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 CCDC147 0 broad.mit.edu 37 10 106207500 106207500 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr10:106207500C>T ENST00000369704.3 + 16 2435 c.2301C>T c.(2299-2301)cgC>cgT p.R767R NM_001008723.1 NP_001008723.1 Q5T655 CC147_HUMAN 52 Colorectal(252;0.103)|Breast(234;0.122) TCTTGGCCCGCCAGCCTGGAC 0.537000 0 SO:0001819 synonymous_variant ENST00000369704.3 0 1 hg19 CCDS31282.1 TCGA-IB-7888-01A-11D-2154-08 CCDC147-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050216.1 1 0 0 29 300 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 1.000000 29 284 0 24 2 -20.000000 1 1 0 0 1 0 1 1 1.870313 1 0.160000 1.960000 0.111675 0.990000 0.700000 1.000000 1.000000 0.945769 0.990000 1 8.500000e-01 1 MKI67 4288 broad.mit.edu 37 10 129906577 129906577 + Missense_Mutation SNP G G A rs117795868 by1000genomes TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr10:129906577G>A ENST00000368654.3 - 13 3902 c.3527C>T c.(3526-3528)aCg>aTg p.T1176M MKI67_ENST00000368653.3_Missense_Mutation_p.T816M NM_002417.4 NP_002408.3 P46013 KI67_HUMAN marker of proliferation Ki-67 159 all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203) TGGTTTGGGCGTAAGCATGGC 0.463000 0 SO:0001583 missense ENST00000368654.3 0 1 hg19 CCDS7659.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 12.05 1.822665 0.32237 . . ENSG00000148773 ENST00000368654;ENST00000368653;ENST00000537609 T;T 0.03301 3.98;3.98 2.74 1.83 0.25207 . 1.848640 0.03443 N 0.209516 T 0.15998 0.0385 M 0.72118 2.19 0.09310 N 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.78314 0.96;0.991;0.989 T 0.06058 -1.0848 10 0.52906 T 0.07 . 5.4955 0.16799 0.1565:0.0:0.8435:0.0 . 1175;816;1176 F5H4V4;P46013-2;P46013 .;.;KI67_HUMAN M 1176;816;1175 ENSP00000357643:T1176M;ENSP00000357642:T816M ENSP00000357642:T816M T - 2 0 MKI67 129796567 0.005000 0.15991 0.002000 0.10522 0.005000 0.04900 0.110000 0.15437 0.740000 0.32651 0.462000 0.41574 ACG TCGA-IB-7888-01A-11D-2154-08 MKI67-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050999.1 0 0 0 9 1605 0 242 0 4.132300e-04 0 5 0 242 2 0 0 0 0 0 2 1 0.993885 10 1587 0 241 2 -2.030090 0 1 121412 29 52 1 0 1 1 1.885195 1 0.160000 1.960000 0.102564 0.060000 0.020000 0.120000 0.070000 0.072004 0.060000 0 4.000000e-02 9.000000e-02 RET 5979 broad.mit.edu 37 10 43596003 43596003 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr10:43596003G>A ENST00000355710.3 + 2 402 c.170G>A c.(169-171)cGg>cAg p.R57Q RET_ENST00000340058.5_Missense_Mutation_p.R57Q NM_020975.4 NP_066124.1 P07949 RET_HUMAN ret proto-oncogene CCDC6/RET(4)|KIF5B/RET(79) 607 Ovarian(717;0.0423) Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398) CATGCCCTGCGGGACGCCCCT 0.622000 1 T, Mis, N, F H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6 medullary thyroid, papillary thyroid, pheochromocytoma, NSCLC medullary thyroid, papillary thyroid, pheochromocytoma Hirschsprung disease Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149) yes Dom yes Multiple endocrine neoplasia 2A/2B 10 10q11.2 5979 ret proto-oncogene yes E, O 0 SO:0001583 missense Familial Cancer Database MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC ENST00000355710.3 1 1 hg19 CCDS7200.1 . . . . . . . . . . G 7.893 0.732679 0.15507 . . ENSG00000165731 ENST00000355710;ENST00000340058;ENST00000535749 T;T 0.80566 -1.27;-1.39 5.51 -2.98 0.05513 . 0.511992 0.21682 N 0.070717 T 0.62159 0.2405 N 0.17474 0.49 0.20703 N 0.999866 B;B 0.27656 0.068;0.184 B;B 0.12156 0.003;0.007 T 0.51395 -0.8711 10 0.59425 D 0.04 . 13.0759 0.59087 0.6294:0.0:0.3706:0.0 . 57;57 P07949;P07949-2 RET_HUMAN;. Q 57 ENSP00000347942:R57Q;ENSP00000344798:R57Q ENSP00000344798:R57Q R + 2 0 RET 42916009 0.007000 0.16637 0.001000 0.08648 0.001000 0.01503 -0.012000 0.12699 -0.533000 0.06323 -1.553000 0.00894 CGG TCGA-IB-7888-01A-11D-2154-08 RET-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047694.2 1 0 0 13 250 0 51 0 2.979146e-03 0 2 0 51 2 0 0 0 0 0 2 1 0.999537 13 247 0 51 2 -3.318794 1 1 121406 1 33 1 0 0 0 1.993230 0 0.160000 1.960000 0.150485 0.610000 0.340000 0.970000 1.000000 0.636909 0.610000 0 4.600000e-01 8.000000e-01 DDX10 1662 broad.mit.edu 37 11 108546412 108546412 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:108546412G>A ENST00000322536.3 + 3 466 c.337G>A c.(337-339)Gcc>Acc p.A113T DDX10_ENST00000526794.1_Missense_Mutation_p.A113T NM_004398.2 NP_004389.2 Q13206 DDX10_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 p.A113T(1) 27 all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729) ACTTGGAGCGGCCAAAACTGG 0.438000 T NUP98 AML* Dom yes 11 11q22-q23 1662 DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 L 1 Substitution - Missense(1) SO:0001583 missense ENST00000322536.3 0 1 hg19 CCDS8342.1 . . . . . . . . . . G 36 5.649371 0.96714 . . ENSG00000178105 ENST00000322536;ENST00000456020;ENST00000526794 T;T 0.22539 1.95;1.95 5.82 5.82 0.92795 DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1); 0.046541 0.85682 N 0.000000 T 0.53302 0.1788 H 0.95679 3.705 0.80722 D 1 P;P 0.48764 0.858;0.915 P;P 0.51055 0.657;0.657 T 0.67921 -0.5545 10 0.87932 D 0 -4.8073 20.1566 0.98115 0.0:0.0:1.0:0.0 . 113;113 Q13206;E9PIF2 DDX10_HUMAN;. T 113 ENSP00000314348:A113T;ENSP00000432032:A113T ENSP00000314348:A113T A + 1 0 DDX10 108051622 1.000000 0.71417 1.000000 0.80357 0.895000 0.52256 9.413000 0.97351 2.779000 0.95612 0.603000 0.83216 GCC TCGA-IB-7888-01A-11D-2154-08 DDX10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390343.1 0 0 0 5 527 0 49 0 7.344143e-03 1 10 0 49 2 0 0 0 0 0 2 1 0.936255 6 522 0 49 2 -1.724912 0 1 0 0 1 0 1 1 2.000262 0 0.160000 1.960000 0.155270 0.120000 0.040000 0.260000 0.120000 0.138238 0.120000 0 7.000000e-02 1.900000e-01 HMBS 3145 broad.mit.edu 37 11 118955763 118955763 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:118955763C>T ENST00000278715.3 + 1 171 c.20C>T c.(19-21)gCg>gTg p.A7V HMBS_ENST00000542729.1_5'UTR|HMBS_ENST00000442944.2_5'UTR|HMBS_ENST00000537841.1_5'UTR|HMBS_ENST00000543090.1_Missense_Mutation_p.A7V|HMBS_ENST00000392841.1_5'Flank|HMBS_ENST00000544387.1_Missense_Mutation_p.A7V NM_000190.3 NP_000181.2 P08397 HEM3_HUMAN hydroxymethylbilane synthase 15 all_hematologic(175;0.0977) Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) AACGGCAATGCGGCTGCAACG 0.667000 0 SO:0001583 missense ENST00000278715.3 0 1 hg19 CCDS8409.1 . . . . . . . . . . C 16.02 3.004515 0.54254 . . ENSG00000256269 ENST00000278715;ENST00000536813;ENST00000546302;ENST00000544387;ENST00000543090 D;D;D;D;D 0.99832 -7.02;-5.71;-6.09;-6.71;-6.91 5.55 -0.207 0.13189 . 0.410282 0.21922 N 0.067144 D 0.97955 0.9327 N 0.22421 0.69 0.18873 N 0.999989 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.0;0.001;0.0 D 0.99023 1.0818 10 0.18276 T 0.48 -1.7114 1.6993 0.02869 0.1664:0.3811:0.2802:0.1723 . 7;7;7 F5H345;G5EA58;P08397 .;.;HEM3_HUMAN V 7 ENSP00000278715:A7V;ENSP00000438726:A7V;ENSP00000445599:A7V;ENSP00000438424:A7V;ENSP00000445429:A7V ENSP00000278715:A7V A + 2 0 HMBS 118460973 0.037000 0.19845 0.044000 0.18714 0.485000 0.33311 0.342000 0.19926 0.062000 0.16340 0.650000 0.86243 GCG TCGA-IB-7888-01A-11D-2154-08 HMBS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399188.1 0 0 0 5 324 0 31 0 2.878254e-02 0 14 0 31 2 0 0 0 0 0 2 1 0.928867 5 307 0 31 2 -3.134256 1 1 0 0 1 0 1 1 2.000262 0 0.160000 1.960000 0.155270 0.200000 0.070000 0.410000 0.190000 0.221602 0.200000 0 1.200000e-01 3.000000e-01 TSPAN18 90139 broad.mit.edu 37 11 44931325 44931325 + Missense_Mutation SNP G G A rs138512957 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:44931325G>A ENST00000520358.2 + 5 548 c.133G>A c.(133-135)Gtg>Atg p.V45M TSPAN18_ENST00000340160.3_Missense_Mutation_p.V45M Q96SJ8 TSN18_HUMAN tetraspanin 18 10 CCGGGAGATCGTGGCTGCCAA 0.697000 0 SO:0001583 missense ENST00000520358.2 0 1 hg19 CCDS7910.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.6|22.6 4.311265|4.311265 0.81358|0.81358 2.27E-4|2.27E-4 1.16E-4|1.16E-4 ENSG00000157570|ENSG00000157570 ENST00000518429|ENST00000533786;ENST00000533202;ENST00000520358;ENST00000520999;ENST00000340160;ENST00000520837 .|T;T;T;T;T;T .|0.80214 .|-1.35;-1.35;-1.35;-1.35;-1.35;-1.35 5.0|5.0 3.1|3.1 0.35709|0.35709 .|. .|0.239380 .|0.41823 .|D .|0.000806 D|D 0.86049|0.86049 0.5840|0.5840 M|M 0.71036|0.71036 2.16|2.16 0.80722|0.80722 D|D 1|1 .|D;D .|0.69078 .|0.996;0.997 .|D;D .|0.67548 .|0.952;0.922 D|D 0.85562|0.85562 0.1228|0.1228 5|10 .|0.59425 .|D .|0.04 .|. 8.9069|8.9069 0.35530|0.35530 0.232:0.0:0.768:0.0|0.232:0.0:0.768:0.0 .|. .|45;45 .|Q8WUV1;Q96SJ8 .|.;TSN18_HUMAN H|M 48|45;45;45;55;45;55 .|ENSP00000433592:V45M;ENSP00000434625:V45M;ENSP00000429993:V45M;ENSP00000427942:V55M;ENSP00000339820:V45M;ENSP00000430343:V55M .|ENSP00000339820:V45M R|V +|+ 2|1 0|0 TSPAN18|TSPAN18 44887901|44887901 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.971000|0.971000 0.66376|0.66376 4.890000|4.890000 0.63178|0.63178 1.105000|1.105000 0.41606|0.41606 0.561000|0.561000 0.74099|0.74099 CGT|GTG TCGA-IB-7888-01A-11D-2154-08 TSPAN18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376197.3 0 0 0 7 553 0 57 0 2.318911e-02 0 16 0 57 2 0 0 0 0 0 2 1 0.978751 7 538 0 56 2 -5.739786 1 1 121408 3 40 1 1 2 3 2.007403 0 0.160000 1.960000 0.163347 0.160000 0.070000 1.000000 0.160000 0.208268 0.160000 0 1.100000e-01 2.500000e-01 CHST1 8534 broad.mit.edu 37 11 45671352 45671352 + Silent SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:45671352G>A ENST00000308064.2 - 4 1792 c.1122C>T c.(1120-1122)aaC>aaT p.N374N CHST1_ENST00000533673.1_5'Flank|RP11-495O11.1_ENST00000525563.1_RNA NM_003654.5 NP_003645.1 O43916 CHST1_HUMAN carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 42 GCTGGCAGGCGTTCTGGGCAA 0.662000 0 SO:0001819 synonymous_variant ENST00000308064.2 1 1 hg19 CCDS7913.1 TCGA-IB-7888-01A-11D-2154-08 CHST1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390127.1 0 0 0 18 459 0 79 0 1.652749e-03 0 2 0 79 2 0 0 0 0 0 2 1 0.999981 18 455 0 79 2 -17.057420 1 1 0 0 1 1 2 3 2.007403 0 0.160000 1.960000 0.163347 0.480000 0.290000 1.000000 0.470000 0.511742 0.480000 0 3.800000e-01 6.200000e-01 OR8K5 219453 broad.mit.edu 37 11 55927158 55927158 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:55927158C>T ENST00000313447.1 - 1 635 c.636G>A c.(634-636)ctG>ctA p.L212L NM_001004058.2 NP_001004058.2 Q8NH50 OR8K5_HUMAN olfactory receptor, family 8, subfamily K, member 5 34 Esophageal squamous(21;0.00693) Lung NSC(402;0.197)|all_epithelial(135;0.236) CTAAGACTATCAGAAAGGAGG 0.378000 0 SO:0001819 synonymous_variant ENST00000313447.1 1 1 hg19 CCDS31521.1 TCGA-IB-7888-01A-11D-2154-08 OR8K5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391543.1 1 0 0 20 306 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.999995 20 302 0 42 2 -3.075367 1 1 121412 1 32 1 1 2 3 2.007403 0 0.160000 1.960000 0.163347 0.780000 0.490000 1.000000 1.000000 0.788623 0.780000 0 6.200000e-01 9.800000e-01 OR1S1 219959 broad.mit.edu 37 11 57982249 57982249 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:57982249C>T ENST00000309433.6 + 1 33 c.33C>T c.(31-33)ggC>ggT p.G11G NM_001004458.1 NP_001004458.1 Q8NH92 OR1S1_HUMAN olfactory receptor, family 1, subfamily S, member 1 48 Breast(21;0.0589) TTCAGATCGGCAGAAATATGC 0.393000 0 SO:0001819 synonymous_variant ENST00000309433.6 0 1 hg19 CCDS31546.1 TCGA-IB-7888-01A-11D-2154-08 OR1S1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394705.1 0 0 0 11 569 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 0.998258 11 563 0 51 2 -3.349171 1 1 0 0 1 1 2 3 2.007403 0 0.160000 1.960000 0.163347 0.240000 0.120000 1.000000 0.240000 0.284717 0.240000 0 1.800000e-01 3.400000e-01 INCENP 3619 broad.mit.edu 37 11 61897787 61897787 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:61897787C>T ENST00000394818.3 + 4 990 c.788C>T c.(787-789)tCc>tTc p.S263F INCENP_ENST00000278849.4_Missense_Mutation_p.S263F NM_001040694.1 NP_001035784.1 Q9NQS7 INCE_HUMAN inner centromere protein antigens 135/155kDa 19 GCGCAGGTCTCCCCTGGCCCA 0.652000 0 SO:0001583 missense ENST00000394818.3 1 1 hg19 CCDS44624.1 . . . . . . . . . . C 13.78 2.338769 0.41398 . . ENSG00000149503 ENST00000394818;ENST00000278849 T;T 0.16597 2.33;2.33 5.3 5.3 0.74995 . 0.412804 0.20464 N 0.091830 T 0.34193 0.0889 L 0.54323 1.7 0.43317 D 0.995338 D;D;P 0.62365 0.991;0.971;0.952 P;P;P 0.60473 0.687;0.875;0.753 T 0.02512 -1.1148 10 0.87932 D 0 . 14.4724 0.67526 0.0:1.0:0.0:0.0 . 263;263;263 B3KPD3;Q9NQS7-2;Q9NQS7 .;.;INCE_HUMAN F 263 ENSP00000378295:S263F;ENSP00000278849:S263F ENSP00000278849:S263F S + 2 0 INCENP 61654363 0.092000 0.21681 0.980000 0.43619 0.238000 0.25445 2.050000 0.41297 2.492000 0.84095 0.462000 0.41574 TCC TCGA-IB-7888-01A-11D-2154-08 INCENP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000394723.2 1 0 0 39 512 0 66 1 4.520780e-01 5 16 0 66 2 0 0 0 0 0 2 1 1.000000 37 498 0 65 2 -3.142702 1 1 0 0 1 0 1 1 2.000262 0 0.160000 1.960000 0.155270 0.870000 0.630000 1.000000 1.000000 0.872899 0.870000 1 7.500000e-01 1 ZBTB3 79842 broad.mit.edu 37 11 62519604 62519604 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:62519604C>T ENST00000394807.3 - 2 1808 c.1683G>A c.