG TCGA-IB-8127-01A-11D-2396-08 KCNB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080374.3 0 0 0 9 839 0 130 0 0 0 1 0 130 2 0 0 0 0 0 2 1 0.993914 9 829 0 128 2 -2.121277 0 1 0 0 1 2 2 4 2.202238 1 0.350000 3.330000 0.518519 0.080000 2.000000e-02 0.150000 0.080000 0.091187 0.080000 0 5.000000e-02 1.200000e-01 BIRC7 79444 broad.mit.edu 37 20 61867525 61867525 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr20:61867525C>T ENST00000217169.3 + 1 291 c.77C>T c.(76-78)aCg>aTg p.T26M BIRC7_ENST00000342412.6_Missense_Mutation_p.T26M|MIR3196_ENST00000579556.1_RNA|BIRC7_ENST00000395306.1_5'Flank NM_139317.1 NP_647478.1 Q96CA5 BIRC7_HUMAN baculoviral IAP repeat containing 7 12 all_cancers(38;2.72e-09) GATGGTCCCACGCAGGAGCGC 0.662000 0 SO:0001583 missense ENST00000217169.3 0 1 hg19 CCDS13513.1 . . . . . . . . . . c 9.412 1.080830 0.20309 . . ENSG00000101197 ENST00000342412;ENST00000217169 T;T 0.57273 0.63;0.41 4.73 -1.7 0.08159 . 1.838210 0.03858 N 0.273537 T 0.30230 0.0758 N 0.14661 0.345 0.09310 N 1 B;B;B 0.14438 0.008;0.009;0.01 B;B;B 0.06405 0.002;0.001;0.002 T 0.08269 -1.0730 10 0.28530 T 0.3 . 1.6898 0.02849 0.157:0.1752:0.156:0.5119 . 26;26;26 Q6R308;Q96CA5;Q96CA5-2 .;BIRC7_HUMAN;. M 26 ENSP00000345213:T26M;ENSP00000217169:T26M ENSP00000217169:T26M T + 2 0 BIRC7 61337970 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 0.061000 0.14366 -0.160000 0.11002 0.506000 0.49869 ACG TCGA-IB-8127-01A-11D-2396-08 BIRC7-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080114.2 1 0 0 17 51 0 8 1 9.969305e-01 13 20 0 8 2 0 0 0 0 0 2 1 0.999982 17 49 0 8 2 -20.000000 1 1 120378 1 29 1 2 2 4 2.202238 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 0.999765 0.990000 1 9.900000e-01 1 CNTNAP5 129684 broad.mit.edu 37 2 125367458 125367458 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:125367458G>A ENST00000431078.1 + 12 2198 c.1834G>A c.(1834-1836)Ggc>Agc p.G612S NM_130773.2 NP_570129.1 Q8WYK1 CNTP5_HUMAN contactin associated protein-like 5 176 AGATGGCAGCGGCCCACTGGG 0.532000 0 SO:0001583 missense ENST00000431078.1 1 1 hg19 CCDS46401.1 . . . . . . . . . . G 34 5.332205 0.95733 . . ENSG00000155052 ENST00000431078 T 0.59772 0.24 5.66 5.66 0.87406 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2); 0.000000 0.50627 D 0.000112 D 0.83348 0.5235 H 0.94385 3.53 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.86857 0.2027 10 0.62326 D 0.03 . 18.6671 0.91495 0.0:0.0:1.0:0.0 . 612 Q8WYK1 CNTP5_HUMAN S 612 ENSP00000399013:G612S ENSP00000399013:G612S G + 1 0 CNTNAP5 125083928 1.000000 0.71417 0.887000 0.34795 0.787000 0.44495 8.884000 0.92432 2.826000 0.97356 0.655000 0.94253 GGC TCGA-IB-8127-01A-11D-2396-08 CNTNAP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330864.3 1 0 0 51 443 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 1.000000 52 441 0 77 2 -3.075755 1 1 120836 2 35 1 2 2 4 2.165928 1 0.350000 3.330000 0.513473 0.790000 5.900000e-01 1.000000 0.790000 0.802997 0.790000 0 6.900000e-01 9.200000e-01 LRP1B 53353 broad.mit.edu 37 2 141457900 141457900 + Nonsense_Mutation SNP G G A rs111904937 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:141457900G>A ENST00000389484.3 - 41 7689 c.6718C>T c.(6718-6720)Cga>Tga p.R2240* NM_018557.2 NP_061027.2 Q9NZR2 LRP1B_HUMAN low density lipoprotein receptor-related protein 1B 606 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) TAAAAGATTCGGTTGGTACCT 0.338000 TSP Lung(27;0.18) Colon(99;50 2074 2507 20106) 0 SO:0001587 stop_gained ENST00000389484.3 0 1 hg19 CCDS2182.1 . . . . . . . . . . G 53 20.963690 0.99936 . . ENSG00000168702 ENST00000389484;ENST00000544579 . . . 4.47 4.47 0.54385 . 0.000000 0.64402 U 0.000004 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 13.3686 0.60701 0.0:0.0:0.8416:0.1584 . . . . X 2240;2178 . ENSP00000374135:R2240X R - 1 2 LRP1B 141174370 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 2.608000 0.46308 2.176000 0.68965 0.585000 0.79938 CGA TCGA-IB-8127-01A-11D-2396-08 LRP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254736.2 1 0 1 173 539 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 170 533 0 85 2 -5.063698 1 1 0 0 1 2 2 4 2.165928 1 0.350000 3.330000 0.513473 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SCN1A 6323 broad.mit.edu 37 2 166911147 166911147 + Splice_Site SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:166911147C>T ENST00000303395.4 - 4 602 c.e4+1 AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Splice_Site|SCN1A_ENST00000409050.1_Splice_Site|SCN1A_ENST00000423058.2_Splice_Site|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA P35498 SCN1A_HUMAN sodium channel, voltage-gated, type I, alpha subunit 200 Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909) AAGGCACTTACGCAAATGTAA 0.343000 0 GRCh37 CS032427 SCN1A S SO:0001630 splice_region_variant ENST00000303395.4 1 1 hg19 CCDS54413.1 . . . . . . . . . . C 27.6 4.844927 0.91197 . . ENSG00000144285 ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050 . . . 