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 RELN 5649 broad.mit.edu 37 7 103180786 103180786 + Frame_Shift_Del DEL T T - TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:103180786delT ENST00000428762.1 - 44 6947 c.6788delA c.(6787-6789)gagfs p.E2263fs RELN_ENST00000343529.5_Frame_Shift_Del_p.E2263fs|RELN_ENST00000424685.2_Frame_Shift_Del_p.E2263fs NM_005045.3 NP_005036.2 P78509 RELN_HUMAN reelin 227 GAAAAGGAACTCCTGAAGAAG 0.542000 NSCLC(146;835 1944 15585 22231 52158) 0 SO:0001589 frameshift_variant ENST00000428762.1 0 1 hg19 CCDS47680.1 TCGA-YY-A8LH-01A-11D-A36O-08 RELN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000348148.1 1 0 0 37 411 0 94 0 0 0 94 0 0 0 0 1 1.000000 37 405 0 90 2 0 0 0 0 0 0 -3.017764 1 1 0 0 1 2 2 4 2.097417 0 0.550000 3.730000 0.709677 0.460000 3.300000e-01 0.620000 0.480000 0.475535 0.460000 0 3.900000e-01 0.550000 INA 9118 broad.mit.edu 37 10 105037160 105037160 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:105037160G>A ENST00000369849.4 + 1 241 c.192G>A c.(190-192)ctG>ctA p.L64L NM_032727.3 NP_116116.1 Q16352 AINX_HUMAN internexin neuronal intermediate filament protein, alpha 13 GCCTCGGCCTGGCCTATCGCC 0.741000 0 SO:0001819 synonymous_variant ENST00000369849.4 1 1 hg19 CCDS7545.1 TCGA-YY-A8LH-01A-11D-A36O-08 INA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050145.1 1 0 0 18 60 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 0.999989 17 58 0 16 2 0 0 0 0 16 2 -20.000000 1 1 0 0 1 2 2 4 2.139192 1 0.550000 3.730000 0.709677 0.990000 8.400000e-01 1.000000 1.000000 0.989482 0.990000 1 9.900000e-01 1.000000 ATRNL1 26033 broad.mit.edu 37 10 117226743 117226743 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:117226743G>A ENST00000355044.3 + 23 3603 c.3477G>A c.(3475-3477)acG>acA p.T1159T ATRNL1_ENST00000303745.7_Intron|ATRNL1_ENST00000423111.2_Silent_p.T210T NM_207303.2 NP_997186.1 Q5VV63 ATRN1_HUMAN attractin-like 1 95 all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234) TCAACATTACGTGGTCTGTCG 0.294000 0 SO:0001819 synonymous_variant ENST00000355044.3 1 1 hg19 CCDS7592.1 TCGA-YY-A8LH-01A-11D-A36O-08 ATRNL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050507.3 1 0 0 20 314 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 0.831260 19 307 1 78 15 0 0 0 0 80 2 -19.999080 1 1 0 0 1 2 2 4 2.139192 1 0.550000 3.730000 0.709677 0.340000 2.100000e-01 0.500000 0.330000 0.351850 0.340000 0 2.700000e-01 0.420000 PNLIPRP3 119548 broad.mit.edu 37 10 118203960 118203960 + Missense_Mutation SNP A A C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:118203960A>C ENST00000369230.3 + 4 537 c.391A>C c.