(1681-1683)ggG>ggA p.G561G NM_024784.3 NP_079060.1 Q9H5J0 ZBTB3_HUMAN zinc finger and BTB domain containing 3 24 CTTTAGGTGGCCCTCCACCAC 0.537000 0 SO:0001819 synonymous_variant ENST00000394807.3 1 1 hg19 CCDS8034.1 TCGA-IB-7888-01A-11D-2154-08 ZBTB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395342.1 1 0 0 20 338 0 49 0 3.535299e-03 0 2 0 49 2 0 0 0 0 0 2 1 0.999995 20 333 0 49 2 -5.638260 1 1 0 0 1 0 1 1 2.000262 0 0.160000 1.960000 0.155270 0.690000 0.440000 1.000000 1.000000 0.711106 0.690000 0 5.500000e-01 8.600000e-01 NOX4 50507 broad.mit.edu 37 11 89106611 89106611 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr11:89106611C>T ENST00000263317.4 - 12 1362 c.1124G>A c.(1123-1125)gGa>gAa p.G375E NOX4_ENST00000535633.1_Missense_Mutation_p.G351E|NOX4_ENST00000528341.1_Missense_Mutation_p.G350E|NOX4_ENST00000542487.1_Missense_Mutation_p.G351E|NOX4_ENST00000534731.1_Missense_Mutation_p.G375E|NOX4_ENST00000531342.1_Missense_Mutation_p.G68E|NOX4_ENST00000532825.1_Missense_Mutation_p.G351E|NOX4_ENST00000527626.1_Missense_Mutation_p.G209E|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Missense_Mutation_p.G351E|NOX4_ENST00000424319.1_Missense_Mutation_p.G351E|NOX4_ENST00000413594.2_Missense_Mutation_p.G396E|NOX4_ENST00000343727.5_Missense_Mutation_p.G351E|NOX4_ENST00000375979.3_Missense_Mutation_p.G68E Q9NPH5 NOX4_HUMAN NADPH oxidase 4 p.G375E(1) 44 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011) TGTCCAGTCTCCTACTATTTT 0.279000 1 Substitution - Missense(1) SO:0001583 missense ENST00000263317.4 0 1 hg19 CCDS8285.1 . . . . . . . . . . C 16.20 3.057366 0.55325 . . ENSG00000086991 ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979 T;T;T;T;T;T;T;T;T;T;T;D;D 0.98012 1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;-4.05;-4.66 5.12 5.12 0.69794 Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.98757 0.9582 M 0.87971 2.92 0.52501 D 0.999951 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 1.0;0.998;0.992;0.998;1.0;0.999;1.0 D 0.99505 1.0954 9 . . . -12.7557 15.4797 0.75514 0.0:1.0:0.0:0.0 . 351;209;350;68;68;375;375 E9PMY6;E9PR43;E9PPP2;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5 .;.;.;.;.;.;NOX4_HUMAN E 351;351;351;375;375;351;351;351;209;350;396;68;68 ENSP00000412446:G351E;ENSP00000440172:G351E;ENSP00000344747:G351E;ENSP00000436892:G375E;ENSP00000263317:G375E;ENSP00000434924:G351E;ENSP00000433797:G351E;ENSP00000439373:G351E;ENSP00000436093:G209E;ENSP00000436970:G350E;ENSP00000405705:G396E;ENSP00000435039:G68E;ENSP00000365146:G68E . G - 2 0 NOX4 88746259 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.868000 0.63021 2.382000 0.81193 0.563000 0.77884 GGA TCGA-IB-7888-01A-11D-2154-08 NOX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394054.1 0 0 0 10 804 0 65 0 1.088310e-01 0 41 0 65 2 0 0 0 0 0 2 1 0.996366 10 779 0 64 2 -1.640117 0 1 0 0 1 0 1 1 2.000262 0 0.160000 1.960000 0.155270 0.150000 0.070000 0.270000 0.150000 0.166443 0.150000 0 1.100000e-01 2.100000e-01 DUSP16 80824 broad.mit.edu 37 12 12629995 12629995 + Silent SNP G G A rs145763524 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr12:12629995G>A ENST00000228862.2 - 7 2401 c.1770C>T c.(1768-1770)tgC>tgT p.C590C DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_5'Flank NM_030640.2 NP_085143.1 Q9BY84 DUS16_HUMAN dual specificity phosphatase 16 26 Prostate(47;0.0687) CTTGGTCTCCGCAAGTGGGCA 0.562000 Ovarian(158;443 1896 15437 36069 46477) 0 SO:0001819 synonymous_variant ENST00000228862.2 0 1 hg19 CCDS8650.1 TCGA-IB-7888-01A-11D-2154-08 DUSP16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400311.1 0 0 0 8 753 0 85 0 1.940647e-01 0 68 0 85 2 0 0 0 0 0 2 1 0.988935 9 744 0 83 2 -2.488069 0 1 121412 1 39 1 0 1 1 2.001092 0 0.160000 1.960000 0.155270 0.130000 0.060000 0.250000 0.130000 0.145571 0.130000 0 9.000000e-02 1.900000e-01 TPTE2 93492 broad.mit.edu 37 13 20048175 20048175 + Missense_Mutation SNP G G C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr13:20048175G>C ENST00000400230.2 - 6 315 c.271C>G c.(271-273)Ctc>Gtc p.L91V TPTE2_ENST00000382977.4_Missense_Mutation_p.L91V|TPTE2_ENST00000382975.4_Missense_Mutation_p.L91V|TPTE2_ENST00000255310.6_Missense_Mutation_p.L54V|TPTE2_ENST00000382978.1_Missense_Mutation_p.L91V|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000390680.2_Missense_Mutation_p.L54V Q6XPS3 TPTE2_HUMAN transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 65 all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) TCGGCAAGGAGGAGAGTGACA 0.294000 0 SO:0001583 missense ENST00000400230.2 0 1 hg19 CCDS45014.1 . . . . . . . . . . g 0 -2.671852 0.00104 . . ENSG00000132958 ENST00000382978;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000343548 D;D;D;D;D;D 0.97553 -4.43;-4.43;-4.43;-4.43;-4.43;-4.43 2.33 -2.98 0.05513 . 0.341290 0.24920 N 0.034543 D 0.87853 0.6282 N 0.11064 0.09 0.09310 N 1 B;B 0.12013 0.005;0.002 B;B 0.06405 0.002;0.002 T 0.79778 -0.1660 9 . . . -2.0597 4.2976 0.10910 0.0:0.4631:0.2199:0.317 . 54;91 Q6XPS3-3;Q6XPS3 .;TPTE2_HUMAN V 91;91;54;54;91;91;91 ENSP00000372438:L91V;ENSP00000383089:L91V;ENSP00000255310:L54V;ENSP00000375098:L54V;ENSP00000372437:L91V;ENSP00000372435:L91V . L - 1 0 TPTE2 18946175 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.850000 0.04317 -0.793000 0.04475 -0.718000 0.03613 CTC TCGA-IB-7888-01A-11D-2154-08 TPTE2-205 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 6 463 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.961525 6 449 0 41 2 -2.146826 0 1 0 0 1 0 1 1 2.005752 0 0.160000 1.960000 0.156627 0.160000 0.060000 0.330000 0.160000 0.182912 0.160000 0 1.100000e-01 2.500000e-01 RCBTB2 1102 broad.mit.edu 37 13 49070346 49070346 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr13:49070346G>A ENST00000344532.3 - 14 1919 c.1496C>T c.(1495-1497)gCg>gTg p.A499V RCBTB2_ENST00000430805.2_Missense_Mutation_p.A504V|RCBTB2_ENST00000544492.1_Missense_Mutation_p.A225V NM_001268.2 NP_001259.1 O95199 RCBT2_HUMAN regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2 31 all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) ATACTTCACCGCAGCCGAGAG 0.478000 0 SO:0001583 missense ENST00000344532.3 0 1 hg19 CCDS9411.1 . . . . . . . . . . g 14.03 2.412381 0.42817 . . ENSG00000136161 ENST00000344532;ENST00000450343;ENST00000452987;ENST00000430805;ENST00000544492 T;T;D 0.84800 -1.03;-1.04;-1.9 5.04 5.04 0.67666 . 0.000000 0.85682 D 0.000000 D 0.86669 0.5988 M 0.82323 2.585 0.80722 D 1 P;P;P;P 0.40144 0.514;0.699;0.704;0.699 B;B;B;B 0.36244 0.086;0.22;0.137;0.22 D 0.89133 0.3511 10 0.66056 D 0.02 . 18.7477 0.91800 0.0:0.0:1.0:0.0 . 225;504;451;499 B4E372;B4DWG0;B3KVB1;O95199 .;.;.;RCBT2_HUMAN V 499;451;504;504;225 ENSP00000345144:A499V;ENSP00000389910:A504V;ENSP00000443862:A225V ENSP00000345144:A499V A - 2 0 RCBTB2 47968347 1.000000 0.71417 0.192000 0.23308 0.093000 0.18481 9.372000 0.97165 2.499000 0.84300 0.558000 0.71614 GCG TCGA-IB-7888-01A-11D-2154-08 RCBTB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044888.2 0 0 0 20 391 1 44 1 5.152384e-02 5 22 1 44 4 0 0 0 0 0 2 0 0.174725 20 388 1 43 27 -2.885646 1 1 121386 1 30 1 0 1 1 2.005752 0 0.160000 1.960000 0.156627 0.600000 0.380000 0.880000 0.600000 0.624406 0.600000 0 4.800000e-01 7.500000e-01 TBC1D4 9882 broad.mit.edu 37 13 75886933 75886933 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr13:75886933C>T ENST00000377636.3 - 13 2670 c.2324G>A c.(2323-2325)cGc>cAc p.R775H TBC1D4_ENST00000377625.2_Missense_Mutation_p.R712H|TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000431480.2_Missense_Mutation_p.R767H NM_014832.2 NP_055647.2 O60343 TBCD4_HUMAN TBC1 domain family, member 4 50 Prostate(6;0.014)|Breast(118;0.0982) GAGGAAAATGCGCTGCCGCCA 0.522000 0 SO:0001583 missense ENST00000377636.3 0 1 hg19 CCDS41901.1 . . . . . . . . . . C 27.9 4.876178 0.91664 0.0 1.2E-4 ENSG00000136111 ENST00000377636;ENST00000431480;ENST00000377625;ENST00000413735 T;T;T;T 0.49720 0.77;0.77;0.77;0.77 5.53 5.53 0.82687 . 0.085211 0.48767 D 0.000171 T 0.64349 0.2590 L 0.50333 1.59 0.80722 D 1 D;D;D 0.89917 0.998;0.999;1.0 P;D;D 0.65443 0.862;0.91;0.935 T 0.63804 -0.6554 10 0.59425 D 0.04 -12.7168 19.8372 0.96661 0.0:1.0:0.0:0.0 . 712;767;775 O60343-2;O60343-3;O60343 .;.;TBCD4_HUMAN H 775;767;712;224 ENSP00000366863:R775H;ENSP00000395986:R767H;ENSP00000366852:R712H;ENSP00000396932:R224H ENSP00000366852:R712H R - 2 0 TBC1D4 74784934 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 5.095000 0.64529 2.770000 0.95276 0.655000 0.94253 CGC TCGA-IB-7888-01A-11D-2154-08 TBC1D4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045283.1 0 0 0 6 400 0 42 0 6.299263e-02 0 23 0 42 2 0 0 0 0 0 2 1 0.964437 6 396 0 42 2 -2.560475 1 1 120902 2 36 1 0 1 1 2.005752 0 0.160000 1.960000 0.156627 0.190000 0.070000 0.370000 0.180000 0.210776 0.190000 0 1.200000e-01 2.800000e-01 STRN3 29966 broad.mit.edu 37 14 31376184 31376184 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr14:31376184C>T ENST00000357479.5 - 14 1983 c.1787G>A c.(1786-1788)gGc>gAc p.G596D STRN3_ENST00000355683.5_Missense_Mutation_p.G512D NM_001083893.1 NP_001077362.1 Q13033 STRN3_HUMAN striatin, calmodulin binding protein 3 20 Hepatocellular(127;0.0877)|Breast(36;0.148) LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805) ATTTTTTATGCCACTATAAGC 0.368000 0 SO:0001583 missense ENST00000357479.5 0 1 hg19 CCDS41938.1 . . . . . . . . . . C 26.5 4.743342 0.89663 . . ENSG00000196792 ENST00000355683;ENST00000357479 T;T 0.59502 0.26;0.26 5.73 5.73 0.89815 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.58495 0.2126 N 0.10733 0.035 0.80722 D 1 P;D 0.64830 0.762;0.994 B;D 0.66351 0.343;0.943 T 0.61322 -0.7086 10 0.30854 T 0.27 -5.1717 19.9019 0.96988 0.0:1.0:0.0:0.0 . 512;596 Q13033-2;Q13033 .;STRN3_HUMAN D 512;596 ENSP00000347909:G512D;ENSP00000350071:G596D ENSP00000347909:G512D G - 2 0 STRN3 30445935 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.498000 0.60373 2.706000 0.92434 0.563000 0.77884 GGC TCGA-IB-7888-01A-11D-2154-08 STRN3-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409713.1 0 0 0 5 461 0 32 0 3.527353e-02 0 22 0 32 2 0 0 0 0 0 2 1 0.936073 5 456 0 31 2 -2.050533 0 1 0 0 1 0 1 1 1.874017 1 0.160000 1.960000 0.113176 0.130000 0.040000 0.280000 0.120000 0.149249 0.130000 0 8.000000e-02 2.100000e-01 ALDH1A3 220 broad.mit.edu 37 15 101438319 101438319 + Missense_Mutation SNP G G A rs147665432 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr15:101438319G>A ENST00000329841.5 + 8 1344 c.812G>A c.(811-813)cGg>cAg p.R271Q RP11-66B24.4_ENST00000560351.1_RNA|ALDH1A3_ENST00000346623.6_Missense_Mutation_p.R164Q NM_000693.2 NP_000684.2 P47895 AL1A3_HUMAN aldehyde dehydrogenase 1 family, member A3 27 Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852) OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103) Vitamin A(DB00162) GCTGCGTCCCGGAGCAATCTG 0.557000 0 SO:0001583 missense ENST00000329841.5 1 1 hg19 CCDS10389.1 . . . . . . . . . . G 15.62 2.886741 0.51908 0.0 3.49E-4 ENSG00000184254 ENST00000329841;ENST00000346623 T 0.15603 2.41 5.76 1.03 0.20045 Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1); 0.354015 0.32935 N 0.005464 T 0.07818 0.0196 N 0.14661 0.345 0.09310 N 1 B;B 0.25521 0.128;0.001 B;B 0.22753 0.041;0.001 T 0.22208 -1.0223 10 0.48119 T 0.1 . 3.9817 0.09498 0.387:0.0:0.4484:0.1646 . 175;271 Q7Z3A2;P47895 .;AL1A3_HUMAN Q 271;175 ENSP00000332256:R271Q ENSP00000332256:R271Q R + 2 0 ALDH1A3 99255842 0.817000 0.29147 0.003000 0.11579 0.960000 0.62799 2.008000 0.40893 0.296000 0.22592 0.555000 0.69702 CGG TCGA-IB-7888-01A-11D-2154-08 ALDH1A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313620.2 1 0 0 29 324 0 29 0 9.996826e-01 0 140 0 29 2 0 0 0 0 0 2 1 1.000000 29 321 0 29 2 -2.920853 1 1 121412 9 40 1 0 1 1 1.999187 0 0.160000 1.960000 0.155270 0.990000 0.700000 1.000000 1.000000 0.944883 0.990000 1 8.400000e-01 1 TGM7 116179 broad.mit.edu 37 15 43579655 43579655 + Splice_Site SNP T T C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr15:43579655T>C ENST00000452443.2 - 6 692 c.688A>G c.(688-690)Atc>Gtc p.I230V NM_052955.2 NP_443187.1 Q96PF1 TGM7_HUMAN transglutaminase 7 39 all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) L-Glutamine(DB00130) TTGCTGTTGATCTGCAGAGGA 0.597000 0 SO:0001630 splice_region_variant ENST00000452443.2 1 0 hg19 CCDS32213.1 . . . . . . . . . . T 14.81 2.647826 0.47258 . . ENSG00000159495 ENST00000452443 D 0.84589 -1.87 5.72 5.72 0.89469 . 0.051682 0.85682 D 0.000000 D 0.85133 0.5627 L 0.28608 0.87 0.39793 D 0.972465 D 0.64830 0.994 D 0.72625 0.978 T 0.80848 -0.1199 10 0.02654 T 1 -28.5987 13.9677 0.64218 0.0:0.0:0.0:1.0 . 230 Q96PF1 TGM7_HUMAN V 230 ENSP00000389466:I230V ENSP00000389466:I230V I - 1 0 TGM7 41366947 0.998000 0.40836 1.000000 0.80357 0.843000 0.47879 0.496000 0.22499 2.189000 0.69895 0.533000 0.62120 ATC TCGA-IB-7888-01A-11D-2154-08 TGM7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432489.1 1 0 0 37 385 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 1.000000 36 378 0 52 2 -20.000000 1 1 0 0 1 0 1 1 2.000515 0 0.160000 1.960000 0.155270 0.990000 0.780000 1.000000 1.000000 0.972449 0.990000 1 9.200000e-01 1 PYGO1 26108 broad.mit.edu 37 15 55838323 55838323 + Silent SNP T T C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr15:55838323T>C ENST00000302000.6 - 3 1252 c.1158A>G c.