5.24 5.24 0.73138 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.1745 0.93599 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . SCN1A 166619393 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.726000 0.84824 2.597000 0.87782 0.561000 0.74099 . TCGA-IB-8127-01A-11D-2396-08 SCN1A-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102661.1 1 0 1 69 235 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 1.000000 69 233 0 21 2 -20.000000 1 1 0 0 1 2 2 4 2.165928 1 0.350000 3.330000 0.513473 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 DOCK10 55619 broad.mit.edu 37 2 225659771 225659771 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:225659771C>T ENST00000258390.7 - 45 5046 c.4979G>A c.(4978-4980)cGt>cAt p.R1660H DOCK10_ENST00000409592.3_Missense_Mutation_p.R1654H NM_014689.2 NP_055504.2 Q96BY6 DOC10_HUMAN dedicator of cytokinesis 10 p.R1658H(1)|p.R198H(1) 87 Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14) AGTCCTTATACGCTTAGTCAG 0.478000 2 Substitution - Missense(2) SO:0001583 missense ENST00000258390.7 0 1 hg19 CCDS46528.1 . . . . . . . . . . C 35 5.577896 0.96565 . . ENSG00000135905 ENST00000409592;ENST00000258390;ENST00000373702 T;T 0.65178 4.66;-0.14 5.8 5.8 0.92144 . 0.000000 0.85682 D 0.000000 D 0.83603 0.5290 M 0.91090 3.175 0.58432 D 0.999999 D;P;D;D 0.76494 0.972;0.95;0.984;0.999 B;B;P;D 0.64410 0.444;0.439;0.74;0.925 D 0.86564 0.1843 10 0.87932 D 0 . 20.0637 0.97700 0.0:1.0:0.0:0.0 . 1660;514;1654;322 Q96BY6;B4DF07;B3FL70;B4DEY4 DOC10_HUMAN;.;.;. H 1654;1660;198 ENSP00000386694:R1654H;ENSP00000258390:R1660H ENSP00000258390:R1660H R - 2 0 DOCK10 225368015 1.000000 0.71417 0.985000 0.45067 0.992000 0.81027 7.487000 0.81328 2.751000 0.94390 0.650000 0.86243 CGT TCGA-IB-8127-01A-11D-2396-08 DOCK10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331246.1 0 0 0 10 713 0 107 0 1.785854e-01 0 50 0 107 2 0 0 0 0 0 2 1 0.996747 10 706 0 107 2 -2.600244 1 1 0 0 1 2 2 4 2.165928 1 0.350000 3.330000 0.513473 0.100000 4.000000e-02 1.000000 0.120000 0.141147 0.100000 0 7.000000e-02 1.600000e-01 ANTXR1 84168 broad.mit.edu 37 2 69409641 69409641 + Missense_Mutation SNP A A G TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:69409641A>G ENST00000303714.4 + 16 1524 c.1202A>G c.(1201-1203)aAg>aGg p.K401R RNA5SP96_ENST00000516041.1_RNA|RNU6-1216P_ENST00000362590.2_RNA NM_032208.2 NP_115584.1 Q9H6X2 ANTR1_HUMAN anthrax toxin receptor 1 29 TGGGGAGAAAAGGGCTCCACA 0.418000 Familial Infantile Hemangioma 0 SO:0001583 missense Familial Cancer Database Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma ENST00000303714.4 0 1 hg19 CCDS1892.1 . . . . . . . . . . A 13.57 2.276887 0.40294 . . ENSG00000169604 ENST00000303714 D 0.82803 -1.65 5.32 5.32 0.75619 Anthrax toxin receptor, C-terminal (2); 0.089199 0.85682 D 0.000000 T 0.73575 0.3604 L 0.28400 0.85 0.80722 D 1 B 0.25105 0.118 B 0.27796 0.083 T 0.71199 -0.4663 10 0.49607 T 0.09 -23.5511 9.1252 0.36810 0.9193:0.0:0.0807:0.0 . 401 Q9H6X2 ANTR1_HUMAN R 401 ENSP00000301945:K401R ENSP00000301945:K401R K + 2 0 ANTXR1 69263145 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 4.689000 0.61723 2.235000 0.73313 0.459000 0.35465 AAG TCGA-IB-8127-01A-11D-2396-08 ANTXR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251770.2 0 0 0 5 444 1 74 0 1.737930e-03 2 446 1 74 20 0 0 0 0 0 2 0 0.001617 5 439 1 74 20 -2.656256 1 1 0 0 1 2 2 4 2.154288 1 0.350000 3.330000 0.510910 0.090000 2.000000e-02 1.000000 0.080000 0.142828 0.090000 0 5.000000e-02 1.500000e-01 CLEC4F 165530 broad.mit.edu 37 2 71036948 71036948 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr2:71036948G>A ENST00000272367.2 - 6 1657 c.1581C>T c.