(391-393)Atc>Ctc p.I131L NM_001011709.2 NP_001011709.2 Q17RR3 LIPR3_HUMAN pancreatic lipase-related protein 3 50 ACGGGAATACATCCATGCTGT 0.318000 0 SO:0001583 missense ENST00000369230.3 0 1 hg19 CCDS31292.1 . . . . . . . . . . A 13.04 2.117608 0.37339 . . ENSG00000203837 ENST00000369230 D 0.90620 -2.7 5.28 -0.352 0.12598 Lipase, N-terminal (1); 0.753542 0.11427 N 0.565260 T 0.82070 0.4957 L 0.33668 1.02 0.09310 N 1 B 0.11235 0.004 B 0.15052 0.012 T 0.69435 -0.5146 10 0.66056 D 0.02 . 2.765 0.05317 0.6175:0.1526:0.1158:0.114 . 131 Q17RR3 LIPR3_HUMAN L 131 ENSP00000358232:I131L ENSP00000358232:I131L I + 1 0 PNLIPRP3 118193950 0.000000 0.05858 0.000000 0.03702 0.059000 0.15707 0.284000 0.18864 -0.211000 0.10124 0.482000 0.46254 ATC TCGA-YY-A8LH-01A-11D-A36O-08 PNLIPRP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050520.1 0 0 0 10 534 0 126 0 0 0 0 126 2 0 0 0 0 0 2 1 0.996720 10 527 0 124 2 0 0 0 0 126 2 -8.530329 1 1 0 0 1 2 2 4 2.139192 1 0.550000 3.730000 0.709677 0.100000 4.000000e-02 0.190000 0.120000 0.113513 0.100000 0 7.000000e-02 0.150000 MKI67 4288 broad.mit.edu 37 10 129905212 129905212 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:129905212C>T ENST00000368654.3 - 13 5267 c.4892G>A c.(4891-4893)cGa>cAa p.R1631Q MKI67_ENST00000368653.3_Missense_Mutation_p.R1271Q 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) CTTGAGCCGTCGCTTGGAGCT 0.502000 0 SO:0001583 missense ENST00000368654.3 0 1 hg19 CCDS7659.1 . . . . . . . . . . C 8.711 0.912034 0.17907 . . ENSG00000148773 ENST00000368654;ENST00000368653;ENST00000537609 T;T 0.03152 4.03;4.03 2.6 0.628 0.17681 . 0.461817 0.16195 N 0.225197 T 0.02230 0.0069 L 0.34521 1.04 0.09310 N 1 B;P;B 0.34562 0.053;0.457;0.275 B;B;B 0.22753 0.007;0.041;0.033 T 0.47355 -0.9124 10 0.25751 T 0.34 . 4.3863 0.11318 0.0:0.5705:0.1925:0.237 . 1630;1271;1631 F5H4V4;P46013-2;P46013 .;.;KI67_HUMAN Q 1631;1271;1630 ENSP00000357643:R1631Q;ENSP00000357642:R1271Q ENSP00000357642:R1271Q R - 2 0 MKI67 129795202 0.001000 0.12720 0.000000 0.03702 0.000000 0.00434 1.262000 0.32992 0.166000 0.19597 -0.244000 0.11960 CGA TCGA-YY-A8LH-01A-11D-A36O-08 MKI67-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050999.1 0 0 0 17 1034 1 300 0 1.510390e-02 0 11 1 300 2 0 0 0 0 0 2 1 0.755046 17 1023 1 294 14 0 0 0 1 300 2 -2.430833 0 1 121412 2 43 1 2 2 4 2.139192 1 0.550000 3.730000 0.709677 0.080000 4.000000e-02 0.150000 0.080000 0.095613 0.080000 0 6.000000e-02 0.120000 RBP3 5949 broad.mit.edu 37 10 48388910 48388910 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:48388910G>A ENST00000224600.4 - 1 2081 c.1968C>T c.(1966-1968)gtC>gtT p.V656V AL731561.2_ENST00000581861.1_RNA NM_002900.2 NP_002891.1 P10745 RET3_HUMAN retinol binding protein 3, interstitial 59 Vitamin A(DB00162) TCTGCCCCACGACCTCTGGCC 0.662000 0 SO:0001819 synonymous_variant ENST00000224600.4 1 1 hg19 CCDS7218.1 TCGA-YY-A8LH-01A-11D-A36O-08 RBP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047888.1 1 0 1 16 91 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999946 15 89 0 32 2 0 0 0 0 32 2 -20.000000 1 1 121162 1 26 1 2 2 4 2.135981 1 0.550000 3.730000 0.709677 0.850000 5.200000e-01 1.000000 1.000000 0.842551 0.850000 1 6.700000e-01 1.000000 C10orf53 282966 broad.mit.edu 37 10 50916592 50916592 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:50916592G>A ENST00000374112.3 + 3 415 c.403G>A c.