(1156-1158)gcA>gcG p.A386A PYGO1_ENST00000563719.1_Silent_p.A386A NM_015617.1 NP_056432.1 Q9Y3Y4 PYGO1_HUMAN pygopus family PHD finger 1 27 ATACTGCAGATGCTTCTGCAG 0.458000 0 SO:0001819 synonymous_variant ENST00000302000.6 1 1 hg19 CCDS10155.1 TCGA-IB-7888-01A-11D-2154-08 PYGO1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000254977.2 1 0 0 40 495 0 39 0 7.181526e-02 0 6 0 39 2 0 0 0 0 0 2 1 1.000000 40 489 0 38 2 -20.000000 1 1 121412 10 40 1 0 1 1 2.000515 0 0.160000 1.960000 0.155270 0.920000 0.670000 1.000000 1.000000 0.907506 0.920000 1 7.900000e-01 1 KIAA0430 9665 broad.mit.edu 37 16 15728761 15728761 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr16:15728761C>T ENST00000396368.3 - 4 1065 c.859G>A c.(859-861)Gct>Act p.A287T KIAA0430_ENST00000602337.1_Missense_Mutation_p.A287T|KIAA0430_ENST00000344181.3_Missense_Mutation_p.A109T|KIAA0430_ENST00000540441.2_Missense_Mutation_p.A287T|KIAA0430_ENST00000548025.1_Missense_Mutation_p.A287T|KIAA0430_ENST00000551742.1_Missense_Mutation_p.A287T NM_001184998.1|NM_001184999.1|NM_014647.3 NP_001171927.1|NP_001171928.1|NP_055462.2 Q9Y4F3 MARF1_HUMAN KIAA0430 40 CAGACTTTAGCCGCATCGATT 0.418000 0 SO:0001583 missense ENST00000396368.3 0 1 hg19 CCDS10562.2 . . . . . . . . . . C 19.81 3.895972 0.72639 . . ENSG00000166783 ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298 . . . 5.42 5.42 0.78866 . 0.211356 0.49916 D 0.000125 T 0.48223 0.1488 L 0.54323 1.7 0.25621 N 0.9864 P;P;P;P 0.48089 0.905;0.817;0.817;0.847 P;B;B;B 0.48654 0.585;0.295;0.295;0.381 T 0.48927 -0.8991 9 0.59425 D 0.04 . 15.1059 0.72322 0.0:0.8589:0.1411:0.0 . 286;287;286;286 Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3 .;.;.;LKAP_HUMAN T 287;287;286;109;287;287;287 . ENSP00000315718:A286T A - 1 0 KIAA0430 15636262 1.000000 0.71417 1.000000 0.80357 0.935000 0.57460 2.818000 0.48041 2.695000 0.91970 0.655000 0.94253 GCT TCGA-IB-7888-01A-11D-2154-08 KIAA0430-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252131.2 0 0 0 8 649 0 73 0 9.480072e-02 0 37 0 73 2 0 0 0 0 0 2 1 0.988951 8 642 0 72 2 -2.666207 1 1 0 0 1 0 1 1 2.005683 0 0.160000 1.960000 0.156627 0.150000 0.070000 0.280000 0.150000 0.168639 0.150000 0 1.000000e-01 2.200000e-01 SLC12A3 6559 broad.mit.edu 37 16 56920970 56920970 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr16:56920970G>A ENST00000563236.1 + 17 2168 c.2143G>A c.(2143-2145)Gag>Aag p.E715K SLC12A3_ENST00000262502.5_Missense_Mutation_p.E714K|SLC12A3_ENST00000438926.2_Missense_Mutation_p.E715K|SLC12A3_ENST00000566786.1_Missense_Mutation_p.E714K P55017 S12A3_HUMAN solute carrier family 12 (sodium/chloride transporter), member 3 50 Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325) TGTCATTGCCGAGGACCTCCG 0.587000 0 SO:0001583 missense ENST00000563236.1 1 1 hg19 CCDS58464.1 . . . . . . . . . . G 16.24 3.068187 0.55539 . . ENSG00000070915 ENST00000438926;ENST00000262502 . . . 5.66 5.66 0.87406 . 0.281585 0.38058 N 0.001840 T 0.51873 0.1700 N 0.21545 0.675 0.53688 D 0.999976 B;B;B 0.26258 0.145;0.051;0.085 B;B;B 0.21546 0.035;0.007;0.035 T 0.45175 -0.9279 9 0.39692 T 0.17 . 19.7573 0.96299 0.0:0.0:1.0:0.0 . 714;715;715 P55017-3;P55017;P55017-2 .;S12A3_HUMAN;. K 714;715 . ENSP00000262502:E715K E + 1 0 SLC12A3 55478471 1.000000 0.71417 0.986000 0.45419 0.557000 0.35523 4.779000 0.62375 2.668000 0.90789 0.551000 0.68910 GAG TCGA-IB-7888-01A-11D-2154-08 SLC12A3-005 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000432337.1 0 0 0 22 455 0 54 0 6.952938e-03 0 3 0 54 2 0 0 0 0 0 2 1 0.999999 22 448 0 54 2 -2.747607 1 1 121412 2 31 1 0 0 0 1.991807 0 0.160000 1.960000 0.150485 0.570000 0.360000 0.820000 0.560000 0.586407 0.570000 0 4.600000e-01 7.000000e-01 DNAH9 1770 broad.mit.edu 37 17 11650990 11650990 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr17:11650990C>T ENST00000262442.4 + 32 6585 c.6517C>T c.(6517-6519)Cgg>Tgg p.R2173W DNAH9_ENST00000454412.2_Missense_Mutation_p.R2173W NM_001372.3 NP_001363.2 Q9NYC9 DYH9_HUMAN dynein, axonemal, heavy chain 9 p.R2173W(1) 290 Breast(5;0.0122)|all_epithelial(5;0.131) GATCATGAAACGGCGCCCCGT 0.542000 1 Substitution - Missense(1) SO:0001583 missense ENST00000262442.4 1 1 hg19 CCDS11160.1 . . . . . . . . . . C 20.4 3.987431 0.74589 . . ENSG00000007174 ENST00000262442;ENST00000454412;ENST00000413703 T;T 0.56103 0.48;0.48 4.5 3.52 0.40303 ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1); 0.385584 0.26638 N 0.023273 T 0.72447 0.3461 M 0.90542 3.125 0.80722 D 1 D 0.76494 0.999 D 0.66716 0.946 T 0.75221 -0.3394 10 0.87932 D 0 . 8.0598 0.30627 0.1561:0.7625:0.0:0.0814 . 2173 Q9NYC9 DYH9_HUMAN W 2173;2173;755 ENSP00000262442:R2173W;ENSP00000414874:R2173W ENSP00000262442:R2173W R + 1 2 DNAH9 11591715 1.000000 0.71417 0.881000 0.34555 0.987000 0.75469 2.893000 0.48633 1.096000 0.41439 0.557000 0.71058 CGG TCGA-IB-7888-01A-11D-2154-08 DNAH9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252756.2 1 0 0 25 425 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 25 417 0 55 2 -20.000000 1 1 121412 2 34 1 0 1 1 1.871319 1 0.160000 1.960000 0.101027 0.640000 0.430000 0.900000 0.640000 0.658160 0.640000 0 5.200000e-01 7.800000e-01 PIGS 94005 broad.mit.edu 37 17 26881272 26881272 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr17:26881272C>T ENST00000308360.7 - 12 2009 c.1634G>A c.(1633-1635)cGc>cAc p.R545H PIGS_ENST00000543734.1_Missense_Mutation_p.R484H|UNC119_ENST00000335765.4_5'Flank|PIGS_ENST00000395346.2_Missense_Mutation_p.R537H|UNC119_ENST00000301032.4_5'Flank|UNC119_ENST00000484980.1_5'Flank NM_033198.3 NP_149975.1 Q96S52 PIGS_HUMAN phosphatidylinositol glycan anchor biosynthesis, class S 16 Lung NSC(42;0.00431) CCAGGACTTGCGGGTCTCCAG 0.547000 0 SO:0001583 missense ENST00000308360.7 0 1 hg19 CCDS11235.1 . . . . . . . . . . c 10.96 1.499138 0.26861 . . ENSG00000087111 ENST00000395346;ENST00000308360;ENST00000543734 T;T;T 0.46819 0.86;0.86;0.86 5.25 -1.09 0.09904 . 0.331862 0.33199 N 0.005180 T 0.43567 0.1253 M 0.79123 2.44 0.09310 N 1 B;B 0.14805 0.011;0.009 B;B 0.14578 0.011;0.01 T 0.42766 -0.9432 10 0.48119 T 0.1 -1.8876 8.6723 0.34159 0.0964:0.5151:0.0:0.3886 . 545;537 Q96S52;Q96S52-2 PIGS_HUMAN;. H 537;545;484 ENSP00000378755:R537H;ENSP00000309430:R545H;ENSP00000438447:R484H ENSP00000309430:R545H R - 2 0 PIGS 23905399 0.394000 0.25246 0.947000 0.38551 0.790000 0.44656 -0.430000 0.06973 -0.251000 0.09542 -1.733000 0.00692 CGC TCGA-IB-7888-01A-11D-2154-08 PIGS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255833.3 0 0 0 5 552 0 81 0 3.483103e-01 0 117 0 81 2 0 0 0 0 0 2 1 0.935091 5 543 0 81 2 -1.828400 0 1 121412 156 52 1 1 2 3 2.007269 0 0.160000 1.960000 0.163347 0.120000 0.040000 1.000000 0.110000 0.166374 0.120000 0 7.000000e-02 2.000000e-01 HAP1 9001 broad.mit.edu 37 17 39883349 39883349 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr17:39883349C>T ENST00000310778.5 - 10 1488 c.1479G>A c.(1477-1479)acG>acA p.T493T JUP_ENST00000540235.1_Intron|HAP1_ENST00000393939.2_Silent_p.T416T|HAP1_ENST00000347901.4_Silent_p.T441T|HAP1_ENST00000341193.5_Silent_p.T424T P54257 HAP1_HUMAN huntingtin-associated protein 1 21 Breast(137;0.000162) BRCA - Breast invasive adenocarcinoma(4;0.0677) TCCTTAGAGACGTTCTGAGCT 0.577000 0 SO:0001819 synonymous_variant ENST00000310778.5 0 1 hg19 TCGA-IB-7888-01A-11D-2154-08 HAP1-006 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000389619.1 0 0 0 4 59 0 10 0 3.637100e-02 0 4 0 10 2 0 0 0 0 0 2 1 0.888797 4 58 0 10 2 -8.658599 1 1 121276 5 34 1 1 2 3 2.007269 0 0.160000 1.960000 0.163347 0.850000 0.290000 1.000000 1.000000 0.792522 0.850000 1 5.200000e-01 1 TP53 7157 broad.mit.edu 37 17 7578275 7578275 + Nonsense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr17:7578275G>A ENST00000269305.4 - 6 763 c.574C>T c.(574-576)Cag>Tag p.Q192* TP53_ENST00000445888.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q192*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q192* 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.Q192*(83)|p.0?(8)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191del(4)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191_Q192delPQ(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ATAAGATGCTGAGGAGGGGCC 0.557000 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 144 Substitution - Nonsense(95)|Deletion - In frame(19)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(6)|Unknown(6)|Insertion - Frameshift(1)|Complex - frameshift(1)|Substitution - Missense(1) SO:0001587 stop_gained Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . G 13.54 2.269040 0.40095 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 . . . 5.41 3.36 0.38483 . 0.242461 0.43260 D 0.000594 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.72032 D 0.01 -22.6404 8.6971 0.34303 0.0:0.1484:0.545:0.3066 . . . . X 192;192;192;192;192;192;181;99;60;99;60 . ENSP00000269305:Q192X Q - 1 0 TP53 7519000 1.000000 0.71417 0.987000 0.45799 0.035000 0.12851 2.163000 0.42377 0.732000 0.32470 0.655000 0.94253 CAG TCGA-IB-7888-01A-11D-2154-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 13 266 0 46 1 5.685033e-01 2 37 0 46 2 1 9.999999e-01 89 1229 1 1227 6 1 0.999557 13 265 0 46 2 -4.489831 1 1 0 0 1 0 1 1 1.871319 1 0.160000 1.960000 0.101027 0.540000 0.300000 0.850000 0.520000 0.562971 0.540000 0 4.100000e-01 7.000000e-01 DNAH2 146754 broad.mit.edu 37 17 7680922 7680922 + Nonsense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr17:7680922G>A ENST00000572933.1 + 33 6677 c.5217G>A c.(5215-5217)tgG>tgA p.W1739* DNAH2_ENST00000389173.2_Nonsense_Mutation_p.W1739* Q9P225 DYH2_HUMAN dynein, axonemal, heavy chain 2 189 all_cancers(10;4.66e-07)|Prostate(122;0.081) CCTTTGACTGGCTCAGCCAAC 0.478000 0 SO:0001587 stop_gained ENST00000572933.1 0 1 hg19 CCDS32551.1 . . . . . . . . . . G 46 12.308359 0.99656 . . ENSG00000183914 ENST00000360606;ENST00000389173 . . . 5.49 5.49 0.81192 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 18.1309 0.89600 0.0:0.0:1.0:0.0 . . . . X 1739 . ENSP00000353818:W1739X W + 3 0 DNAH2 7621647 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.405000 0.97313 2.569000 0.86673 0.585000 0.79938 TGG TCGA-IB-7888-01A-11D-2154-08 DNAH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000440241.1 0 0 0 10 1786 0 215 0 4.076339e-05 0 2 0 215 2 0 0 0 0 0 2 1 0.996730 10 1772 0 212 2 -2.444690 0 1 0 0 1 0 1 1 1.871319 1 0.160000 1.960000 0.101027 0.060000 0.020000 0.120000 0.070000 0.071104 0.060000 0 4.000000e-02 9.000000e-02 CILP2 148113 broad.mit.edu 37 19 19655205 19655205 + Silent SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:19655205G>A ENST00000291495.5 + 8 1936 c.1851G>A c.(1849-1851)tcG>tcA p.S617S CILP2_ENST00000586018.1_Silent_p.S623S NM_153221.2 NP_694953.2 Q8IUL8 CILP2_HUMAN cartilage intermediate layer protein 2 32 ACCTCACCTCGGCGGCGTCTG 0.697000 0 SO:0001819 synonymous_variant ENST00000291495.5 1 1 hg19 CCDS12405.1 TCGA-IB-7888-01A-11D-2154-08 CILP2-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000459738.3 1 0 0 42 626 0 95 0 0 0 1 0 95 2 0 0 0 0 0 2 1 1.000000 42 613 0 94 2 -3.017761 1 1 0 0 1 0 1 1 2.000492 0 0.160000 1.960000 0.155270 0.770000 0.570000 1.000000 1.000000 0.788764 0.770000 0 6.600000e-01 9.000000e-01 NPHS1 4868 broad.mit.edu 37 19 36322199 36322199 + Splice_Site SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:36322199G>A ENST00000378910.5 - 26 3385 c.3386C>T c.(3385-3387)aCg>aTg p.T1129M NPHS1_ENST00000353632.6_Splice_Site_p.T1089M NM_004646.3 NP_004637.1 O60500 NPHN_HUMAN nephrosis 1, congenital, Finnish type (nephrin) 74 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) CCCACTTACCGTGGAGCTCTG 0.607000 0 SO:0001630 splice_region_variant ENST00000378910.5 1 0 hg19 CCDS32996.1 . . . . . . . . . . G 6.172 0.399943 0.11696 . . ENSG00000161270 ENST00000378910;ENST00000353632 T;T 0.75154 -0.79;-0.91 5.07 1.79 0.24919 . 0.218040 0.40144 N 0.001180 T 0.57227 0.2039 L 0.29908 0.895 0.23969 N 0.996316 B 0.13145 0.007 B 0.11329 0.006 T 0.41324 -0.9515 10 0.29301 T 0.29 -2.7895 7.28 0.26306 0.2727:0.0:0.7273:0.0 . 1129 O60500 NPHN_HUMAN M 1129;1089 ENSP00000368190:T1129M;ENSP00000343634:T1089M ENSP00000343634:T1089M T - 2 0 NPHS1 41014039 0.000000 0.05858 0.392000 0.26245 0.023000 0.10783 -0.642000 0.05427 0.336000 0.23639 0.442000 0.29010 ACG TCGA-IB-7888-01A-11D-2154-08 NPHS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452553.1 1 0 0 30 451 0 63 0 0 0 1 0 63 2 0 0 0 0 0 2 1 1.000000 30 449 0 60 2 -7.324553 1 1 121412 2 39 1 0 1 1 2.000492 0 0.160000 1.960000 0.155270 0.770000 0.530000 1.000000 1.000000 0.783806 0.770000 0 6.400000e-01 9.200000e-01 TYROBP 7305 broad.mit.edu 37 19 36398352 36398352 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:36398352C>T ENST00000262629.4 - 3 291 c.225G>A c.(223-225)gcG>gcA p.A75A TYROBP_ENST00000589517.1_Silent_p.A75A|TYROBP_ENST00000424586.3_Silent_p.A64A|TYROBP_ENST00000585901.2_Silent_p.A75A|TYROBP_ENST00000544690.2_Silent_p.A64A NM_003332.3|NM_198125.2 NP_003323.1|NP_937758.1 O43914 TYOBP_HUMAN TYRO protein tyrosine kinase binding protein 8 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) ACTCACCCTCCGCAGCCCCTC 0.632000 0 SO:0001819 synonymous_variant ENST00000262629.4 1 1 hg19 CCDS12482.1 TCGA-IB-7888-01A-11D-2154-08 TYROBP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000457397.1 1 0 0 28 539 0 50 0 9.999998e-01 1 475 0 50 2 0 0 0 0 0 2 1 1.000000 27 531 0 48 2 -3.144665 1 1 121408 6 39 1 0 1 1 2.000492 0 0.160000 1.960000 0.155270 0.610000 0.410000 0.850000 0.610000 0.627357 0.610000 0 5.000000e-01 7.400000e-01 AXL 558 broad.mit.edu 37 19 41745081 41745081 + Missense_Mutation SNP A A G TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:41745081A>G ENST00000301178.4 + 9 1337 c.1147A>G c.