(1579-1581)atC>atT p.I527I CLEC4F_ENST00000426626.1_Silent_p.I527I NM_001258027.1|NM_173535.2 NP_001244956.1|NP_775806.2 Q8N1N0 CLC4F_HUMAN C-type lectin domain family 4, member F 37 CAGTGAGACCGATCCAGTAGT 0.562000 Colon(107;10 2157 6841 26035) 0 SO:0001819 synonymous_variant ENST00000272367.2 1 1 hg19 CCDS1910.1 TCGA-IB-8127-01A-11D-2396-08 CLEC4F-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251922.1 0 0 1 150 578 1 123 0 4.416022e-01 0 7 1 123 2 0 0 0 0 0 2 1 1.000000 149 573 0 123 2 -3.801580 1 1 121412 1 32 1 2 2 4 2.154288 1 0.350000 3.330000 0.510910 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ANKRD28 23243 broad.mit.edu 37 3 15731728 15731728 + Splice_Site SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr3:15731728C>T ENST00000399451.2 - 18 2039 c.e18-1 ANKRD28_ENST00000497037.1_Splice_Site|ANKRD28_ENST00000383777.1_Splice_Site NM_001195098.1|NM_001195099.1|NM_015199.3 NP_001182027.1|NP_001182028.1|NP_056014.2 O15084 ANR28_HUMAN ankyrin repeat domain 28 6 CATGATAGGCCTAGAAATAAA 0.318000 0 SO:0001630 splice_region_variant ENST00000399451.2 0 1 hg19 CCDS46769.1 . . . . . . . . . . C 23.7 4.451013 0.84209 . . ENSG00000206560 ENST00000399451;ENST00000383777;ENST00000412318 . . . 5.53 5.53 0.82687 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.472 0.94966 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . ANKRD28 15706732 1.000000 0.71417 1.000000 0.80357 0.940000 0.58332 7.480000 0.81109 2.585000 0.87301 0.655000 0.94253 . TCGA-IB-8127-01A-11D-2396-08 ANKRD28-003 PUTATIVE basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000339758.1 1 0 0 4 53 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 0.892791 4 53 0 8 2 -8.743280 1 1 0 0 1 0 4 4 1.801629 1 0.350000 3.330000 0.408015 0.550000 1.700000e-01 1.000000 1.000000 0.608595 0.550000 0 3.200000e-01 1 NAALADL2 254827 broad.mit.edu 37 3 174815006 174815006 + Nonsense_Mutation SNP C C A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr3:174815006C>A ENST00000454872.1 + 2 598 c.470C>A c.(469-471)tCa>tAa p.S157* NAALADL2_ENST00000473253.1_3'UTR|NAALADL2-AS3_ENST00000453180.1_RNA NM_207015.2 NP_996898.2 Q58DX5 NADL2_HUMAN N-acetylated alpha-linked acidic dipeptidase-like 2 49 Ovarian(172;0.0102) all_cancers(1;0.0272)|all_epithelial(1;0.0553) OV - Ovarian serous cystadenocarcinoma(80;9.26e-28) GCTCCATCTTCAGGAACAGTT 0.358000 0 SO:0001587 stop_gained ENST00000454872.1 0 1 hg19 CCDS46960.1 . . . . . . . . . . C 24.8 4.573879 0.86542 . . ENSG00000177694 ENST00000454872 . . . 5.63 5.63 0.86233 . 0.321256 0.22752 N 0.056073 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . -7.1618 16.3124 0.82883 0.1327:0.8672:0.0:0.0 . . . . X 157 . . S + 2 0 NAALADL2 176297700 1.000000 0.71417 0.857000 0.33713 0.752000 0.42762 3.818000 0.55678 2.803000 0.96430 0.585000 0.79938 TCA TCGA-IB-8127-01A-11D-2396-08 NAALADL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347390.2 0 0 0 8 634 0 92 0 3.681114e-02 0 21 0 92 2 0 0 0 0 0 2 1 0.989085 7 630 0 92 2 -2.506986 1 1 0 0 1 1 2 3 1.903978 1 0.350000 3.330000 0.446809 0.080000 3.000000e-02 0.160000 0.090000 0.093701 0.080000 0 5.000000e-02 1.300000e-01 SCN5A 6331 broad.mit.edu 37 3 38627422 38627422 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr3:38627422G>A ENST00000333535.4 - 16 2696 c.2547C>T c.(2545-2547)atC>atT p.I849I SCN5A_ENST00000450102.2_Silent_p.I849I|SCN5A_ENST00000451551.2_Silent_p.I849I|SCN5A_ENST00000413689.1_Silent_p.I849I|SCN5A_ENST00000423572.2_Silent_p.I849I|SCN5A_ENST00000455624.2_Silent_p.I849I|SCN5A_ENST00000443581.1_Silent_p.I849I|SCN5A_ENST00000425664.1_Silent_p.I849I|SCN5A_ENST00000449557.2_Silent_p.I849I|SCN5A_ENST00000414099.2_Silent_p.I849I Q14524 SCN5A_HUMAN sodium channel, voltage-gated, type V, alpha subunit 107 Medulloblastoma(35;0.163) Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909) AGATGAACACGATGATGGCTA 0.567000 0 SO:0001819 synonymous_variant ENST00000333535.4 1 1 hg19 CCDS46796.1 TCGA-IB-8127-01A-11D-2396-08 SCN5A-014 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000377958.1 1 0 1 63 463 0 83 0 0 0 1 0 83 2 0 0 0 0 0 2 1 1.000000 62 460 0 83 2 -19.999760 1 1 0 0 1 0 4 4 1.801629 1 0.350000 3.330000 0.408015 0.770000 5.900000e-01 1.000000 0.740000 0.805043 0.770000 0 6.700000e-01 1 DHX15 1665 broad.mit.edu 37 4 24578266 24578266 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr4:24578266C>T ENST00000336812.4 - 2 263 c.107G>A c.(106-108)cGg>cAg p.R36Q NM_001358.2 NP_001349.2 O43143 DHX15_HUMAN DEAH (Asp-Glu-Ala-His) box helicase 15 30 Breast(46;0.0503) ATCTTTAGACCGATCTTCACG 0.418000 0 SO:0001583 missense ENST00000336812.4 1 1 hg19 CCDS33966.1 . . . . . . . . . . C 19.52 3.842965 0.71488 . . ENSG00000109606 ENST00000336812 T 0.60920 0.15 5.59 4.74 0.60224 . 