(403-405)Gac>Aac p.D135N C10orf53_ENST00000535836.1_Missense_Mutation_p.D135N NM_182554.2 NP_872360.2 Q8N6V4 CJ053_HUMAN chromosome 10 open reading frame 53 7 all_neural(218;0.107) caatctttgtgacctgggttg 0.488000 0 SO:0001583 missense ENST00000374112.3 0 1 hg19 CCDS31202.1 . . . . . . . . . . G 11.29 1.594908 0.28445 . . ENSG00000178645 ENST00000374112;ENST00000535836 . . . 1.65 1.65 0.23941 . . . . . T 0.12987 0.0315 N 0.08118 0 0.09310 N 1 P 0.41947 0.766 B 0.33521 0.165 T 0.10268 -1.0637 8 0.87932 D 0 . 6.7374 0.23417 0.0:0.0:1.0:0.0 . 135 B9ZVK6 . N 135 . ENSP00000363226:D135N D + 1 0 C10orf53 50586598 0.028000 0.19301 0.022000 0.16811 0.046000 0.14306 0.550000 0.23345 1.229000 0.43630 0.491000 0.48974 GAC TCGA-YY-A8LH-01A-11D-A36O-08 C10orf53-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000048006.1 0 0 0 8 521 0 166 0 0 0 0 166 2 0 0 0 0 0 2 1 0.988876 8 514 0 166 2 0 0 0 0 166 2 -2.976057 1 1 0 0 1 2 2 4 2.135981 1 0.550000 3.730000 0.709677 0.080000 2.000000e-02 0.170000 0.080000 0.095784 0.080000 0 5.000000e-02 0.130000 PCDH15 65217 broad.mit.edu 37 10 55849770 55849770 + Silent SNP A A G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:55849770A>G ENST00000320301.6 - 16 2365 c.1971T>C c.(1969-1971)ccT>ccC p.P657P PCDH15_ENST00000395433.1_Silent_p.P635P|PCDH15_ENST00000373965.2_Silent_p.P664P|PCDH15_ENST00000395430.1_Silent_p.P657P|PCDH15_ENST00000373957.3_Silent_p.P635P|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Silent_p.P657P|PCDH15_ENST00000409834.1_Silent_p.P268P|PCDH15_ENST00000395438.1_Silent_p.P657P|PCDH15_ENST00000361849.3_Silent_p.P657P|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000395445.1_Silent_p.P664P|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Silent_p.P620P|PCDH15_ENST00000373955.1_Silent_p.P657P|PCDH15_ENST00000414778.1_Silent_p.P662P NM_033056.3 NP_149045.3 Q96QU1 PCD15_HUMAN protocadherin-related 15 237 Melanoma(3;0.117)|Lung SC(717;0.238) AAACTCTCTGAGGATCTCCAT 0.338000 HNSCC(58;0.16) 0 SO:0001819 synonymous_variant ENST00000320301.6 1 1 hg19 CCDS7248.1 TCGA-YY-A8LH-01A-11D-A36O-08 PCDH15-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000048121.2 0 0 0 14 650 0 135 0 0 0 0 135 2 0 0 0 0 0 2 1 0.999731 14 641 0 134 2 0 0 0 0 135 2 -4.304782 1 1 0 0 1 2 2 4 2.135981 1 0.550000 3.730000 0.709677 0.110000 5.000000e-02 0.200000 0.120000 0.126801 0.110000 0 8.000000e-02 0.160000 ANKRD2 26287 broad.mit.edu 37 10 99338074 99338074 + Silent SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr10:99338074C>A ENST00000307518.5 + 3 615 c.348C>A c.