(1147-1149)Ata>Gta p.I383V AXL_ENST00000359092.3_Missense_Mutation_p.I383V|AXL_ENST00000593513.1_Missense_Mutation_p.I115V NM_001278599.1|NM_021913.3 NP_001265528.1|NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase 48 GCTAATGGACATAGGGCTAAG 0.572000 0 SO:0001583 missense ENST00000301178.4 1 1 hg19 CCDS12575.1 . . . . . . . . . . a 1.232 -0.623935 0.03636 . . ENSG00000167601 ENST00000301178;ENST00000359092 T;T 0.57107 0.42;0.42 4.31 -2.42 0.06542 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.576798 0.16485 N 0.212370 T 0.27489 0.0675 N 0.17312 0.475 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.04013 0.001;0.001 T 0.31888 -0.9927 10 0.05959 T 0.93 -1.1005 11.2374 0.48949 0.2549:0.0:0.7451:0.0 . 383;383 P30530-2;P30530 .;UFO_HUMAN V 383 ENSP00000301178:I383V;ENSP00000351995:I383V ENSP00000301178:I383V I + 1 0 AXL 46436921 0.002000 0.14202 0.135000 0.22099 0.952000 0.60782 -0.610000 0.05629 -0.465000 0.06953 0.317000 0.21355 ATA TCGA-IB-7888-01A-11D-2154-08 AXL-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000463323.2 1 0 0 20 274 0 32 0 9.415436e-01 0 68 0 32 2 0 0 0 0 0 2 1 0.999995 20 270 0 32 2 -19.999980 1 1 0 0 1 1 2 3 2.007548 0 0.160000 1.960000 0.166005 0.870000 0.550000 1.000000 1.000000 0.858844 0.870000 1 6.900000e-01 1 MEGF8 1954 broad.mit.edu 37 19 42873053 42873053 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:42873053C>T ENST00000251268.6 + 37 6540 c.6540C>T c.(6538-6540)gaC>gaT p.D2180D MEGF8_ENST00000378073.4_5'Flank|MEGF8_ENST00000334370.4_Silent_p.D2113D NM_001271938.1 NP_001258867.1 Q7Z7M0 MEGF8_HUMAN multiple EGF-like-domains 8 50 Prostate(69;0.00682) CCCCTGAGGACGAGTGTGCAA 0.612000 0 SO:0001819 synonymous_variant ENST00000251268.6 1 1 hg19 TCGA-IB-7888-01A-11D-2154-08 MEGF8-002 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000463854.1 1 0 0 31 462 0 58 0 1.125161e-01 0 9 0 58 2 0 0 0 0 0 2 1 1.000000 31 457 0 58 2 -3.221907 1 1 121408 12 41 1 1 2 3 2.007548 0 0.160000 1.960000 0.166005 0.800000 0.550000 1.000000 1.000000 0.813853 0.800000 0 6.700000e-01 9.900000e-01 ZNF155 7711 broad.mit.edu 37 19 44495748 44495748 + Missense_Mutation SNP C C G TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:44495748C>G ENST00000270014.2 + 3 192 c.64C>G c.(64-66)Ctg>Gtg p.L22V ZNF155_ENST00000590615.1_Missense_Mutation_p.L22V|ZNF155_ENST00000407951.2_Missense_Mutation_p.L33V NM_001260487.1|NM_198089.2 NP_001247416|NP_932355 Q12901 ZN155_HUMAN zinc finger protein 155 15 Prostate(69;0.0352) TGAGGAGGAGCTGGGGCTGCT 0.532000 NSCLC(61;554 1277 20909 42067 42312) 0 SO:0001583 missense ENST00000270014.2 1 1 hg19 CCDS12634.1 . . . . . . . . . . c 13.84 2.356298 0.41700 . . ENSG00000204920 ENST00000407951;ENST00000270014 T;T 0.01787 4.64;4.64 1.64 1.64 0.23874 Krueppel-associated box (4); . . . . T 0.06508 0.0167 M 0.68317 2.08 0.23546 N 0.997442 D;D 0.89917 0.999;1.0 D;D 0.91635 0.999;0.996 T 0.30475 -0.9977 9 0.87932 D 0 . 3.5586 0.07873 0.0:0.6202:0.0:0.3798 . 33;22 B4DM95;Q12901 .;ZN155_HUMAN V 33;22 ENSP00000385163:L33V;ENSP00000270014:L22V ENSP00000270014:L22V L + 1 2 ZNF155 49187588 0.980000 0.34600 1.000000 0.80357 0.940000 0.58332 -0.002000 0.12924 1.202000 0.43218 0.462000 0.41574 CTG TCGA-IB-7888-01A-11D-2154-08 ZNF155-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000460074.1 0 0 0 44 1272 0 167 0 1.620949e-02 1 5 0 167 2 0 0 0 0 0 2 1 1.000000 42 1249 0 165 2 -2.880287 1 1 121412 2 31 1 0 1 1 2.005789 0 0.160000 1.960000 0.156627 0.410000 0.300000 0.540000 0.410000 0.423340 0.410000 0 3.500000e-01 4.800000e-01 CD33 945 broad.mit.edu 37 19 51728620 51728620 + Missense_Mutation SNP C C T rs138300409 byFrequency TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:51728620C>T ENST00000262262.4 + 2 205 c.184C>T c.(184-186)Cgg>Tgg p.R62W CD33_ENST00000421133.2_Intron|CD33_ENST00000436584.2_Intron|CD33_ENST00000391796.3_Missense_Mutation_p.R62W NM_001772.3 NP_001763.3 P20138 CD33_HUMAN CD33 molecule 24 all_neural(266;0.0199) Gemtuzumab ozogamicin(DB00056) TTACTGGTTCCGGGAAGGAGC 0.537000 0 SO:0001583 missense ENST00000262262.4 1 1 hg19 CCDS33084.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 . 13.98 2.398956 0.42512 0.002724 0.0 ENSG00000105383 ENST00000262262;ENST00000391796 T;T 0.70986 -0.53;-0.53 3.49 2.41 0.29592 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 1.872790 0.03872 N 0.275685 T 0.78641 0.4315 M 0.84433 2.695 0.34210 D 0.674215 P;P 0.52061 0.95;0.908 B;P 0.47162 0.32;0.54 T 0.71424 -0.4597 10 0.59425 D 0.04 . 8.0281 0.30448 0.2431:0.7569:0.0:0.0 . 62;62 F8WAL2;P20138 .;CD33_HUMAN W 62 ENSP00000262262:R62W;ENSP00000375673:R62W ENSP00000262262:R62W R + 1 2 CD33 56420432 0.000000 0.05858 0.293000 0.24932 0.544000 0.35116 -0.589000 0.05767 0.778000 0.33520 0.655000 0.94253 CGG TCGA-IB-7888-01A-11D-2154-08 CD33-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000464199.2 1 0 0 53 594 0 60 0 2.000260e-01 0 10 0 60 2 0 0 0 0 0 2 1 1.000000 52 585 0 60 2 -2.774725 1 1 121412 34 48 1 0 1 1 2.005789 0 0.160000 1.960000 0.156627 0.990000 0.770000 1.000000 1.000000 0.959666 0.990000 1 8.800000e-01 1 ZNF480 147657 broad.mit.edu 37 19 52825191 52825191 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:52825191C>T ENST00000595962.1 + 5 754 c.688C>T c.(688-690)Cct>Tct p.P230S ZNF480_ENST00000334564.7_Missense_Mutation_p.P187S|ZNF480_ENST00000490272.1_3'UTR|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000335090.6_Missense_Mutation_p.P153S NM_144684.2 NP_653285.2 Q8WV37 ZN480_HUMAN zinc finger protein 480 12 TGTAGAGAAACCTTACAAATG 0.358000 0 SO:0001583 missense ENST00000595962.1 1 1 hg19 CCDS12850.2 . . . . . . . . . . C 10.56 1.385181 0.25031 . . ENSG00000198464 ENST00000468240;ENST00000334564;ENST00000335090 T;T;T 0.28454 1.61;1.61;1.61 1.99 1.99 0.26369 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.25791 0.0628 L 0.49640 1.575 0.24874 N 0.992269 B;B 0.28552 0.215;0.097 B;B 0.23852 0.049;0.026 T 0.22138 -1.0225 9 0.66056 D 0.02 . 7.3747 0.26821 0.0:1.0:0.0:0.0 . 187;230 F8WEZ9;Q8WV37 .;ZN480_HUMAN S 230;187;153 ENSP00000417424:P230S;ENSP00000334164:P187S;ENSP00000335670:P153S ENSP00000334164:P187S P + 1 0 ZNF480 57517003 0.000000 0.05858 0.041000 0.18516 0.050000 0.14768 0.441000 0.21611 1.080000 0.41073 0.467000 0.42956 CCT TCGA-IB-7888-01A-11D-2154-08 ZNF480-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000349001.3 1 0 0 24 347 0 51 0 4.659431e-03 0 2 0 51 2 0 0 0 1 0 0 2 1 1.000000 24 342 0 51 2 -20.000000 1 1 0 0 1 1 2 3 2.034393 0 0.160000 1.960000 0.169304 0.840000 0.540000 1.000000 1.000000 0.840870 0.840000 0 6.800000e-01 1 ZNF578 147660 broad.mit.edu 37 19 53015104 53015104 + Missense_Mutation SNP G G C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:53015104G>C ENST00000421239.2 + 6 1714 c.1470G>C c.(1468-1470)aaG>aaC p.K490N CTD-3099C6.5_ENST00000599143.1_RNA NM_001099694.1 NP_001093164.1 Q96N58 ZN578_HUMAN zinc finger protein 578 AGTGTCACAAGACCTTCAGTC 0.393000 0 SO:0001583 missense ENST00000421239.2 0 1 hg19 CCDS54310.1 . . . . . . . . . . - 11.14 1.552309 0.27739 . . ENSG00000258405 ENST00000553364 . . . 1.54 0.276 0.15663 . . . . . T 0.64438 0.2598 M 0.85373 2.75 0.09310 N 1 D 0.89917 1.0 D 0.79784 0.993 T 0.52208 -0.8606 7 . . . . 3.0654 0.06213 0.1691:0.0:0.5654:0.2655 . 490 G3V4F6 . N 490 . . K + 3 2 ZNF578 57706916 0.001000 0.12720 0.000000 0.03702 0.074000 0.17049 -0.210000 0.09345 -0.031000 0.13781 0.306000 0.20318 AAG TCGA-IB-7888-01A-11D-2154-08 ZNF578-001 KNOWN not_best_in_genome_evidence|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344298.3 0 0 0 9 498 0 60 0 0 0 1 0 60 2 0 0 0 0 0 2 1 0.994088 9 494 0 60 2 -7.785121 1 1 0 0 1 1 2 3 2.034393 0 0.160000 1.960000 0.169304 0.240000 0.110000 1.000000 0.220000 0.330088 0.240000 0 1.600000e-01 3.800000e-01 VN1R4 317703 broad.mit.edu 37 19 53770125 53770125 + Missense_Mutation SNP A A G TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:53770125A>G ENST00000311170.4 - 1 847 c.794T>C c.(793-795)tTa>tCa p.L265S CTD-2245F17.9_ENST00000599803.1_lincRNA NM_173857.2 NP_776256.2 Q7Z5H5 VN1R4_HUMAN vomeronasal 1 receptor 4 22 GTTCACCAGTAAACTATTGGG 0.453000 HNSCC(26;0.072) 0 SO:0001583 missense ENST00000311170.4 1 1 hg19 CCDS33099.1 . . . . . . . . . . A 7.798 0.713095 0.15306 . . ENSG00000228567 ENST00000311170 T 0.09723 2.95 2.28 -2.0 0.07433 GPCR, rhodopsin-like superfamily (1); 1.998760 0.03487 N 0.216036 T 0.14787 0.0357 M 0.66939 2.045 0.09310 N 1 P 0.34724 0.465 B 0.38458 0.274 T 0.31971 -0.9924 10 0.62326 D 0.03 . 4.3774 0.11277 0.4545:0.3629:0.0:0.1826 . 265 Q7Z5H5 VN1R4_HUMAN S 265 ENSP00000310856:L265S ENSP00000310856:L265S L - 2 0 VN1R4 58461937 0.000000 0.05858 0.000000 0.03702 0.020000 0.10135 -1.932000 0.01554 -0.543000 0.06240 0.445000 0.29226 TTA TCGA-IB-7888-01A-11D-2154-08 VN1R4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464287.1 0 0 0 11 303 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 0.998261 10 299 0 35 2 -3.073324 1 1 121412 12 18 1 1 2 3 2.034393 0 0.160000 1.960000 0.169304 0.470000 0.240000 1.000000 0.440000 0.531349 0.470000 0 3.400000e-01 7.000000e-01 OR7D4 125958 broad.mit.edu 37 19 9325369 9325369 + Missense_Mutation SNP C C T rs112089905 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr19:9325369C>T ENST00000308682.2 - 1 173 c.145G>A c.(145-147)Gtc>Atc p.V49I NM_001005191.2 NP_001005191.1 Q8NG98 OR7D4_HUMAN olfactory receptor, family 7, subfamily D, member 4 26 TCAGAGCTGACGGCCAGAATG 0.552000 0 SO:0001583 missense ENST00000308682.2 0 1 hg19 CCDS32901.1 . . . . . . . . . . C 0.018 -1.485647 0.01018 . . ENSG00000174667 ENST00000308682 T 0.01422 4.91 4.0 -3.92 0.04155 GPCR, rhodopsin-like superfamily (1); 0.997135 0.08123 N 0.994431 T 0.00637 0.0021 N 0.02802 -0.49 0.09310 N 1 B 0.11235 0.004 B 0.10450 0.005 T 0.46884 -0.9159 10 0.06625 T 0.88 . 7.4819 0.27411 0.0:0.4152:0.1191:0.4657 . 49 Q8NG98 OR7D4_HUMAN I 49 ENSP00000310488:V49I ENSP00000310488:V49I V - 1 0 OR7D4 9186369 0.000000 0.05858 0.001000 0.08648 0.037000 0.13140 -3.502000 0.00449 -1.075000 0.03129 -0.441000 0.05720 GTC TCGA-IB-7888-01A-11D-2154-08 OR7D4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449004.1 0 0 0 7 618 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 0.980242 7 614 0 80 2 -2.597637 1 1 121412 4 40 1 1 2 3 2.008981 0 0.160000 1.960000 0.164013 0.150000 0.060000 1.000000 0.140000 0.198449 0.150000 0 1.000000e-01 2.300000e-01 SCNN1D 6339 broad.mit.edu 37 1 1225872 1225872 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr1:1225872G>A ENST00000338555.2 + 11 2448 c.1304G>A c.(1303-1305)cGc>cAc p.R435H SCNN1D_ENST00000379116.5_Missense_Mutation_p.R599H|SCNN1D_ENST00000325425.8_Missense_Mutation_p.R501H|SCNN1D_ENST00000400928.3_Missense_Mutation_p.R435H P51172 SCNND_HUMAN sodium channel, non-voltage-gated 1, delta subunit 7 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) Amiloride(DB00594)|Triamterene(DB00384) TGCTTCTACCGCCTCTACCAG 0.667000 0 SO:0001583 missense ENST00000338555.2 0 1 hg19 . . . . . . . . . . G 11.04 1.522663 0.27211 0.0 1.16E-4 ENSG00000162572 ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928 T;T;T;T 0.64085 -0.08;-0.08;-0.08;-0.08 4.05 -0.816 0.10839 . 1.672600 0.03725 N 0.252521 T 0.50820 0.1638 L 0.34521 1.04 0.19300 N 0.999974 P;P;P 0.47350 0.894;0.869;0.456 B;B;B 0.40565 0.273;0.333;0.018 T 0.49995 -0.8879 10 0.52906 T 0.07 . 7.7318 0.28791 0.5569:0.0:0.4431:0.0 . 257;435;599 B1AMF2;P51172;A6NNF7 .;SCNND_HUMAN;. H 466;599;435;501;435 ENSP00000368411:R599H;ENSP00000339504:R435H;ENSP00000321594:R501H;ENSP00000383717:R435H ENSP00000321594:R501H R + 2 0 SCNN1D 1215735 0.000000 0.05858 0.745000 0.31077 0.243000 0.25628 -0.215000 0.09279 -0.054000 0.13266 -0.350000 0.07774 CGC TCGA-IB-7888-01A-11D-2154-08 SCNN1D-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000005802.2 0 0 0 7 634 0 95 0 0 0 1 0 95 2 0 0 0 0 0 2 1 0.967663 7 545 0 92 2 -2.715278 1 1 120860 29 46 1 1 2 3 2.027057 0 0.160000 1.960000 0.167328 0.150000 0.060000 1.000000 0.140000 0.230713 0.150000 0 9.000000e-02 2.400000e-01 CSMD2 114784 broad.mit.edu 37 1 33999485 33999485 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr1:33999485C>T ENST00000373381.4 - 63 10078 c.9902G>A c.(9901-9903)cGt>cAt p.R3301H NM_001281956.1|NM_052896.3 NP_001268885.1|NP_443128.2 Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) TTTTTGACAACGGAAGAGGAC 0.562000 0 SO:0001583 missense ENST00000373381.4 1 1 hg19 . . . . . . . . . . C 15.17 2.753862 0.49362 . . ENSG00000121904 ENST00000373381 T 0.64991 -0.13 5.33 3.45 0.39498 Complement control module (2);Sushi/SCR/CCP (3); 0.324034 0.31010 N 0.008421 T 0.57140 0.2033 N 0.12961 0.28 0.80722 D 1 B;D 0.59357 0.014;0.985 B;D 0.65323 0.015;0.934 T 0.51411 -0.8709 10 0.20046 T 0.44 . 9.63 0.39774 0.0:0.7703:0.0:0.2297 . 3157;3301 Q7Z408;E7EUA6 CSMD2_HUMAN;. H 3301 ENSP00000362479:R3301H ENSP00000241312:R3157H R - 2 0 CSMD2 33772072 0.958000 0.32768 0.903000 0.35520 0.527000 0.34593 1.098000 0.31000 1.248000 0.43934 0.591000 0.81541 CGT TCGA-IB-7888-01A-11D-2154-08 CSMD2-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 0 17 218 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.999965 17 214 0 29 2 -19.981070 1 1 121412 8 36 1 0 1 1 2.003071 0 0.160000 1.960000 0.155949 0.900000 0.550000 1.000000 1.000000 0.871378 0.900000 1 7.100000e-01 1 GRIK3 2899 broad.mit.edu 37 1 37282815 37282815 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr1:37282815G>A ENST00000373091.3 - 13 1953 c.1937C>T c.