0.070853 0.56097 D 0.000027 T 0.29652 0.0740 N 0.08118 0 0.80722 D 1 P 0.43352 0.804 B 0.30316 0.114 T 0.24012 -1.0172 10 0.13853 T 0.58 -7.751 14.6282 0.68638 0.0:0.9285:0.0:0.0715 . 36 O43143 DHX15_HUMAN Q 36 ENSP00000336741:R36Q ENSP00000336741:R36Q R - 2 0 DHX15 24187364 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 5.772000 0.68889 2.648000 0.89879 0.650000 0.86243 CGG TCGA-IB-8127-01A-11D-2396-08 DHX15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360143.1 1 0 1 93 151 0 47 1 1 155 185 0 47 2 0 0 0 0 0 2 1 1.000000 93 149 0 46 2 -13.396250 1 1 0 0 1 1 2 3 1.936336 1 0.350000 3.330000 0.446809 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 KCTD8 386617 broad.mit.edu 37 4 44176848 44176848 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr4:44176848G>A ENST00000360029.3 - 2 1664 c.1381C>T c.(1381-1383)Cgc>Tgc p.R461C NM_198353.2 NP_938167.1 Q6ZWB6 KCTD8_HUMAN potassium channel tetramerization domain containing 8 p.R461C(1) 41 TGCCATTGGCGTTTGCGCTCT 0.363000 HNSCC(17;0.042) 1 Substitution - Missense(1) SO:0001583 missense ENST00000360029.3 1 1 hg19 CCDS3467.1 . . . . . . . . . . G 15.83 2.948563 0.53186 . . ENSG00000183783 ENST00000360029 T 0.44083 0.93 4.91 4.91 0.64330 . 0.000000 0.52532 D 0.000075 T 0.50154 0.1599 N 0.24115 0.695 0.46798 D 0.999203 D 0.89917 1.0 D 0.64595 0.927 T 0.54636 -0.8264 10 0.72032 D 0.01 . 17.6253 0.88092 0.0:0.0:1.0:0.0 . 461 Q6ZWB6 KCTD8_HUMAN C 461 ENSP00000353129:R461C ENSP00000353129:R461C R - 1 0 KCTD8 43871605 1.000000 0.71417 1.000000 0.80357 0.853000 0.48598 3.936000 0.56568 2.699000 0.92147 0.650000 0.86243 CGC TCGA-IB-8127-01A-11D-2396-08 KCTD8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216868.1 1 0 1 89 561 0 120 0 5.229704e-02 0 3 0 120 2 0 0 0 0 0 2 1 1.000000 89 557 0 120 2 -20.000000 1 1 121410 11 43 1 1 2 3 1.972835 1 0.350000 3.330000 0.446809 0.910000 7.400000e-01 1.000000 1.000000 0.913954 0.910000 1 8.200000e-01 1 MMRN1 22915 broad.mit.edu 37 4 90872776 90872776 + Silent SNP C C A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr4:90872776C>A ENST00000394980.1 + 8 3458 c.3139C>A c.(3139-3141)Cgg>Agg p.R1047R MMRN1_ENST00000394981.1_Silent_p.R350R|MMRN1_ENST00000264790.2_Silent_p.R1047R|MMRN1_ENST00000508372.1_Silent_p.R789R Q13201 MMRN1_HUMAN multimerin 1 72 Hepatocellular(203;0.114) AAGCTGTAGTCGGCATCCGTG 0.433000 0 SO:0001819 synonymous_variant ENST00000394980.1 0 1 hg19 CCDS3635.1 TCGA-IB-8127-01A-11D-2396-08 MMRN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253546.2 0 0 0 8 308 0 37 0 1.407274e-01 0 23 0 37 2 0 0 0 0 0 2 1 0.989190 8 305 0 37 2 -3.730222 1 1 121382 12 38 1 1 3 4 2.072452 1 0.350000 3.330000 0.499037 0.200000 8.000000e-02 1.000000 0.190000 0.303103 0.200000 0 1.400000e-01 3.400000e-01 PCDHGA1 56114 broad.mit.edu 37 5 140712339 140712339 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr5:140712339G>A ENST00000517417.1 + 1 2088 c.2088G>A c.(2086-2088)gcG>gcA p.A696A PCDHGA1_ENST00000378105.3_Silent_p.A696A NM_018912.2 NP_061735.1 Q9Y5H4 PCDG1_HUMAN protocadherin gamma subfamily A, 1 p.A696A(4) 78 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGGTGGTGGCGGCGGCCGCGG 0.672000 4 Substitution - coding silent(4) SO:0001819 synonymous_variant ENST00000517417.1 1 1 hg19 CCDS54922.1 TCGA-IB-8127-01A-11D-2396-08 PCDHGA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000374737.1 1 0 1 151 997 0 137 1 5.260277e-01 5 8 0 137 2 0 0 0 0 0 2 1 1.000000 142 959 0 140 2 -2.879461 1 1 121398 2 37 1 2 2 4 2.234259 1 0.350000 3.330000 0.518519 0.990000 8.600000e-01 1.000000 1.000000 0.977311 0.990000 1 9.300000e-01 1 PCDHGA9 56107 broad.mit.edu 37 5 140783647 140783647 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr5:140783647C>T ENST00000573521.1 + 1 1128 c.1128C>T c.(1126-1128)tcC>tcT p.S376S PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron NM_018921.2|NM_032089.1 NP_061744.1|NP_114478.1 Q9Y5G4 PCDG9_HUMAN protocadherin gamma subfamily A, 9 5 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ACCGAGACTCCGGGAAGAATG 0.408000 0 SO:0001819 synonymous_variant ENST00000573521.1 1 1 hg19 CCDS58981.1 TCGA-IB-8127-01A-11D-2396-08 PCDHGA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437105.1 1 0 1 103 219 0 52 0 7.085715e-01 1 6 0 52 2 0 0 0 0 0 2 1 1.000000 101 218 0 52 2 -9.703541 1 1 120866 1 28 1 2 2 4 2.234259 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TNIP1 10318 broad.mit.edu 37 5 150422486 150422486 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr5:150422486G>A ENST00000389378.2 - 10 1561 c.973C>T c.(973-975)Cgg>Tgg p.R325W TNIP1_ENST00000520931.1_Missense_Mutation_p.R272W|TNIP1_ENST00000523200.1_Missense_Mutation_p.R325W|TNIP1_ENST00000522226.1_Missense_Mutation_p.R325W|TNIP1_ENST00000518977.1_Missense_Mutation_p.R325W|TNIP1_ENST00000521591.1_Missense_Mutation_p.R325W|TNIP1_ENST00000521423.1_Intron|TNIP1_ENST00000315050.7_Missense_Mutation_p.R325W|TNIP1_ENST00000524280.1_Missense_Mutation_p.R325W|TNIP1_ENST00000523338.1_Missense_Mutation_p.R325W NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4 NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3 Q15025 TNIP1_HUMAN TNFAIP3 interacting protein 1 23 Medulloblastoma(196;0.0911)|all_hematologic(541;0.207) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) TTCATGGACCGGAAATGCTGG 0.552000 0 SO:0001583 missense ENST00000389378.2 0 1 hg19 CCDS34280.1 . . . . . . . . . . G 22.8 4.337020 0.81801 . . ENSG00000145901 ENST00000520931;ENST00000389378;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840 T;T;T;T;T;T;T;T;T 0.61859 2.23;2.26;2.26;2.26;2.26;2.26;2.26;0.07;2.3 5.47 5.47 0.80525 . 0.106709 0.64402 D 0.000004 T 0.77572 0.4150 M 0.83223 2.63 0.44780 D 0.997788 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.999;1.0;0.999;1.0;1.0;0.998;0.999 T 0.80797 -0.1222 10 0.87932 D 0 -33.1055 14.6438 0.68745 0.0:0.0:0.8538:0.1461 . 325;279;279;325;325;325;325 B7Z8K2;A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025 .;.;.;.;.;.;TNIP1_HUMAN W 272;325;325;325;282;282;287;325;325;325;325;325;282 ENSP00000429891:R272W;ENSP00000374029:R325W;ENSP00000317891:R325W;ENSP00000428243:R325W;ENSP00000428187:R325W;ENSP00000430760:R325W;ENSP00000430971:R325W;ENSP00000429912:R325W;ENSP00000431105:R325W ENSP00000317891:R325W R - 1 2 TNIP1 150402679 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.685000 0.54678 2.561000 0.86390 0.650000 0.86243 CGG TCGA-IB-8127-01A-11D-2396-08 TNIP1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374914.1 0 0 0 9 1761 0 303 1 7.962232e-01 2 578 0 303 2 0 0 0 0 0 2 1 0.994002 9 1749 0 300 2 -1.820619 0 1 121412 3 37 1 2 2 4 2.234259 1 0.350000 3.330000 0.518519 0.030000 0 0.080000 0.040000 0.041968 0.030000 0 1.000000e-02 6.000000e-02 GABRB2 2561 broad.mit.edu 37 5 160721244 160721244 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr5:160721244C>T ENST00000393959.1 - 10 1382 c.1383G>A c.(1381-1383)gcG>gcA p.A461A GABRB2_ENST00000517901.1_Silent_p.A360A|GABRB2_ENST00000517547.1_Silent_p.A263A|GABRB2_ENST00000353437.6_Silent_p.A423A|GABRB2_ENST00000274547.2_Silent_p.A461A|GABRB2_ENST00000520240.1_Silent_p.A423A P47870 GBRB2_HUMAN gamma-aminobutyric acid (GABA) A receptor, beta 2 26 Renal(175;0.00259) Medulloblastoma(196;0.021)|all_neural(177;0.0463) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) TTTTCTTTTGCGCCACATGTC 0.517000 0 SO:0001819 synonymous_variant ENST00000393959.1 1 1 hg19 CCDS4355.1 TCGA-IB-8127-01A-11D-2396-08 GABRB2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252704.1 1 0 1 115 301 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 1.000000 114 296 0 79 2 -20.000000 1 1 121412 20 44 1 2 2 4 2.234259 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 IRF4 3662 broad.mit.edu 37 6 401644 401644 + Silent SNP C C T rs113364548 by1000genomes TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr6:401644C>T ENST00000380956.4 + 7 1092 c.966C>T c.(964-966)gaC>gaT p.D322D NM_001195286.1|NM_002460.3 NP_001182215.1|NP_002451.2 Q15306 IRF4_HUMAN interferon regulatory factor 4 5 Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895) TGGCCCCCGACGGGCTCTATG 0.607000 T IGH@ MM Dom yes 6 6p25-p23 3662 interferon regulatory factor 4 L 0 SO:0001819 synonymous_variant ENST00000380956.4 1 1 hg19 CCDS4469.1 TCGA-IB-8127-01A-11D-2396-08 IRF4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043638.1 1 0 1 93 175 0 47 0 9.763307e-01 0 14 0 47 2 0 0 0 0 0 2 1 1.000000 89 172 0 44 2 -20.000000 1 1 121412 6 40 1 0 2 2 1.684488 1 0.350000 3.330000 0.350000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PPP1R3A 5506 broad.mit.edu 37 7 113518727 113518727 + Nonsense_Mutation SNP A A C TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr7:113518727A>C ENST00000284601.3 - 4 2488 c.2420T>G c.