(1936-1938)aCg>aTg p.T646M GRIK3_ENST00000373093.4_Missense_Mutation_p.T646M NM_000831.3 NP_000822.2 Q13003 GRIK3_HUMAN glutamate receptor, ionotropic, kainate 3 89 Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169) GATGATGAGCGTGAAGAACCA 0.547000 0 SO:0001583 missense ENST00000373091.3 1 1 hg19 CCDS416.1 . . . . . . . . . . G 29.6 5.021642 0.93462 . . ENSG00000163873 ENST00000373091;ENST00000373093 D;D 0.97455 -4.39;-4.39 5.74 5.74 0.90152 Ionotropic glutamate receptor (2); 0.000000 0.85682 D 0.000000 D 0.98642 0.9545 M 0.84948 2.725 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.998 D 0.99402 1.0928 10 0.87932 D 0 . 19.9326 0.97124 0.0:0.0:1.0:0.0 . 646;646 A9Z1Z8;Q13003 .;GRIK3_HUMAN M 646 ENSP00000362183:T646M;ENSP00000362185:T646M ENSP00000362183:T646M T - 2 0 GRIK3 37055402 1.000000 0.71417 0.999000 0.59377 0.997000 0.91878 9.869000 0.99810 2.720000 0.93068 0.650000 0.86243 ACG TCGA-IB-7888-01A-11D-2154-08 GRIK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012053.1 1 0 0 31 463 0 61 0 4.232465e-03 0 2 0 61 2 0 0 0 0 0 2 1 1.000000 30 460 0 61 2 -7.096011 1 1 0 0 1 0 1 1 2.003071 0 0.160000 1.960000 0.155949 0.780000 0.540000 1.000000 1.000000 0.788689 0.780000 0 6.500000e-01 9.200000e-01 PTBP2 58155 broad.mit.edu 37 1 97250690 97250690 + Missense_Mutation SNP G G C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr1:97250690G>C ENST00000426398.2 + 8 827 c.784G>C c.(784-786)Gta>Cta p.V262L PTBP2_ENST00000370198.1_Missense_Mutation_p.V262L|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000541987.1_Missense_Mutation_p.V231L|PTBP2_ENST00000609116.1_Missense_Mutation_p.V262L|PTBP2_ENST00000370197.1_Missense_Mutation_p.V262L|PTBP2_ENST00000394184.3_Missense_Mutation_p.V273L NM_021190.2 NP_067013.1 Q9UKA9 PTBP2_HUMAN polypyrimidine tract binding protein 2 26 all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171) GAATTTGAATGTAAAATACAA 0.388000 0 SO:0001583 missense ENST00000426398.2 1 1 hg19 CCDS754.1 . . . . . . . . . . G 18.57 3.652675 0.67472 . . ENSG00000117569 ENST00000236228;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184;ENST00000541987;ENST00000394176 T;T;T;T;T;D 0.83837 0.25;0.29;0.3;0.25;0.29;-1.77 5.57 5.57 0.84162 Nucleotide-binding, alpha-beta plait (1); 0.000000 0.85682 D 0.000000 D 0.91164 0.7217 M 0.81341 2.54 0.80722 D 1 B;B;P;B;B;B 0.34800 0.06;0.339;0.469;0.006;0.004;0.046 B;P;P;B;B;B 0.59115 0.18;0.716;0.852;0.118;0.227;0.235 D 0.90767 0.4669 10 0.87932 D 0 . 19.5464 0.95299 0.0:0.0:1.0:0.0 . 270;273;262;262;262;262 B4DSU5;B4DSS8;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3 .;.;.;PTBP2_HUMAN;.;. L 262;262;262;262;273;231;252 ENSP00000236228:V262L;ENSP00000359217:V262L;ENSP00000359216:V262L;ENSP00000412788:V262L;ENSP00000377738:V273L;ENSP00000442475:V231L ENSP00000236228:V262L V + 1 0 PTBP2 97023278 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.476000 0.97823 2.629000 0.89072 0.591000 0.81541 GTA TCGA-IB-7888-01A-11D-2154-08 PTBP2-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000029453.1 1 0 0 24 435 0 55 0 6.763151e-02 1 7 0 55 2 0 0 0 0 0 2 1 1.000000 24 431 0 55 2 -5.277491 1 1 0 0 1 0 1 1 2.003071 0 0.160000 1.960000 0.155949 0.650000 0.430000 0.920000 0.640000 0.666091 0.650000 0 5.300000e-01 7.900000e-01 RALGAPA2 57186 broad.mit.edu 37 20 20493321 20493321 + Missense_Mutation SNP A A C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr20:20493321A>C ENST00000202677.7 - 32 4699 c.4692T>G c.(4690-4692)atT>atG p.I1564M NM_020343.3 NP_065076.2 Q2PPJ7 RGPA2_HUMAN Ral GTPase activating protein, alpha subunit 2 (catalytic) 54 TTTGGCGCAAAATGACCTCAA 0.473000 0 SO:0001583 missense ENST00000202677.7 1 1 hg19 CCDS46584.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 12.96|12.96 2.094340|2.094340 0.36952|0.36952 .|. .|. ENSG00000188559|ENSG00000188559 ENST00000430436|ENST00000202677 .|D .|0.93953 .|-3.32 5.97|5.97 -2.19|-2.19 0.07015|0.07015 .|. .|0.185757 .|0.47093 .|D .|0.000246 D|D 0.92967|0.92967 0.7762|0.7762 M|M 0.84326|0.84326 2.69|2.69 0.23150|0.23150 N|N 0.998215|0.998215 .|P;P;P .|0.52463 .|0.745;0.953;0.852 .|B;P;P .|0.54924 .|0.41;0.737;0.764 D|D 0.85470|0.85470 0.1172|0.1172 5|9 .|. .|. .|. .|. 0.7294|0.7294 0.00955|0.00955 0.3729:0.2028:0.2455:0.1788|0.3729:0.2028:0.2455:0.1788 .|. .|1402;1564;1564 .|A8MSM5;Q2PPJ7-2;Q2PPJ7 .|.;.;RGPA2_HUMAN C|M 1381|1564 .|ENSP00000202677:I1564M .|. F|I -|- 2|3 0|3 RALGAPA2|RALGAPA2 20441321|20441321 0.025000|0.025000 0.19082|0.19082 0.786000|0.786000 0.31890|0.31890 0.938000|0.938000 0.57974|0.57974 -0.042000|-0.042000 0.12063|0.12063 -0.312000|-0.312000 0.08741|0.08741 0.459000|0.459000 0.35465|0.35465 TTT|ATT TCGA-IB-7888-01A-11D-2154-08 RALGAPA2-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000471941.1 1 0 1 21 345 0 29 1 5.994290e-01 8 26 0 29 2 0 0 0 0 0 2 1 0.999998 22 342 0 29 2 -19.999920 1 1 0 0 1 1 2 3 2.007114 0 0.160000 1.960000 0.163347 0.730000 0.460000 1.000000 1.000000 0.745524 0.730000 0 5.800000e-01 9.200000e-01 ZCCHC3 85364 broad.mit.edu 37 20 279077 279077 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr20:279077C>T ENST00000382352.3 + 1 1341 c.850C>T c.(850-852)Ccg>Tcg p.P284S NM_033089.6 NP_149080 Q9NUD5 ZCHC3_HUMAN zinc finger, CCHC domain containing 3 8 all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231) OV - Ovarian serous cystadenocarcinoma(29;0.149) GCTGGCCGTGCCGGTGAAAGT 0.627000 0 SO:0001583 missense ENST00000382352.3 0 1 hg19 CCDS42844.1 . . . . . . . . . . C 16.02 3.003893 0.54254 . . ENSG00000177764 ENST00000382352 . . . 5.2 5.2 0.72013 . 0.169587 0.37304 N 0.002143 T 0.49575 0.1565 N 0.11560 0.145 0.36834 D 0.887039 D 0.76494 0.999 D 0.66716 0.946 T 0.58346 -0.7652 9 0.52906 T 0.07 -21.2771 9.6167 0.39696 0.0:0.9079:0.0:0.0921 . 284 Q9NUD5 ZCHC3_HUMAN S 284 . ENSP00000371789:P284S P + 1 0 ZCCHC3 227077 1.000000 0.71417 1.000000 0.80357 0.959000 0.62525 2.058000 0.41374 2.707000 0.92482 0.555000 0.69702 CCG TCGA-IB-7888-01A-11D-2154-08 ZCCHC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077447.1 0 0 0 6 572 0 59 0 5.782568e-02 0 31 0 59 2 0 0 0 0 0 2 1 0.963188 6 562 0 59 2 -2.079961 0 1 0 0 1 1 2 3 2.007114 0 0.160000 1.960000 0.163347 0.140000 0.050000 1.000000 0.130000 0.182398 0.140000 0 9.000000e-02 2.200000e-01 KCNB1 3745 broad.mit.edu 37 20 47990860 47990860 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr20:47990860C>T ENST00000371741.4 - 2 1403 c.1237G>A c.(1237-1239)Gtc>Atc p.V413I 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) AAGTTATTGACGATGATGGGG 0.507000 0 SO:0001583 missense ENST00000371741.4 1 1 hg19 CCDS13418.1 . . . . . . . . . . C 19.89 3.910860 0.72983 . . ENSG00000158445 ENST00000371741;ENST00000538812 D 0.97620 -4.46 6.07 6.07 0.98685 . 0.132027 0.49305 D 0.000146 D 0.98388 0.9464 M 0.74258 2.255 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 D 0.98623 1.0668 10 0.62326 D 0.03 . 20.2543 0.98414 0.0:1.0:0.0:0.0 . 413 Q14721 KCNB1_HUMAN I 413;368 ENSP00000360806:V413I ENSP00000360806:V413I V - 1 0 KCNB1 47424267 1.000000 0.71417 0.999000 0.59377 0.995000 0.86356 7.818000 0.86416 2.884000 0.98904 0.655000 0.94253 GTC TCGA-IB-7888-01A-11D-2154-08 KCNB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080374.3 0 0 0 17 467 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 0.999965 17 465 0 63 2 -3.817906 1 1 0 0 1 1 2 3 2.007114 0 0.160000 1.960000 0.163347 0.450000 0.270000 1.000000 0.440000 0.480415 0.450000 0 3.500000e-01 5.800000e-01 ZNF70 7621 broad.mit.edu 37 22 24086567 24086567 + Missense_Mutation SNP C C G TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr22:24086567C>G ENST00000341976.3 - 2 1221 c.761G>C c.(760-762)tGt>tCt p.C254S NM_021916.2 NP_068735.1 Q9UC06 ZNF70_HUMAN zinc finger protein 70 21 ACATTCCTTACACTGATAAGG 0.512000 0 SO:0001583 missense ENST00000341976.3 1 1 hg19 CCDS13812.1 . . . . . . . . . . C 19.48 3.836062 0.71373 . . ENSG00000187792 ENST00000341976 D 0.85171 -1.95 3.34 3.34 0.38264 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . D 0.94248 0.8153 H 0.95884 3.735 0.42002 D 0.990899 D 0.89917 1.0 D 0.97110 1.0 D 0.95533 0.8605 9 0.87932 D 0 -14.9537 13.0199 0.58779 0.0:1.0:0.0:0.0 . 254 Q9UC06 ZNF70_HUMAN S 254 ENSP00000339314:C254S ENSP00000339314:C254S C - 2 0 ZNF70 22416567 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 7.099000 0.76981 2.175000 0.68902 0.456000 0.33151 TGT TCGA-IB-7888-01A-11D-2154-08 ZNF70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319881.1 1 0 0 20 360 0 26 0 3.141319e-03 0 2 0 26 2 0 0 0 0 0 2 1 0.999996 21 358 0 26 2 -19.985140 1 1 0 0 1 0.160000 1.960000 0 0 HOXD1 3231 broad.mit.edu 37 2 177054575 177054575 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr2:177054575C>T ENST00000331462.4 + 2 915 c.692C>T c.(691-693)gCg>gTg p.A231V HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000436126.1_RNA NM_024501.2 NP_078777.1 Q9GZZ0 HXD1_HUMAN homeobox D1 10 OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226) CCCTCCAGCGCGATCCGCACG 0.557000 0 SO:0001583 missense ENST00000331462.4 0 1 hg19 CCDS2271.1 . . . . . . . . . . C 20.1 3.934471 0.73442 . . ENSG00000128645 ENST00000331462 D 0.95656 -3.77 5.45 4.56 0.56223 Homeodomain-related (1);Homeobox (2);Homeodomain-like (1); 0.288296 0.25122 N 0.032971 D 0.91676 0.7369 L 0.46157 1.445 0.43342 D 0.99539 P;B 0.44006 0.824;0.209 B;B 0.32465 0.146;0.073 D 0.90160 0.4227 10 0.33940 T 0.23 . 15.8297 0.78741 0.0:0.8637:0.1363:0.0 . 231;231 Q96CA4;Q9GZZ0 .;HXD1_HUMAN V 231 ENSP00000328598:A231V ENSP00000328598:A231V A + 2 0 HOXD1 176762821 1.000000 0.71417 0.982000 0.44146 0.976000 0.68499 6.063000 0.71162 1.273000 0.44346 0.655000 0.94253 GCG TCGA-IB-7888-01A-11D-2154-08 HOXD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255693.2 0 0 0 15 980 0 106 0 8.054221e-04 0 3 0 106 2 0 0 0 0 0 2 1 0.999847 15 961 0 105 2 -2.967410 1 1 121412 1 33 1 1 2 3 2.011184 0 0.160000 1.960000 0.164013 0.190000 0.100000 1.000000 0.190000 0.238081 0.190000 0 1.400000e-01 2.600000e-01 ZAP70 7535 broad.mit.edu 37 2 98354224 98354224 + Missense_Mutation SNP G G A rs150631046 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr2:98354224G>A ENST00000264972.5 + 12 1702 c.1487G>A c.(1486-1488)cGc>cAc p.R496H ZAP70_ENST00000451498.2_Missense_Mutation_p.R189H|ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Missense_Mutation_p.R370H NM_001079.3 NP_001070.2 P43403 ZAP70_HUMAN zeta-chain (TCR) associated protein kinase 70kDa 29 CCCCAGGCCCGCTCAGCAGGG 0.627000 0 SO:0001583 missense ENST00000264972.5 0 1 hg19 CCDS33254.1 . . . . . . . . . . G 21.8 4.206886 0.79127 0.0 1.16E-4 ENSG00000115085 ENST00000264972;ENST00000442208;ENST00000451498 D;D;D 0.83250 -1.7;-1.7;-1.7 5.2 5.2 0.72013 Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.000000 0.44902 D 0.000406 T 0.80839 0.4700 N 0.24115 0.695 0.51233 D 0.99991 D;D 0.76494 0.999;0.999 P;D 0.62955 0.864;0.909 T 0.75371 -0.3341 10 0.15952 T 0.53 . 10.1268 0.42654 0.0915:0.0:0.9085:0.0 . 370;496 P43403-3;P43403 .;ZAP70_HUMAN H 496;370;189 ENSP00000264972:R496H;ENSP00000411141:R370H;ENSP00000400475:R189H ENSP00000264972:R496H R + 2 0 ZAP70 97720656 1.000000 0.71417 1.000000 0.80357 0.938000 0.57974 6.334000 0.72944 2.610000 0.88304 0.655000 0.94253 CGC TCGA-IB-7888-01A-11D-2154-08 ZAP70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329278.1 0 0 0 6 787 0 94 0 1.762158e-02 0 22 0 94 2 0 0 0 0 0 2 1 0.962626 6 770 0 91 2 -2.317295 0 1 121412 1 28 1 0 1 1 1.892716 1 0.160000 1.960000 0.119866 0.090000 0.030000 0.190000 0.090000 0.104071 0.090000 0 6.000000e-02 1.400000e-01 MUC4 4585 broad.mit.edu 37 3 195515980 195515980 + Nonsense_Mutation SNP G G T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr3:195515980G>T ENST00000463781.3 - 2 2930 c.2471C>A c.(2470-2472)tCa>tAa p.S824* MUC4_ENST00000475231.1_Nonsense_Mutation_p.S824*|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron NM_018406.6 NP_060876.5 Q99102 MUC4_HUMAN mucin 4, cell surface associated 51 all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) CGTCTCTCCTGAGGTGGATAT 0.577000 0 SO:0001587 stop_gained ENST00000463781.3 0 1 hg19 CCDS54700.1 . . . . . . . . . . - 37 6.249658 0.97412 . . ENSG00000145113 ENST00000463781;ENST00000475231;ENST00000392409 . . . 3.5 1.63 0.23807 . 2.354170 0.02108 N 0.054574 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -2.5202 5.4797 0.16717 0.1201:0.2045:0.6753:0.0 . . . . X 824;824;798 . ENSP00000376209:S798X S - 2 0 MUC4 197000375 0.027000 0.19231 0.000000 0.03702 0.004000 0.04260 3.437000 0.52863 0.260000 0.21731 0.627000 0.83407 TCA TCGA-IB-7888-01A-11D-2154-08 MUC4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000324081.6 1 0 0 41 473 0 48 0 5.692764e-02 1 4 0 48 2 0 0 0 0 0 2 1 1.000000 41 466 0 48 2 -3.142702 1 1 0 0 1 0 1 1 2.003901 0 0.160000 1.960000 0.155949 0.980000 0.720000 1.000000 1.000000 0.942069 0.980000 1 8.400000e-01 1 CACNA2D3 55799 broad.mit.edu 37 3 54798357 54798357 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr3:54798357C>T ENST00000474759.1 + 13 1407 c.1359C>T c.(1357-1359)acC>acT p.T453T CACNA2D3_ENST00000490478.1_Silent_p.T359T|CACNA2D3_ENST00000415676.2_Silent_p.T453T|CACNA2D3_ENST00000288197.5_Silent_p.T453T NM_018398.2 NP_060868.2 Q8IZS8 CA2D3_HUMAN calcium channel, voltage-dependent, alpha 2/delta subunit 3 59 Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421) TGGTGTGGACCGAAGCTTACA 0.507000 0 SO:0001819 synonymous_variant ENST00000474759.1 1 1 hg19 CCDS54598.1 TCGA-IB-7888-01A-11D-2154-08 CACNA2D3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351402.1 1 0 0 30 433 0 56 0 1.308691e-02 0 3 0 56 2 0 0 0 0 0 2 1 1.000000 30 430 0 56 2 -2.429504 0 1 120972 1 35 1 0 1 1 2.003901 0 0.160000 1.960000 0.155949 0.800000 0.550000 1.000000 1.000000 0.811147 0.800000 0 6.700000e-01 9.600000e-01 C4orf21 0 broad.mit.edu 37 4 113460845 113460845 + Splice_Site SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr4:113460845C>T ENST00000505019.1 - 28 6298 c.6173G>A c.(6172-6174)gGa>gAa p.G2058E RP11-402J6.1_ENST00000504009.1_RNA NM_018392.4 NP_060862.3 Q86YA3 ZGRF1_HUMAN 45 Ovarian(17;0.156) ATCTTCCCTTCCTTAAAAAAA 0.373000 0 SO:0001630 splice_region_variant ENST00000505019.1 0 1 hg19 . . . . . . . . . . C 14.33 2.504359 0.44558 . . ENSG00000138658 ENST00000505019 D 0.81659 -1.52 5.37 5.37 0.77165 . 0.229935 0.38436 N 0.001681 T 0.70850 0.3271 L 0.34521 1.04 0.80722 D 1 B;B 0.33637 0.42;0.016 B;B 0.35240 0.198;0.008 T 0.66763 -0.5841 10 0.21540 T 0.41 -21.145 12.0989 0.53772 0.0:0.9203:0.0:0.0797 . 2058;516 G5EA02;B3KQX2 .;. E 2058 ENSP00000424737:G2058E ENSP00000424737:G2058E G - 2 0 C4orf21 113680294 0.955000 0.32602 0.986000 0.45419 0.904000 0.53231 0.837000 0.27558 2.678000 0.91216 0.555000 0.69702 GGA TCGA-IB-7888-01A-11D-2154-08 C4orf21-003 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000256413.1 0 0 0 11 109 0 16 0 2.222264e-01 0 9 0 16 2 0 0 0 0 0 2 1 0.998525 11 108 0 16 2 -6.664263 1 1 0 0 1 1 2 3 2.007896 0 0.160000 1.960000 0.163347 0.990000 0.620000 1.000000 1.000000 0.950493 0.990000 1 8.600000e-01 1 TLL1 7092 broad.mit.edu 37 4 166978413 166978413 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr4:166978413G>A ENST00000061240.2 + 14 2445 c.1798G>A c.(1798-1800)Gcc>Acc p.A600T TLL1_ENST00000507499.1_Missense_Mutation_p.A623T NM_012464.4 NP_036596.3 O43897 TLL1_HUMAN tolloid-like 1 77 all_hematologic(180;0.221) Melanoma(52;0.0315)|Prostate(90;0.0405) TTACCAGTGTGCCTGTGAGCC 0.512000 0 SO:0001583 missense ENST00000061240.2 0 1 hg19 CCDS3811.1 . . . . . . . . . . G 13.64 2.296332 0.40594 . . ENSG00000038295 ENST00000061240;ENST00000507499 D;D 0.97016 -4.21;-4.21 5.96 1.33 0.21861 EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.201206 0.42172 N 0.000746 D 0.90683 0.7077 N 0.04669 -0.19 0.50813 D 0.99989 B;P 0.42584 0.088;0.784 B;P 0.51657 0.054;0.676 D 0.83697 0.0180 10 0.20519 T 0.43 . 6.019 0.19618 0.1836:0.0:0.5477:0.2687 . 623;600 E9PD25;O43897 .;TLL1_HUMAN T 600;623 ENSP00000061240:A600T;ENSP00000426082:A623T ENSP00000061240:A600T A + 1 0 TLL1 167197863 0.980000 0.34600 0.005000 0.12908 0.779000 0.44077 2.781000 0.47750 -0.066000 0.12998 -0.143000 0.13931 GCC TCGA-IB-7888-01A-11D-2154-08 TLL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000363821.1 0 0 0 6 462 0 42 0 2.424630e-03 0 5 0 42 2 0 0 0 0 0 2 1 0.964492 6 459 0 42 2 -5.501510 1 1 0 0 1 1 2 3 2.007896 0 0.160000 1.960000 0.163347 0.170000 0.060000 1.000000 0.160000 0.215827 0.170000 0 1.100000e-01 2.700000e-01 KDR 3791 broad.mit.edu 37 4 55956204 55956204 + Silent SNP C C T rs147630437 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr4:55956204C>T ENST00000263923.4 - 23 3406 c.3111G>A c.(3109-3111)tcG>tcA p.S1037S RP11-530I17.1_ENST00000511222.1_RNA NM_002253.2 NP_002244.1 P35968 VGFR2_HUMAN kinase insert domain receptor (a type III receptor tyrosine kinase) 135 all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101) Epithelial(7;0.189) Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268) CGTTCTTCTCCGATAAGAGGA 0.428000 Mis NSCLC, angiosarcoma TSP Lung(20;0.16) Dom yes 4 4q11-q12 3791 vascular endothelial growth factor receptor 2 E 0 SO:0001819 synonymous_variant ENST00000263923.4 1 1 hg19 CCDS3497.1 TCGA-IB-7888-01A-11D-2154-08 KDR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250645.1 1 0 0 36 448 0 58 0 8.836514e-01 0 49 0 58 2 0 0 0 0 0 2 1 1.000000 36 443 0 58 2 -2.578431 1 1 121412 9 40 1 1 2 3 2.007896 0 0.160000 1.960000 0.163347 0.940000 0.670000 1.000000 1.000000 0.911841 0.940000 1 7.900000e-01 1 SLC6A19 340024 broad.mit.edu 37 5 1208876 1208876 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr5:1208876C>T ENST00000304460.10 + 2 274 c.218C>T c.(217-219)cCg>cTg p.P73L NM_001003841.2 NP_001003841.1 Q695T7 S6A19_HUMAN solute carrier family 6 (neutral amino acid transporter), member 19 44 all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10) Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185) TTCATGATCCCGTTCCTCATC 0.657000 0 SO:0001583 missense ENST00000304460.10 1 1 hg19 CCDS34130.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 26.6 4.754281 0.89843 0.0 1.16E-4 ENSG00000174358 ENST00000304460 D 0.86865 -2.18 4.55 4.55 0.56014 . 0.000000 0.85682 D 0.000000 D 0.94968 0.8372 M 0.92691 3.335 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 D 0.96314 0.9231 10 0.72032 D 0.01 . 17.3733 0.87384 0.0:1.0:0.0:0.0 . 73 Q695T7 S6A19_HUMAN L 73 ENSP00000305302:P73L ENSP00000305302:P73L P + 2 0 SLC6A19 1261876 1.000000 0.71417 0.919000 0.36401 0.935000 0.57460 5.849000 0.69465 2.091000 0.63221 0.485000 0.47835 CCG TCGA-IB-7888-01A-11D-2154-08 SLC6A19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365557.1 1 0 0 54 658 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 54 652 0 70 2 -2.287385 0 1 121408 12 44 1 0 1 1 2.003436 0 0.160000 1.960000 0.155949 0.930000 0.710000 1.000000 1.000000 0.921879 0.930000 1 8.200000e-01 1 PCDHGA8 9708 broad.mit.edu 37 5 140774356 140774356 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr5:140774356C>T ENST00000398604.2 + 1 1976 c.1976C>T c.(1975-1977)aCg>aTg p.T659M 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|PCDHGB4_ENST00000519479.1_Intron NM_032088.1 NP_114477.1 Q9Y5G5 PCDG8_HUMAN protocadherin gamma subfamily A, 8 51 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCCACTGTCACGCTCACCGTA 0.642000 0 SO:0001583 missense ENST00000398604.2 1 1 hg19 CCDS47291.1 . . . . . . . . . . . 10.15 1.270078 0.23221 . . ENSG00000253767 ENST00000398604 T 0.55588 0.51 4.99 0.815 0.18763 Cadherin (4);Cadherin-like (1); 0.284430 0.17574 U 0.169343 T 0.64260 0.2582 M 0.77103 2.36 0.09310 N 0.999997 D;D 0.71674 0.974;0.998 P;P 0.58820 0.656;0.846 T 0.56123 -0.8031 10 0.72032 D 0.01 . 8.7668 0.34708 0.0:0.6668:0.1188:0.2144 . 659;659 Q9Y5G5;Q9Y5G5-2 PCDG8_HUMAN;. M 659 ENSP00000381605:T659M ENSP00000381605:T659M T + 2 0 PCDHGA8 140754540 0.000000 0.05858 0.009000 0.14445 0.315000 0.28087 0.251000 0.18257 0.182000 0.20032 -0.156000 0.13503 ACG TCGA-IB-7888-01A-11D-2154-08 PCDHGA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376972.1 1 0 0 21 354 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 0.999992 18 315 0 37 2 -19.999590 1 1 0 0 1 0 1 1 2.003436 0 0.160000 1.960000 0.155949 0.690000 0.440000 1.000000 1.000000 0.712766 0.690000 0 5.600000e-01 8.600000e-01 PCDHGB7 56099 broad.mit.edu 37 5 140797472 140797472 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr5:140797472G>A ENST00000398594.2 + 1 46 c.46G>A c.(46-48)Gta>Ata p.V16I 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|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron NM_018927.3 NP_061750.1 Q9Y5F8 PCDGJ_HUMAN protocadherin gamma subfamily B, 7 56 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) cccgcggcAGGTACTATTTCC 0.642000 OREG0016863 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000398594.2 0 1 hg19 CCDS47293.1 . . . . . . . . . . g 16.24 3.066765 0.55539 . . ENSG00000254122 ENST00000398594 T 0.49432 0.78 5.92 5.92 0.95590 . 0.310523 0.16999 U 0.190963 T 0.44644 0.1303 N 0.08118 0 0.22199 N 0.999295 P;P 0.50617 0.63;0.937 B;P 0.52554 0.407;0.702 T 0.47129 -0.9141 10 0.39692 T 0.17 . 20.3343 0.98733 0.0:0.0:1.0:0.0 . 16;16 Q9Y5F8;Q9Y5F8-2 PCDGJ_HUMAN;. I 16 ENSP00000381594:V16I ENSP00000381594:V16I V + 1 0 PCDHGB7 140777656 1.000000 0.71417 1.000000 0.80357 0.507000 0.33981 7.377000 0.79668 2.822000 0.97130 0.650000 0.86243 GTA TCGA-IB-7888-01A-11D-2154-08 PCDHGB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376973.1 0 0 0 4 72 0 9 0 0 0 0 9 2 0 0 0 0 0 2 1 0.885874 4 70 0 9 2 -8.332241 1 1 0 0 1 0 1 1 2.003436 0 0.160000 1.960000 0.155949 0.690000 0.240000 1.000000 1.000000 0.696963 0.690000 0 4.200000e-01 1 SLC1A3 6507 broad.mit.edu 37 5 36684084 36684084 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr5:36684084G>A ENST00000265113.4 + 9 1884 c.1408G>A c.(1408-1410)Gcg>Acg p.A470T SLC1A3_ENST00000381918.3_Intron|CTD-2353F22.1_ENST00000510740.1_RNA NM_004172.4 NP_004163.3 P43003 EAA1_HUMAN solute carrier family 1 (glial high affinity glutamate transporter), member 3 41 all_lung(31;0.000245) Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) GCTCATCATCGCGGTGGACTG 0.587000 0 SO:0001583 missense ENST00000265113.4 1 1 hg19 CCDS3919.1 . . . . . . . . . . G 36 5.635976 0.96693 . . ENSG00000079215 ENST00000265113;ENST00000427100 T 0.64260 -0.09 5.74 5.74 0.90152 . 0.000000 0.85682 D 0.000000 T 0.79592 0.4472 M 0.78456 2.415 0.80722 D 1 D 0.89917 1.0 D 0.63793 0.918 T 0.79938 -0.1592 10 0.54805 T 0.06 -18.3873 19.9326 0.97124 0.0:0.0:1.0:0.0 . 470 P43003 EAA1_HUMAN T 470;418 ENSP00000265113:A470T ENSP00000265113:A470T A + 1 0 SLC1A3 36719841 1.000000 0.71417 0.972000 0.41901 0.977000 0.68977 9.768000 0.98965 2.720000 0.93068 0.650000 0.86243 GCG TCGA-IB-7888-01A-11D-2154-08 SLC1A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207579.2 1 0 0 60 690 0 71 0 7.535664e-01 0 33 0 71 2 0 0 0 1 0 0 2 1 1.000000 59 685 0 70 2 -14.296970 1 1 121412 1 33 1 0 1 1 2.003436 0 0.160000 1.960000 0.155949 0.990000 0.760000 1.000000 1.000000 0.951944 0.990000 1 8.700000e-01 1 BDP1 55814 broad.mit.edu 37 5 70840231 70840231 + Missense_Mutation SNP C C A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr5:70840231C>A ENST00000358731.4 + 31 6723 c.6460C>A c.(6460-6462)Ctc>Atc p.L2154I BDP1_ENST00000380675.2_Missense_Mutation_p.L290I NM_018429.2 NP_060899.2 A6H8Y1 BDP1_HUMAN B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 72 Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198) AAATAAAAACCTCGGACCAGT 0.358000 0 SO:0001583 missense ENST00000358731.4 1 1 hg19 CCDS43328.1 . . . . . . . . . . C 9.258 1.042474 0.19748 . . ENSG00000145734 ENST00000358731;ENST00000451951;ENST00000380675;ENST00000545546 T;T 0.49139 3.67;0.79 5.24 0.299 0.15771 . 0.742384 0.12025 N 0.506463 T 0.40196 0.1107 M 0.64997 1.995 0.09310 N 1 B;B 0.21147 0.052;0.005 B;B 0.22601 0.04;0.004 T 0.35773 -0.9775 10 0.42905 T 0.14 . 4.7548 0.13078 0.0:0.5134:0.1484:0.3382 . 2154;2154 A6H8Y1;A6H8Y1-2 BDP1_HUMAN;. I 2154;1702;290;290 ENSP00000351575:L2154I;ENSP00000370050:L290I ENSP00000351575:L2154I L + 1 0 BDP1 70875987 0.000000 0.05858 0.001000 0.08648 0.669000 0.39330 -0.816000 0.04477 0.037000 0.15575 -0.122000 0.15005 CTC TCGA-IB-7888-01A-11D-2154-08 BDP1-016 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000374681.2 1 0 0 41 507 0 53 0 9.569440e-02 0 7 0 53 2 0 0 0 0 0 2 1 1.000000 41 500 0 53 2 -2.879461 1 1 0 0 1 0 1 1 2.003436 0 0.160000 1.960000 0.155949 0.920000 0.680000 1.000000 1.000000 0.908874 0.920000 1 7.900000e-01 1 POLK 51426 broad.mit.edu 37 5 74893770 74893770 + Missense_Mutation SNP T T C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr5:74893770T>C ENST00000241436.4 + 15 2712 c.2540T>C c.(2539-2541)aTg>aCg p.M847T POLK_ENST00000506928.1_3'UTR|POLK_ENST00000508526.1_Missense_Mutation_p.M649T|POLK_ENST00000380481.3_Missense_Mutation_p.M757T|CTC-366B18.2_ENST00000511329.1_RNA|POLK_ENST00000504026.1_3'UTR|POLK_ENST00000352007.5_Missense_Mutation_p.M649T NM_016218.2 NP_057302.1 Q9UBT6 POLK_HUMAN polymerase (DNA directed) kappa 27 all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184) CCAGGATTGATGACAAAGTAC 0.244000 DNA polymerases (catalytic subunits) 0 SO:0001583 missense ENST00000241436.4 0 1 hg19 CCDS4030.1 . . . . . . . . . . T 10.08 1.252983 0.22965 . . ENSG00000122008 ENST00000241436;ENST00000352007;ENST00000508526;ENST00000380481 T;T;T;T 0.52754 1.38;0.65;0.65;1.38 5.22 -2.08 0.07254 . 0.820001 0.11842 N 0.524186 T 0.24431 0.0592 L 0.34521 1.04 0.09310 N 1 B;B 0.06786 0.0;0.001 B;B 0.06405 0.001;0.002 T 0.32295 -0.9912 10 0.02654 T 1 -0.5908 3.4503 0.07495 0.4082:0.2354:0.0:0.3564 . 649;847 Q9UBT6-3;Q9UBT6 .;POLK_HUMAN T 847;649;649;757 ENSP00000241436:M847T;ENSP00000342256:M649T;ENSP00000426853:M649T;ENSP00000369848:M757T ENSP00000241436:M847T M + 2 0 POLK 74929526 0.000000 0.05858 0.004000 0.12327 0.939000 0.58152 -0.694000 0.05115 -0.514000 0.06488 -0.333000 0.08304 ATG TCGA-IB-7888-01A-11D-2154-08 POLK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219945.3 1 0 0 19 208 0 8 1 7.891585e-01 4 30 0 8 2 0 0 0 0 0 2 1 0.999991 19 204 0 8 2 -19.999990 1 1 0 0 1 0 1 1 2.003436 0 0.160000 1.960000 0.155949 0.990000 0.650000 1.000000 1.000000 0.939041 0.990000 1 8.300000e-01 1 DDO 8528 broad.mit.edu 37 6 110714483 110714483 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr6:110714483G>A ENST00000368924.3 - 5 620 c.605C>T c.(604-606)cCg>cTg p.P202L DDO_ENST00000368923.3_Missense_Mutation_p.P143L NM_003649.2 NP_003640.2 Q99489 OXDD_HUMAN D-aspartate oxidase 24 all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327) GTCAAAGGACGGATGAAGTTC 0.502000 0 SO:0001583 missense ENST00000368924.3 1 1 hg19 CCDS5082.1 . . . . . . . . . . G 3.961 -0.010388 0.07727 0.0 1.16E-4 ENSG00000203797 ENST00000368924;ENST00000368923;ENST00000368925 T;T;T 0.35421 1.31;1.31;1.31 5.95 1.93 0.25924 . 