(2419-2421)tTa>tGa p.L807* NM_002711.3 NP_002702.2 Q16821 PPR3A_HUMAN protein phosphatase 1, regulatory subunit 3A 121 ACAAATACCTAAACGTGATTC 0.383000 0 SO:0001587 stop_gained ENST00000284601.3 0 1 hg19 CCDS5759.1 . . . . . . . . . . A 34 5.312369 0.95655 . . ENSG00000154415 ENST00000284601 . . . 5.92 2.29 0.28610 . 0.536654 0.17154 N 0.184937 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -0.2057 9.3856 0.38340 0.7344:0.0:0.2656:0.0 . . . . X 807 . ENSP00000284601:L807X L - 2 0 PPP1R3A 113305963 1.000000 0.71417 0.285000 0.24819 0.850000 0.48378 1.634000 0.37123 0.154000 0.19237 -0.297000 0.09499 TTA TCGA-IB-8127-01A-11D-2396-08 PPP1R3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346724.1 1 0 1 136 389 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 1.000000 133 386 0 95 2 -20.000000 1 1 0 0 1 2 2 4 2.189630 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CALN1 83698 broad.mit.edu 37 7 71252799 71252799 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr7:71252799C>T ENST00000329008.5 - 6 919 c.621G>A c.(619-621)ctG>ctA p.L207L CALN1_ENST00000405452.2_Silent_p.L207L|CALN1_ENST00000412588.1_Silent_p.L249L|CALN1_ENST00000431984.1_Silent_p.L207L|CALN1_ENST00000395275.2_Silent_p.L249L|CALN1_ENST00000395276.2_Silent_p.L207L NM_001017440.2 NP_001017440.1 Q9BXU9 CABP8_HUMAN calneuron 1 p.L249L(1)|p.L207L(1) 32 all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161) TGGCTGCAATCAGCATGACAC 0.592000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000329008.5 1 1 hg19 CCDS5541.1 TCGA-IB-8127-01A-11D-2396-08 CALN1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320044.2 1 0 1 90 242 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 89 239 0 53 2 -20.000000 1 1 0 0 1 2 2 4 2.189630 1 0.350000 3.330000 0.518519 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ENDOG 2021 broad.mit.edu 37 9 131584646 131584646 + Silent SNP C C A rs141194619 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:131584646C>A ENST00000372642.4 + 3 862 c.651C>A c.(649-651)gtC>gtA p.V217V C9orf114_ENST00000361256.5_3'UTR NM_004435.2 NP_004426.2 Q14249 NUCG_HUMAN endonuclease G AGTACCAGGTCATCGGCAAGA 0.587000 0 SO:0001819 synonymous_variant ENST00000372642.4 0 1 hg19 CCDS6912.1 TCGA-IB-8127-01A-11D-2396-08 ENDOG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054505.1 1 0 0 19 153 0 24 1 9.999978e-01 28 164 0 24 2 0 0 0 0 0 2 1 0.999993 19 153 0 24 2 -20.000000 1 1 0 0 1 2 2 4 2.120770 1 0.350000 3.330000 0.504384 0.860000 5.300000e-01 1.000000 1.000000 0.847254 0.860000 1 6.800000e-01 1 USP20 10868 broad.mit.edu 37 9 132640646 132640646 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:132640646G>A ENST00000315480.4 + 23 2597 c.2439G>A c.(2437-2439)tcG>tcA p.S813S USP20_ENST00000372429.3_Silent_p.S813S|USP20_ENST00000358355.1_Silent_p.S813S Q9Y2K6 UBP20_HUMAN ubiquitin specific peptidase 20 11 Ovarian(14;0.00556) CCGAGGAGTCGCCGGGCGTCA 0.607000 0 SO:0001819 synonymous_variant ENST00000315480.4 1 1 hg19 CCDS43892.1 TCGA-IB-8127-01A-11D-2396-08 USP20-003 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054604.2 1 0 1 22 67 0 15 1 9.999996e-01 19 70 0 15 2 0 0 0 0 0 2 1 1.000000 22 66 0 15 2 -20.000000 1 1 120628 3 27 1 2 2 4 2.120770 1 0.350000 3.330000 0.504384 0.990000 9.900000e-01 1.000000 1.000000 0.999901 0.990000 1 9.900000e-01 1 C9orf172 389813 broad.mit.edu 37 9 139739952 139739952 + Silent SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:139739952C>T ENST00000436881.1 + 1 1086 c.1086C>T c.(1084-1086)ccC>ccT p.P362P NM_001080482.2 NP_001073951.2 C9J069 CI172_HUMAN chromosome 9 open reading frame 172 9 GCTATGTCCCCGAGGAGCCCC 0.697000 0 SO:0001819 synonymous_variant ENST00000436881.1 0 1 hg19 CCDS48059.1 TCGA-IB-8127-01A-11D-2396-08 C9orf172-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 0 15 59 0 10 1 5.826610e-01 2 7 0 10 2 0 0 0 0 0 2 1 0.999893 14 56 0 10 2 -20.000000 1 1 0 0 1 2 2 4 2.120770 1 0.350000 3.330000 0.504384 0.990000 9.400000e-01 1.000000 1.000000 0.996087 0.990000 1 9.900000e-01 1 CACNA1B 774 broad.mit.edu 37 9 140880965 140880965 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:140880965G>A ENST00000371372.1 + 14 2015 c.1870G>A c.