0.501675 0.22971 N 0.053429 T 0.09686 0.0238 L 0.46157 1.445 0.09310 N 1 P;B 0.34662 0.462;0.121 B;B 0.17722 0.01;0.019 T 0.11470 -1.0586 10 0.31617 T 0.26 -13.5945 7.5782 0.27948 0.0:0.3124:0.3619:0.3257 . 143;202 Q99489-4;Q99489-3 .;. L 202;143;174 ENSP00000357920:P202L;ENSP00000357919:P143L;ENSP00000357921:P174L ENSP00000357919:P143L P - 2 0 DDO 110821176 0.000000 0.05858 0.018000 0.16275 0.049000 0.14656 0.680000 0.25306 0.804000 0.34136 0.563000 0.77884 CCG TCGA-IB-7888-01A-11D-2154-08 DDO-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041796.1 1 0 0 57 944 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 1.000000 57 935 0 86 2 -2.578427 1 1 121412 13 44 1 0 1 1 1.995738 0 0.160000 1.960000 0.154589 0.700000 0.540000 0.890000 0.710000 0.714213 0.700000 0 6.100000e-01 8.000000e-01 TCP10 6953 broad.mit.edu 37 6 167789540 167789540 + Missense_Mutation SNP G G A rs28637384 TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr6:167789540G>A ENST00000397829.4 - 6 769 c.602C>T c.(601-603)cCg>cTg p.P201L TCP10_ENST00000366827.2_Missense_Mutation_p.P201L NM_004610.3 NP_004601.3 Q12799 TCP10_HUMAN t-complex 10 18 Breast(66;1.53e-05)|Ovarian(120;0.024) GGAGTTTTGCGGACTTCGGGA 0.612000 0 SO:0001583 missense ENST00000397829.4 0 1 hg19 CCDS43527.1 10 0.004578754578754579 4 0.008130081300813009 1 0.0027624309392265192 3 0.005244755244755245 2 0.002638522427440633 G 0.115 -1.133580 0.01756 0.006612 3.59E-4 ENSG00000203690 ENST00000366827;ENST00000397829 T;T 0.14266 2.52;2.52 1.65 -1.01 0.10169 . . . . . T 0.01092 0.0036 N 0.08118 0 0.09310 N 0.999998 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.47522 -0.9111 9 0.02654 T 1 . 5.1124 0.14815 0.7913:0.0:0.2087:0.0 rs28637384 228;228 Q12799;Q12799-2 TCP10_HUMAN;. L 201 ENSP00000355792:P201L;ENSP00000380929:P201L ENSP00000355792:P201L P - 2 0 TCP10 167709530 0.001000 0.12720 0.001000 0.08648 0.020000 0.10135 0.285000 0.18883 -0.248000 0.09583 -0.699000 0.03677 CCG TCGA-IB-7888-01A-11D-2154-08 TCP10-008 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000365570.1 1 0 0 6 207 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 0.963528 6 203 0 25 2 -2.847517 1 1 120932 189 47 1 1 2 3 2.019436 0 0.160000 1.960000 0.166005 0.390000 0.160000 1.000000 0.360000 0.443821 0.390000 0 2.500000e-01 6.100000e-01 PHF10 55274 broad.mit.edu 37 6 170118958 170118958 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr6:170118958G>A ENST00000339209.4 - 3 374 c.251C>T c.(250-252)aCa>aTa p.T84I PHF10_ENST00000366780.4_Missense_Mutation_p.T84I|PHF10_ENST00000464779.1_5'UTR NM_018288.3|NM_133325.2 NP_060758.2|NP_579866.2 Q8WUB8 PHF10_HUMAN PHD finger protein 10 14 Breast(66;5.08e-05)|Ovarian(120;0.208) GTATTCTCCTGTTTCATCAGG 0.313000 0 SO:0001583 missense ENST00000339209.4 0 1 hg19 CCDS5308.2 . . . . . . . . . . G 18.46 3.629915 0.67015 . . ENSG00000130024 ENST00000366780;ENST00000339209 T;T 0.29397 1.57;1.57 5.49 5.49 0.81192 . . . . . T 0.19927 0.0479 L 0.44542 1.39 0.53005 D 0.999969 B;B 0.34329 0.449;0.321 B;B 0.35413 0.202;0.1 T 0.03483 -1.1032 9 0.59425 D 0.04 . 16.8851 0.86074 0.0:0.0:1.0:0.0 . 84;84 Q8WUB8-2;Q8WUB8 .;PHF10_HUMAN I 84 ENSP00000355743:T84I;ENSP00000341805:T84I ENSP00000341805:T84I T - 2 0 PHF10 169860883 1.000000 0.71417 0.999000 0.59377 0.985000 0.73830 7.257000 0.78362 2.724000 0.93272 0.557000 0.71058 ACA TCGA-IB-7888-01A-11D-2154-08 PHF10-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000346732.1 0 0 0 8 451 0 29 0 2.212888e-01 0 45 0 29 2 0 0 0 0 0 2 1 0.989113 8 447 0 29 2 -3.105146 1 1 0 0 1 1 2 3 2.019436 0 0.160000 1.960000 0.166005 0.230000 0.100000 1.000000 0.210000 0.298149 0.230000 0 1.600000e-01 3.500000e-01 RREB1 6239 broad.mit.edu 37 6 7229365 7229365 + Nonsense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr6:7229365C>T ENST00000349384.6 + 10 1347 c.1033C>T c.(1033-1035)Caa>Taa p.Q345* RREB1_ENST00000379938.2_Nonsense_Mutation_p.Q345*|RREB1_ENST00000334984.6_Nonsense_Mutation_p.Q345*|RREB1_ENST00000379933.3_Nonsense_Mutation_p.Q345* NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) AGACCAGGGTCAAGAAAAGCC 0.627000 0 SO:0001587 stop_gained ENST00000349384.6 0 1 hg19 CCDS34336.1 . . . . . . . . . . C 16.68 3.191693 0.58017 . . ENSG00000124782 ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150 . . . 5.7 2.61 0.31194 . 0.654137 0.12867 N 0.432616 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.10111 T 0.7 -5.9613 4.9171 0.13851 0.329:0.4924:0.0998:0.0788 . . . . X 345 . ENSP00000335574:Q345X Q + 1 0 RREB1 7174364 0.000000 0.05858 0.001000 0.08648 0.054000 0.15201 0.831000 0.27476 0.754000 0.32968 0.455000 0.32223 CAA TCGA-IB-7888-01A-11D-2154-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 1 0 1 11 177 0 26 1 3.810143e-01 6 15 0 26 2 0 0 0 0 0 2 1 0.998344 11 174 0 25 2 -15.022750 1 0 0 0 1 0 0 0 1.991081 0 0.160000 1.960000 0.150485 0.730000 0.390000 1.000000 1.000000 0.740569 0.730000 0 5.400000e-01 9.600000e-01 RREB1 6239 broad.mit.edu 37 6 7229368 7229368 + Nonsense_Mutation SNP G G T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr6:7229368G>T ENST00000349384.6 + 10 1350 c.1036G>T c.(1036-1038)Gaa>Taa p.E346* RREB1_ENST00000379938.2_Nonsense_Mutation_p.E346*|RREB1_ENST00000334984.6_Nonsense_Mutation_p.E346*|RREB1_ENST00000379933.3_Nonsense_Mutation_p.E346* NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) CCAGGGTCAAGAAAAGCCGCA 0.632000 0 SO:0001587 stop_gained ENST00000349384.6 0 1 hg19 CCDS34336.1 . . . . . . . . . . G 18.90 3.720585 0.68959 . . ENSG00000124782 ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150 . . . 5.44 5.44 0.79542 . 0.520225 0.17251 N 0.181180 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.52906 T 0.07 -9.0175 12.5884 0.56430 0.0761:0.0:0.9239:0.0 . . . . X 346 . ENSP00000335574:E346X E + 1 0 RREB1 7174367 1.000000 0.71417 0.030000 0.17652 0.053000 0.15095 4.178000 0.58284 2.547000 0.85894 0.455000 0.32223 GAA TCGA-IB-7888-01A-11D-2154-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 1 0 0 10 182 0 25 1 3.530145e-01 8 14 0 25 2 0 0 0 0 0 2 1 0.996872 10 179 0 24 2 -13.174810 1 0 0 0 1 0 0 0 1.991081 0 0.160000 1.960000 0.150485 0.650000 0.340000 1.000000 1.000000 0.672841 0.650000 0 4.700000e-01 8.700000e-01 CFTR 1080 broad.mit.edu 37 7 117171027 117171027 + Missense_Mutation SNP A A C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr7:117171027A>C ENST00000003084.6 + 4 480 c.348A>C c.(346-348)gaA>gaC p.E116D CFTR_ENST00000454343.1_Missense_Mutation_p.E116D NM_000492.3 NP_000483.3 P13569 CFTR_HUMAN cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) 69 Lung NSC(10;0.00148)|all_lung(10;0.00171) STAD - Stomach adenocarcinoma(10;0.000534) Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820) ACAAGGAGGAACGCTCTATCG 0.448000 Cystic Fibrosis 0 SO:0001583 missense Familial Cancer Database CF ENST00000003084.6 0 1 hg19 CCDS5773.1 . . . . . . . . . . A 16.08 3.022693 0.54683 . . ENSG00000001626 ENST00000446805;ENST00000003084;ENST00000454343;ENST00000426809 D;D;D;D 0.99748 -6.62;-2.63;-2.63;-2.63 5.73 -1.17 0.09648 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.000000 0.85682 D 0.000000 D 0.98713 0.9568 N 0.17872 0.535 0.42468 D 0.992811 D 0.76494 0.999 D 0.83275 0.996 D 0.96486 0.9360 10 0.22109 T 0.4 -17.2878 5.6679 0.17704 0.6179:0.0:0.2697:0.1124 . 116 P13569 CFTR_HUMAN D 35;116;116;116 ENSP00000417012:E35D;ENSP00000003084:E116D;ENSP00000403677:E116D;ENSP00000389119:E116D ENSP00000003084:E116D E + 3 2 CFTR 116958263 1.000000 0.71417 0.935000 0.37517 0.096000 0.18686 0.836000 0.27545 -0.336000 0.08438 -0.388000 0.06559 GAA TCGA-IB-7888-01A-11D-2154-08 CFTR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059397.3 0 0 0 4 200 0 21 0 5.561244e-02 1 14 0 21 2 0 0 0 0 0 2 1 0.888885 4 198 0 21 2 -3.449250 1 1 0 0 1 0 1 1 2.001689 0 0.160000 1.960000 0.155949 0.260000 0.090000 0.570000 0.240000 0.293962 0.260000 0 1.600000e-01 4.100000e-01 ASB15 142685 broad.mit.edu 37 7 123270139 123270139 + Silent SNP A A G TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr7:123270139A>G ENST00000451558.1 + 13 2081 c.1560A>G c.(1558-1560)gtA>gtG p.V520V ASB15_ENST00000275699.3_Silent_p.V520V|ASB15_ENST00000451215.1_Silent_p.V520V|ASB15_ENST00000434204.1_Silent_p.V520V|ASB15_ENST00000540573.1_Silent_p.V520V Q8WXK1 ASB15_HUMAN ankyrin repeat and SOCS box containing 15 12 CACTAGAAGTACAGAGAGAAT 0.368000 0 SO:0001819 synonymous_variant ENST00000451558.1 1 1 hg19 CCDS34742.1 TCGA-IB-7888-01A-11D-2154-08 ASB15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347493.1 1 0 0 24 328 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 1.000000 24 324 0 42 2 -20.000000 1 1 0 0 1 0 1 1 2.001689 0 0.160000 1.960000 0.155949 0.840000 0.560000 1.000000 1.000000 0.843403 0.840000 0 6.900000e-01 1 NXPH1 30010 broad.mit.edu 37 7 8790918 8790918 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr7:8790918C>T ENST00000405863.1 + 3 1246 c.335C>T c.(334-336)aCg>aTg p.T112M NXPH1_ENST00000497400.1_3'UTR|NXPH1_ENST00000602349.1_5'UTR NM_152745.2 NP_689958.1 P58417 NXPH1_HUMAN neurexophilin 1 17 Ovarian(82;0.0628) ATTGTTAAAACGGGCAAGTTT 0.473000 0 SO:0001583 missense ENST00000405863.1 1 1 hg19 CCDS47540.1 . . . . . . . . . . C 16.79 3.220768 0.58560 . . ENSG00000122584 ENST00000405863;ENST00000438764;ENST00000429542 . . . 6.07 5.19 0.71726 . 0.000000 0.85682 D 0.000000 T 0.79458 0.4449 M 0.75447 2.3 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.82293 -0.0529 9 0.72032 D 0.01 -8.2624 16.7467 0.85474 0.1304:0.8696:0.0:0.0 . 112 P58417 NXPH1_HUMAN M 112 . ENSP00000384551:T112M T + 2 0 NXPH1 8757443 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.792000 0.85828 1.553000 0.49476 0.655000 0.94253 ACG TCGA-IB-7888-01A-11D-2154-08 NXPH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324591.1 1 0 0 30 402 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 1.000000 29 397 0 52 2 -8.202104 1 1 120786 5 38 1 1 2 3 2.008079 0 0.160000 1.960000 0.163347 0.880000 0.600000 1.000000 1.000000 0.869109 0.880000 1 7.300000e-01 1 SLC7A2 6542 broad.mit.edu 37 8 17415826 17415826 + Missense_Mutation SNP C C G rs148874201 byFrequency TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr8:17415826C>G ENST00000494857.1 + 9 1436 c.1218C>G c.(1216-1218)gaC>gaG p.D406E SLC7A2_ENST00000470360.1_Missense_Mutation_p.D445E|SLC7A2_ENST00000522656.1_Missense_Mutation_p.D406E|SLC7A2_ENST00000398090.3_Missense_Mutation_p.D445E|SLC7A2_ENST00000004531.10_Missense_Mutation_p.D446E NM_001008539.3 NP_001008539.3 P52569 CTR2_HUMAN solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 25 L-Lysine(DB00123)|L-Ornithine(DB00129) TTCTGTTTGACCTGAAGGCGC 0.507000 0 SO:0001583 missense ENST00000494857.1 1 0 hg19 CCDS34852.1 . . . . . . . . . . C 13.17 2.157068 0.38119 . . ENSG00000003989 ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090 D;D;D;D;D 0.90133 -2.62;-2.62;-2.62;-2.62;-2.62 5.38 5.38 0.77491 Amino acid permease domain (1); 0.000000 0.85682 D 0.000000 D 0.91181 0.7222 L 0.57130 1.785 0.58432 D 0.999999 B;P;D 0.55172 0.141;0.859;0.97 B;B;P 0.55455 0.132;0.367;0.776 D 0.87579 0.2483 10 0.12430 T 0.62 . 12.823 0.57704 0.0:0.9251:0.0:0.0748 . 446;445;406 P52569-3;P52569-2;P52569 .;.;CTR2_HUMAN E 406;406;445;446;445 ENSP00000419140:D406E;ENSP00000430464:D406E;ENSP00000419873:D445E;ENSP00000004531:D446E;ENSP00000381164:D445E ENSP00000004531:D446E D + 3 2 SLC7A2 17460118 1.000000 0.71417 1.000000 0.80357 0.918000 0.54935 4.982000 0.63825 2.691000 0.91804 0.561000 0.74099 GAC TCGA-IB-7888-01A-11D-2154-08 SLC7A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253367.3 1 0 0 22 346 0 46 0 7.163784e-01 0 41 0 46 2 0 0 0 0 0 2 1 0.999999 22 342 0 46 2 -16.208110 1 1 0 0 1 1 2 3 2.011730 0 0.160000 1.960000 0.164678 0.760000 0.490000 1.000000 1.000000 0.777142 0.760000 0 6.100000e-01 9.600000e-01 PTK2B 2185 broad.mit.edu 37 8 27288476 27288476 + Silent SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr8:27288476C>T ENST00000397501.1 + 13 1561 c.753C>T c.(751-753)ttC>ttT p.F251F PTK2B_ENST00000544172.1_Silent_p.F251F|PTK2B_ENST00000338238.4_Silent_p.F251F|PTK2B_ENST00000346049.5_Silent_p.F251F|PTK2B_ENST00000397497.4_5'UTR|PTK2B_ENST00000517339.1_Silent_p.F251F|PTK2B_ENST00000420218.2_Silent_p.F251F NM_173174.2 NP_775266.1 Q14289 FAK2_HUMAN protein tyrosine kinase 2 beta 47 Ovarian(32;2.72e-05) Leflunomide(DB01097) TGAAGTTCTTCAACACTCTCG 0.577000 0 SO:0001819 synonymous_variant ENST00000397501.1 1 1 hg19 CCDS6057.1 . . . . . . . . . . C 11.33 1.608253 0.28623 . . ENSG00000120899 ENST00000519512 . . . 5.8 5.8 0.92144 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 13.1808 0.59653 0.0:0.8401:0.1599:0.0 . . . . X 25 . . Q + 1 0 PTK2B 27344393 0.998000 0.40836 1.000000 0.80357 0.968000 0.65278 0.490000 0.22403 2.735000 0.93741 0.655000 0.94253 CAA TCGA-IB-7888-01A-11D-2154-08 PTK2B-009 PUTATIVE alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219916.1 1 0 1 28 486 0 75 1 8.909084e-01 12 57 0 75 2 0 0 0 0 0 2 1 1.000000 28 481 0 74 2 -5.730829 1 1 0 0 1 1 2 3 2.011730 0 0.160000 1.960000 0.164678 0.690000 0.470000 1.000000 0.680000 0.715459 0.690000 0 5.700000e-01 8.600000e-01 CSMD1 64478 broad.mit.edu 37 8 3165343 3165343 + Splice_Site SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr8:3165343G>A ENST00000520002.1 - 26 4382 c.3827C>T c.