(1870-1872)Gcc>Acc p.A624T CACNA1B_ENST00000277551.2_Missense_Mutation_p.A624T|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A625T|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A624T|CACNA1B_ENST00000371357.1_Missense_Mutation_p.A625T NM_000718.3|NM_001243812.1 NP_000709.1|NP_001230741.1 Q00975 CAC1B_HUMAN calcium channel, voltage-dependent, N type, alpha 1B subunit 80 all_cancers(76;0.166) Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661) TGTGGTCTTCGCCCTGCTGGG 0.597000 0 SO:0001583 missense ENST00000371372.1 0 1 hg19 CCDS59522.1 . . . . . . . . . . G 21.0 4.082671 0.76528 . . ENSG00000148408 ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355 D;D;D;D;D 0.98400 -4.91;-4.91;-4.91;-4.91;-4.91 4.35 4.35 0.52113 . 0.000000 0.85682 D 0.000000 D 0.99013 0.9663 M 0.87381 2.88 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.99719 1.1009 10 0.87932 D 0 . 17.2437 0.87021 0.0:0.0:1.0:0.0 . 624;624 B1AQK4;B1AQK6 .;. T 624;624;624;625;625 ENSP00000360423:A624T;ENSP00000277551:A624T;ENSP00000360414:A624T;ENSP00000360408:A625T;ENSP00000360406:A625T ENSP00000277551:A624T A + 1 0 CACNA1B 140000786 1.000000 0.71417 0.982000 0.44146 0.975000 0.68041 9.499000 0.97975 2.107000 0.64212 0.462000 0.41574 GCC TCGA-IB-8127-01A-11D-2396-08 CACNA1B-001 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000055380.1 1 0 1 22 182 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.999999 22 181 0 23 2 -9.997785 1 1 0 0 1 2 2 4 2.120770 1 0.350000 3.330000 0.504384 0.830000 5.300000e-01 1.000000 1.000000 0.833704 0.830000 0 6.700000e-01 1 CDKN2A 1029 broad.mit.edu 37 9 21971096 21971096 + Nonsense_Mutation SNP C C A rs121913384 TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:21971096C>A ENST00000304494.5 - 2 532 c.262G>T c.(262-264)Gag>Tag p.E88* CDKN2A_ENST00000530628.2_Missense_Mutation_p.G102V|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.E88*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.G102V|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.E37*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.E37*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.E37*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.E88*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.G143V|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.E37*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.E88*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.E37* NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.E88*(15)|p.E88K(3)|p.H83fs*2(2)|p.D84_F90del(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.G143V(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.V82_E88del(1)|p.E87K(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) AGGAAGCCCTCCCGGGCAGCG 0.756000 E88*(CAL33_UPPER_AERODIGESTIVE_TRACT) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1388 Whole gene deletion(1316)|Unknown(44)|Substitution - Nonsense(15)|Substitution - Missense(5)|Deletion - Frameshift(4)|Deletion - In frame(3)|Complex - deletion inframe(1) GRCh37 CM034218 CDKN2A M rs121913384 SO:0001587 stop_gained ENST00000304494.5 0 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 39|39 7.530771|7.530771 0.98342|0.98342 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000304494;ENST00000446177|ENST00000361570;ENST00000530628 .|D;D .|0.87412 .|-2.25;-2.14 5.93|5.93 5.93|5.93 0.95920|0.95920 .|. .|0.215520 .|0.23483 .|N .|0.047681 .|D .|0.89287 .|0.6672 L|L 0.32530|0.32530 0.975|0.975 0.58432|0.58432 D|D 0.999998|0.999998 .|D .|0.63880 .|0.993 .|P .|0.58660 .|0.843 .|D .|0.89966 .|0.4090 .|10 0.24483|0.87932 T|D 0.36|0 .|. 19.1221|19.1221 0.93367|0.93367 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|143 .|Q8N726 .|CD2A2_HUMAN X|V 88|143;102 .|ENSP00000355153:G143V;ENSP00000432664:G102V ENSP00000307101:E88X|ENSP00000355153:G143V E|G -|- 1|2 0|0 CDKN2A|CDKN2A 21961096|21961096 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.984000|0.984000 0.73092|0.73092 3.901000|3.901000 0.56303|0.56303 2.808000|2.808000 0.96608|0.96608 0.655000|0.655000 0.94253|0.94253 GAG|GGA TCGA-IB-8127-01A-11D-2396-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 49 100 0 20 1 1 165 9 0 20 2 1 1 64 99 0 179 2 1 1.000000 45 89 0 17 2 -20.000000 1 1 0 0 1 0 2 2 1.636910 1 0.350000 3.330000 0.350000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 LINGO2 158038 broad.mit.edu 37 9 27949236 27949236 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:27949236G>A ENST00000379992.2 - 6 1883 c.1434C>T c.(1432-1434)agC>agT p.S478S LINGO2_ENST00000308675.3_Silent_p.S478S NM_152570.2 NP_689783.1 Q7L985 LIGO2_HUMAN leucine rich repeat and Ig domain containing 2 44 Melanoma(11;0.242) all_neural(11;2.78e-09) CATACATCCCGCTGTCTTGAT 0.502000 0 SO:0001819 synonymous_variant ENST00000379992.2 0 1 hg19 CCDS6524.1 TCGA-IB-8127-01A-11D-2396-08 LINGO2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051978.2 0 0 0 5 344 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 0.935098 5 338 0 78 2 -4.239472 1 1 121408 6 38 1 0 2 2 1.636910 1 0.350000 3.330000 0.350000 0.080000 2.000000e-02 0.180000 0.080000 0.097146 0.080000 0 5.000000e-02 1.300000e-01 DOCK8 81704 broad.mit.edu 37 9 372257 372257 + Missense_Mutation SNP C C T TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:372257C>T ENST00000453981.1 + 18 2192 c.2080C>T c.(2080-2082)Cca>Tca p.P694S DOCK8_ENST00000432829.2_Missense_Mutation_p.P626S|DOCK8_ENST00000382331.1_5'UTR|DOCK8_ENST00000382329.1_Missense_Mutation_p.P161S|DOCK8_ENST00000469391.1_Missense_Mutation_p.P626S Q8NF50 DOCK8_HUMAN dedicator of cytokinesis 8 65 all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128) GGAAAAATTGCCACCCAACTA 0.448000 0 SO:0001583 missense ENST00000453981.1 0 1 hg19 CCDS6440.2 . . . . . . . . . . C 28.8 4.948470 0.92593 . . ENSG00000107099 ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329 T;T;T;T 0.14766 2.48;2.48;2.48;2.48 5.63 5.63 0.86233 . 0.000000 0.85682 D 0.000000 T 0.42653 0.1212 M 0.78223 2.4 0.80722 D 1 D;D;D 0.89917 1.0;0.999;1.0 D;D;D 0.97110 1.0;0.996;1.0 T 0.24261 -1.0165 10 0.72032 D 0.01 . 20.0442 0.97604 0.0:1.0:0.0:0.0 . 626;161;694 E9PH09;A2A369;Q8NF50 .;.;DOCK8_HUMAN S 694;694;626;626;161 ENSP00000408464:P694S;ENSP00000394888:P626S;ENSP00000419438:P626S;ENSP00000371766:P161S ENSP00000287364:P694S P + 1 0 DOCK8 362257 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.329000 0.79170 2.814000 0.96858 0.655000 0.94253 CCA TCGA-IB-8127-01A-11D-2396-08 DOCK8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171792.5 0 0 0 5 420 0 76 0 1.055717e-01 0 38 0 76 2 0 0 0 0 0 2 1 0.934722 5 412 0 76 2 -2.041525 0 1 0 0 1 0 2 2 1.636910 1 0.350000 3.330000 0.350000 0.070000 2.000000e-02 0.150000 0.070000 0.079925 0.070000 0 4.000000e-02 1.100000e-01 WNK2 65268 broad.mit.edu 37 9 96080243 96080243 + Silent SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chr9:96080243G>A ENST00000297954.4 + 30 6828 c.6828G>A c.(6826-6828)ccG>ccA p.P2276P WNK2_ENST00000427277.2_Intron|WNK2_ENST00000395477.2_Intron|WNK2_ENST00000349097.3_Intron|WNK2_ENST00000356055.3_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000395475.2_Intron NM_001282394.1 NP_001269323.1 Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 54 GCACTCAGCCGCGAGGGGGAC 0.672000 0 SO:0001819 synonymous_variant ENST00000297954.4 1 1 hg19 TCGA-IB-8127-01A-11D-2396-08 WNK2-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000317359.1 0 0 0 68 181 0 42 1 8.436209e-01 3 8 0 42 2 0 0 0 0 0 2 1 1.000000 67 180 0 42 2 -20.000000 1 1 116238 12 41 1 2 2 4 2.120118 1 0.350000 3.330000 0.503058 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 SERPINA7 6906 broad.mit.edu 37 X 105277592 105277592 + Missense_Mutation SNP G G A TCGA-IB-8127-01A-11D-2396-08 TCGA-IB-8127-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3f827515-ef77-4787-9d36-0df578e74dd8 d887d823-1afd-4869-bdbf-896901450ece g.chrX:105277592G>A ENST00000327674.4 - 4 1482 c.1147C>T c.(1147-1149)Cct>Tct p.P383S SERPINA7_ENST00000487487.1_5'Flank|SERPINA7_ENST00000372563.1_Missense_Mutation_p.P383S P05543 THBG_HUMAN serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7 24 Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583) TGGATAATAGGGTGTAGGAAA 0.438000 0 SO:0001583 missense ENST00000327674.4 1 1 hg19 CCDS14518.1 . . . . . . . . . . G 10.06 1.246856 0.22796 . . ENSG00000123561 ENST00000327674;ENST00000372563 D;D 0.84370 -1.84;-1.84 4.9 -3.02 0.05446 Serpin domain (3); 0.262727 0.32444 N 0.006089 T 0.75686 0.3883 L 0.48174 1.505 0.09310 N 1 P 0.41188 0.741 B 0.41619 0.361 T 0.68168 -0.5480 10 0.42905 T 0.14 . 5.562 0.17150 0.3419:0.3906:0.2675:0.0 . 383 P05543 THBG_HUMAN S 383 ENSP00000329374:P383S;ENSP00000361644:P383S ENSP00000329374:P383S P - 1 0 SERPINA7 105164248 0.910000 0.30920 0.000000 0.03702 0.039000 0.13416 3.651000 0.54431 -0.590000 0.05866 0.594000 0.82650 CCT TCGA-IB-8127-01A-11D-2396-08 SERPINA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057790.1 1 0 1 586 596 0 187 0 0 0 0 187 2 0 0 0 0 0 2 1 1.000000 579 592 0 185 2 -20.000000 1 1 0 0 1 0 1 1 0.350000 3.330000 0.350000 0.990000 9.800000e-01 1.000000 1.000000 0.998096 0.990000 1 9.800000e-01 1