(3826-3828)gCg>gTg p.A1276V CSMD1_ENST00000542608.1_Splice_Site_p.A1275V|CSMD1_ENST00000602557.1_Splice_Site_p.A1276V|CSMD1_ENST00000537824.1_Splice_Site_p.A1275V|CSMD1_ENST00000400186.3_Splice_Site_p.A1276V|CSMD1_ENST00000602723.1_Splice_Site_p.A1276V|CSMD1_ENST00000539096.1_Splice_Site_p.A1275V Q96PZ7 CSMD1_HUMAN CUB and Sushi multiple domains 1 25 all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234) ACCACATTCCGCTGTAGAAGA 0.448000 0 SO:0001630 splice_region_variant ENST00000520002.1 1 0 hg19 . . . . . . . . . . G 34 5.328932 0.95733 0.0 1.19E-4 ENSG00000183117 ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096 T;T;T;T;T 0.24908 1.83;1.83;1.83;1.83;1.83 4.86 4.86 0.63082 Complement control module (2);Sushi/SCR/CCP (1); 0.069339 0.56097 D 0.000026 T 0.55178 0.1904 M 0.84156 2.68 0.80722 D 1 P;D;D 0.89917 0.847;1.0;0.981 B;D;P 0.73380 0.129;0.98;0.832 T 0.60767 -0.7198 10 0.49607 T 0.09 . 18.0036 0.89203 0.0:0.0:1.0:0.0 . 1276;1276;1276 E5RIG2;Q96PZ7;Q96PZ7-4 .;CSMD1_HUMAN;. V 1276;1276;1138;1275;1275;1275 ENSP00000383047:A1276V;ENSP00000430733:A1276V;ENSP00000441462:A1275V;ENSP00000446243:A1275V;ENSP00000441675:A1275V ENSP00000320445:A1138V A - 2 0 CSMD1 3152750 1.000000 0.71417 0.996000 0.52242 0.866000 0.49608 9.606000 0.98325 2.241000 0.73720 0.655000 0.94253 GCG TCGA-IB-7888-01A-11D-2154-08 CSMD1-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000374500.2 1 0 0 31 381 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 30 380 0 47 2 -3.318793 1 1 120976 18 44 1 1 2 3 2.028523 0 0.160000 1.960000 0.167987 0.970000 0.660000 1.000000 1.000000 0.922793 0.970000 1 8.000000e-01 1 ASTN2 23245 broad.mit.edu 37 9 119188282 119188282 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr9:119188282C>T ENST00000313400.4 - 23 3968 c.3868G>A c.(3868-3870)Gtg>Atg p.V1290M ASTN2_ENST00000373996.3_Missense_Mutation_p.V1286M|ASTN2_ENST00000361209.2_Missense_Mutation_p.V1239M|ASTN2_ENST00000341734.4_Missense_Mutation_p.V342M|ASTN2_ENST00000288520.5_Missense_Mutation_p.V391M|ASTN2_ENST00000361477.3_Missense_Mutation_p.V342M O75129 ASTN2_HUMAN astrotactin 2 102 ACTGTTTCCACGCGGCTCTGG 0.582000 0 SO:0001583 missense ENST00000313400.4 1 1 hg19 . . . . . . . . . . C 15.58 2.877017 0.51801 . . ENSG00000148219 ENST00000313400;ENST00000373996;ENST00000288520;ENST00000341734;ENST00000373986;ENST00000361209;ENST00000361477 T;T;T;T;T;T;T 0.14766 2.9;2.9;2.48;2.49;2.72;2.91;2.49 5.86 5.86 0.93980 . 0.187931 0.46442 D 0.000285 T 0.10551 0.0258 N 0.08118 0 0.39656 D 0.970535 P;P;D;D;D;P;P 0.63046 0.567;0.567;0.992;0.987;0.989;0.567;0.882 B;B;P;B;P;B;B 0.51193 0.141;0.141;0.607;0.403;0.662;0.216;0.388 T 0.07520 -1.0768 10 0.51188 T 0.08 -23.4177 7.6948 0.28587 0.0:0.808:0.0:0.192 . 342;342;1239;1290;1286;342;391 B7ZKP4;B7ZKP5;O75129-2;O75129;O75129-3;O75129-6;O75129-4 .;.;.;ASTN2_HUMAN;.;.;. M 1290;1286;391;342;1013;1239;342 ENSP00000314038:V1290M;ENSP00000363108:V1286M;ENSP00000288520:V391M;ENSP00000339925:V342M;ENSP00000363098:V1013M;ENSP00000354504:V1239M;ENSP00000355116:V342M ENSP00000288520:V391M V - 1 0 ASTN2 118228103 1.000000 0.71417 0.966000 0.40874 0.836000 0.47400 4.208000 0.58486 2.761000 0.94854 0.655000 0.94253 GTG TCGA-IB-7888-01A-11D-2154-08 ASTN2-201 KNOWN basic protein_coding protein_coding 1 0 0 12 213 0 28 0 1.119584e-01 0 10 0 28 2 0 0 0 0 0 2 1 0.999146 12 211 0 27 2 -15.089070 1 1 121412 4 33 1 0 1 1 2.003816 0 0.160000 1.960000 0.155949 0.670000 0.370000 1.000000 1.000000 0.688759 0.670000 0 5.000000e-01 8.700000e-01 COL5A1 1289 broad.mit.edu 37 9 137658318 137658318 + Missense_Mutation SNP G G C TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 G C G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr9:137658318G>C ENST00000371817.3 + 22 2521 c.2107G>C c.(2107-2109)Ggc>Cgc p.G703R NM_000093.3|NM_001278074.1 NP_000084.3|NP_001265003.1 P20908 CO5A1_HUMAN collagen, type V, alpha 1 115 Myeloproliferative disorder(178;0.0341) GGGTATGGACGGCCAGCCGGG 0.542000 0 SO:0001583 missense ENST00000371817.3 0 1 hg19 CCDS6982.1 . . . . . . . . . . G 11.38 1.620563 0.28801 . . ENSG00000130635 ENST00000371817 D 0.99186 -5.53 4.71 3.79 0.43588 . 0.000000 0.64402 U 0.000001 D 0.99318 0.9761 H 0.98314 4.2 0.47819 D 0.999522 D 0.63046 0.992 P 0.53722 0.733 D 0.98691 1.0696 10 0.87932 D 0 . 10.0654 0.42299 0.0:0.0:0.7989:0.2011 . 703 P20908 CO5A1_HUMAN R 703 ENSP00000360882:G703R ENSP00000360882:G703R G + 1 0 COL5A1 136798139 1.000000 0.71417 0.559000 0.28332 0.315000 0.28087 6.660000 0.74417 0.933000 0.37291 0.655000 0.94253 GGC TCGA-IB-7888-01A-11D-2154-08 COL5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054954.2 0 0 0 10 224 0 30 0 9.943699e-01 0 206 0 30 2 0 0 0 0 0 2 1 0.996863 10 222 0 30 2 -3.884504 1 1 0 0 1 0 1 1 2.003816 0 0.160000 1.960000 0.155949 0.540000 0.280000 0.900000 0.520000 0.565456 0.540000 0 3.900000e-01 7.200000e-01 DOCK8 81704 broad.mit.edu 37 9 328114 328114 + Silent SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr9:328114G>A ENST00000453981.1 + 9 1099 c.987G>A c.(985-987)gcG>gcA p.A329A DOCK8_ENST00000432829.2_Silent_p.A261A|DOCK8_ENST00000469391.1_Silent_p.A261A 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) CAAGTCAGGCGAGATCTGCAG 0.458000 0 SO:0001819 synonymous_variant ENST00000453981.1 1 1 hg19 CCDS6440.2 TCGA-IB-7888-01A-11D-2154-08 DOCK8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171792.5 1 0 0 25 255 0 30 0 7.295541e-01 0 28 0 30 2 0 0 0 0 0 2 1 1.000000 25 255 0 29 2 -2.966611 1 1 0 0 1 0 1 1 2.003816 0 0.160000 1.960000 0.155949 0.990000 0.740000 1.000000 1.000000 0.967088 0.990000 1 9.100000e-01 1 MELK 9833 broad.mit.edu 37 9 36670999 36670999 + Missense_Mutation SNP C C T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chr9:36670999C>T ENST00000298048.2 + 16 1694 c.1510C>T c.(1510-1512)Cgc>Tgc p.R504C MELK_ENST00000541717.1_Missense_Mutation_p.R463C|MELK_ENST00000543751.1_Missense_Mutation_p.R472C|MELK_ENST00000536329.1_Missense_Mutation_p.R433C|MELK_ENST00000545008.1_Missense_Mutation_p.R433C|MELK_ENST00000538311.1_Missense_Mutation_p.R310C|MELK_ENST00000536987.1_Missense_Mutation_p.R373C|MELK_ENST00000536860.1_Missense_Mutation_p.R456C NM_014791.3 NP_055606.1 Q14680 MELK_HUMAN maternal embryonic leucine zipper kinase p.R504C(2) 29 Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06) STAD - Stomach adenocarcinoma(86;0.228) TTTCAGGTGCCGCTCAGTGGA 0.488000 Ovarian(82;980 1317 7225 14391 18624) 2 Substitution - Missense(2) SO:0001583 missense ENST00000298048.2 1 1 hg19 CCDS6606.1 . . . . . . . . . . C 23.8 4.455826 0.84209 0.0 1.16E-4 ENSG00000165304 ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751 T;T;T;T;T;T;T;T 0.73789 -0.58;0.39;0.17;0.71;0.08;-0.78;-0.56;-0.59 5.95 5.95 0.96441 . 0.099925 0.64402 D 0.000001 D 0.85279 0.5660 M 0.63843 1.955 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;0.999;0.999;1.0;0.999;0.999 D;D;D;D;D;P;P 0.70716 0.97;0.97;0.921;0.921;0.911;0.886;0.886 D 0.84401 0.0560 10 0.54805 T 0.06 -9.996 20.3932 0.98965 0.0:1.0:0.0:0.0 . 424;433;456;463;433;472;504 B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680 .;.;.;.;.;.;MELK_HUMAN C 504;310;373;433;456;433;463;472 ENSP00000298048:R504C;ENSP00000438226:R310C;ENSP00000439184:R373C;ENSP00000445452:R433C;ENSP00000439792:R456C;ENSP00000443550:R433C;ENSP00000437804:R463C;ENSP00000441596:R472C ENSP00000298048:R504C R + 1 0 MELK 36660999 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 3.420000 0.52735 2.824000 0.97209 0.655000 0.94253 CGC TCGA-IB-7888-01A-11D-2154-08 MELK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052428.3 1 0 0 29 487 0 41 1 9.344850e-02 2 7 0 41 2 0 0 0 0 0 2 1 1.000000 28 484 0 41 2 -2.642034 1 1 121412 4 39 1 0 1 1 2.003816 0 0.160000 1.960000 0.155949 0.690000 0.480000 0.960000 0.690000 0.711876 0.690000 0 5.800000e-01 8.300000e-01 LAMP2 3920 broad.mit.edu 37 X 119576496 119576496 + Missense_Mutation SNP G G T TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chrX:119576496G>T ENST00000200639.4 - 7 1022 c.886C>A c.(886-888)Ctg>Atg p.L296M LAMP2_ENST00000434600.2_Missense_Mutation_p.L296M|LAMP2_ENST00000538785.1_Missense_Mutation_p.L185M|LAMP2_ENST00000371335.4_Missense_Mutation_p.L296M|LAMP2_ENST00000540603.1_Missense_Mutation_p.L249M P13473 LAMP2_HUMAN lysosomal-associated membrane protein 2 15 ACTTCCTTCAGATAAAATCGG 0.383000 0 SO:0001583 missense ENST00000200639.4 1 1 hg19 CCDS14599.1 . . . . . . . . . . G 17.93 3.510196 0.64522 . . ENSG00000005893 ENST00000434600;ENST00000538785;ENST00000200639;ENST00000371335;ENST00000540603 T;T;T;T;T 0.55234 0.53;0.53;0.53;0.53;0.53 5.34 4.48 0.54585 . 0.000000 0.64402 D 0.000002 T 0.76557 0.4004 M 0.91038 3.17 0.48288 D 0.999626 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0 T 0.80625 -0.1299 10 0.72032 D 0.01 -9.4133 11.8331 0.52307 0.0878:0.0:0.9122:0.0 . 249;185;296;296;296 B4E2S7;B7Z2R9;P13473-2;P13473;Q6Q3G8 .;.;.;LAMP2_HUMAN;. M 296;185;296;296;249 ENSP00000408411:L296M;ENSP00000440506:L185M;ENSP00000200639:L296M;ENSP00000360386:L296M;ENSP00000440479:L249M ENSP00000200639:L296M L - 1 2 LAMP2 119460524 1.000000 0.71417 1.000000 0.80357 0.912000 0.54170 5.599000 0.67592 1.011000 0.39340 0.594000 0.82650 CTG TCGA-IB-7888-01A-11D-2154-08 LAMP2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000058099.1 1 0 1 87 1288 0 158 1 1 101 299 0 158 2 0 0 0 0 0 2 1 1.000000 87 1276 0 158 2 -12.721170 1 1 0 0 1 0 1 1 0.160000 1.960000 0.160000 0.780000 0.630000 0.950000 0.790000 0.795474 0.780000 0 7.000000e-01 8.700000e-01 CSF2RA 1438 broad.mit.edu 37 X 1428355 1428355 + Missense_Mutation SNP G G A rs139686363 byFrequency TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chrX:1428355G>A ENST00000381524.3 + 13 1372 c.1186G>A c.(1186-1188)Gtg>Atg p.V396M CSF2RA_ENST00000381500.1_3'UTR|CSF2RA_ENST00000381529.3_Missense_Mutation_p.V396M|CSF2RA_ENST00000417535.2_Missense_Mutation_p.V430M|CSF2RA_ENST00000361536.3_3'UTR|CSF2RA_ENST00000355432.3_Missense_Mutation_p.R336H|CSF2RA_ENST00000501036.2_Missense_Mutation_p.V263M|CSF2RA_ENST00000432318.2_Missense_Mutation_p.V396M|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000355805.2_3'UTR|CSF2RA_ENST00000498153.1_3'UTR P15509 CSF2R_HUMAN colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) 45 all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122) Sargramostim(DB00020) GGTCTTGACCGTGAAGGAAAT 0.527000 Esophageal Squamous(131;723 1707 25334 40494 41806) 0 SO:0001583 missense ENST00000381524.3 0 1 hg19 CCDS35191.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 11.17|11.17 1.559304|1.559304 0.27827|0.27827 0.0|0.0 3.49E-4|3.49E-4 ENSG00000198223|ENSG00000198223 ENST00000355432|ENST00000381529;ENST00000432318;ENST00000501036;ENST00000381524;ENST00000417535 T|D;D;D;D;D 0.46451|0.95272 0.87|-3.53;-3.53;-3.66;-3.53;-3.32 0.69|0.69 0.69|0.69 0.18039|0.18039 .|. .|. .|. .|. .|. D|D 0.95522|0.95522 0.8545|0.8545 .|. .|. .|. 0.09310|0.09310 N|N 1|1 D|D;D 0.54207|0.76494 0.965|0.999;0.997 B|P;P 0.32864|0.61201 0.154|0.885;0.838 D|D 0.88243|0.88243 0.2911|0.2911 7|7 0.87932|0.66056 D|D 0|0.02 .|. .|. .|. .|. .|. 337|430;396 P15509-5|A7J003;P15509 .|.;CSF2R_HUMAN H|M 336|396;396;263;396;430 ENSP00000347606:R336H|ENSP00000370940:V396M;ENSP00000416437:V396M;ENSP00000440491:V263M;ENSP00000370935:V396M;ENSP00000394227:V430M ENSP00000347606:R336H|ENSP00000370935:V396M R|V +|+ 2|1 0|0 CSF2RA|CSF2RA 1388355|1388355 0.007000|0.007000 0.16637|0.16637 0.020000|0.020000 0.16555|0.16555 0.092000|0.092000 0.18411|0.18411 1.192000|1.192000 0.32150|0.32150 0.658000|0.658000 0.30925|0.30925 0.110000|0.110000 0.15639|0.15639 CGT|GTG TCGA-IB-7888-01A-11D-2154-08 CSF2RA-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000035013.2 0 0 0 6 878 0 91 0 4.139506e-02 0 39 0 91 2 0 0 0 0 0 2 1 0.964281 6 872 0 91 2 -2.034825 0 1 121412 18 48 1 0 1 1 0.160000 1.960000 0.160000 0.080000 0.030000 0.180000 0.080000 0.098159 0.080000 0 5.000000e-02 1.300000e-01 STS 412 broad.mit.edu 37 X 7267976 7267976 + Missense_Mutation SNP G G A TCGA-IB-7888-01A-11D-2154-08 TCGA-IB-7888-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 848ffe2a-2771-4f43-8b27-d59425f52af4 8f106862-2abd-4d1f-b9af-8d584a18d612 g.chrX:7267976G>A ENST00000217961.4 + 10 1646 c.1426G>A c.(1426-1428)Gtg>Atg p.V476M NM_000351.4 NP_000342.2 P08842 STS_HUMAN steroid sulfatase (microsomal), isozyme S 27 Colorectal(8;0.0136)|Medulloblastoma(8;0.184) Norelgestromin(DB06713) CTTCAACCCCGTGGGTTCCAA 0.473000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000217961.4 0 1 hg19 CCDS14127.1 3 0.0018083182640144665 0 0.0 0 0.0 1 0.0017605633802816902 0 0.0 G 8.477 0.858878 0.17178 . . ENSG00000101846 ENST00000217961 D 0.89415 -2.51 4.22 3.35 0.38373 Sulfatase (1);Alkaline-phosphatase-like, core domain (1); 0.537990 0.20281 N 0.095442 T 0.70413 0.3221 N 0.03608 -0.345 0.09310 N 0.999996 P 0.41498 0.752 B 0.33339 0.162 T 0.65146 -0.6239 10 0.56958 D 0.05 . 7.1491 0.25599 0.2151:0.0:0.7849:0.0 . 476 P08842 STS_HUMAN M 476 ENSP00000217961:V476M ENSP00000217961:V476M V + 1 0 STS 7277976 0.042000 0.20092 0.064000 0.19789 0.004000 0.04260 1.805000 0.38883 0.627000 0.30340 0.594000 0.82650 GTG TCGA-IB-7888-01A-11D-2154-08 STS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055686.1 0 0 0 6 871 0 92 0 1.467889e-01 0 83 0 92 2 0 0 0 1 0 0 2 1 0.963373 6 858 0 91 2 -2.891929 1 1 121388 32 49 1 0 1 1 0.160000 1.960000 0.160000 0.080000 0.030000 0.180000 0.080000 0.098936 0.080000 0 5.000000e-02 1.300000e-01