(346-348)atC>atA p.I116I ANKRD2_ENST00000455090.1_Silent_p.I89I|ANKRD2_ENST00000370655.1_Silent_p.I89I|ANKRD2_ENST00000298808.5_Silent_p.I116I Q9GZV1 ANKR2_HUMAN ankyrin repeat domain 2 (stretch responsive muscle) 7 all_hematologic(284;1.95e-06)|Colorectal(252;0.0163) AGAACCTCATCGAGCTGCGGA 0.662000 0 SO:0001819 synonymous_variant ENST00000307518.5 1 1 hg19 CCDS7466.1 TCGA-YY-A8LH-01A-11D-A36O-08 ANKRD2-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 40 147 0 50 0 0 0 1 0 50 2 0 0 0 0 0 2 1 1.000000 39 145 0 48 2 0 0 0 0 50 2 -20.000000 1 1 0 0 1 2 2 4 2.139192 1 0.550000 3.730000 0.709677 0.990000 8.900000e-01 1.000000 1.000000 0.993634 0.990000 1 9.900000e-01 1.000000 MRVI1 10335 broad.mit.edu 37 11 10622527 10622527 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr11:10622527G>A ENST00000436272.1 - 14 1952 c.1874C>T c.(1873-1875)gCg>gTg p.A625V MRVI1_ENST00000534266.2_Missense_Mutation_p.A337V|MRVI1_ENST00000545852.1_Missense_Mutation_p.A337V|MRVI1_ENST00000531107.1_Missense_Mutation_p.A644V|MRVI1_ENST00000547195.1_Missense_Mutation_p.A561V|MRVI1_ENST00000423302.2_Missense_Mutation_p.A652V|MRVI1_ENST00000527509.2_Missense_Mutation_p.A561V|MRVI1-AS1_ENST00000529979.1_RNA|MRVI1_ENST00000541483.1_Missense_Mutation_p.A446V|MRVI1-AS1_ENST00000525578.1_RNA|MRVI1-AS1_ENST00000529829.1_RNA|MRVI1_ENST00000558540.1_Missense_Mutation_p.A337V|MRVI1_ENST00000552103.1_Missense_Mutation_p.A561V|MRVI1_ENST00000424001.1_Missense_Mutation_p.A337V|MRVI1_ENST00000421747.1_Missense_Mutation_p.A643V|LYVE1_ENST00000531706.1_Intron Q9Y6F6 MRVI1_HUMAN murine retrovirus integration site 1 homolog 22 CATGAGCTCCGCATGGTCCTT 0.517000 0 SO:0001583 missense ENST00000436272.1 0 1 hg19 . . . . . . . . . . G 35 5.484238 0.96307 0.0 1.21E-4 ENSG00000072952 ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509 T;T;T;T;T;T;T;T;T;T 0.26810 1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71 5.44 5.44 0.79542 . 0.000000 0.85682 D 0.000000 T 0.54351 0.1853 M 0.76574 2.34 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.994;0.999;0.999;0.998 T 0.57075 -0.7873 10 0.72032 D 0.01 -10.4332 19.2679 0.93997 0.0:0.0:1.0:0.0 . 446;625;644;643 F5H6A1;Q9Y6F6;E9PQY6;Q9Y6F6-4 .;MRVI1_HUMAN;.;. V 643;626;625;561;561;337;337;652;446;644;561 ENSP00000414598:A643V;ENSP00000412229:A625V;ENSP00000448278:A561V;ENSP00000446764:A561V;ENSP00000441971:A337V;ENSP00000401205:A337V;ENSP00000412130:A652V;ENSP00000437784:A446V;ENSP00000432436:A644V;ENSP00000432067:A561V ENSP00000307885:A626V A - 2 0 MRVI1 10579103 1.000000 0.71417 0.997000 0.53966 0.993000 0.82548 9.476000 0.97823 2.557000 0.86248 0.557000 0.71058 GCG TCGA-YY-A8LH-01A-11D-A36O-08 MRVI1-203 KNOWN basic protein_coding protein_coding 0 0 0 8 633 0 202 0 2.166691e-04 0 2 0 202 2 0 0 0 0 0 2 1 0.988944 8 626 0 200 2 0 0 0 0 202 2 -2.353778 0 1 120882 9 46 1 2 3 5 2.070863 1 0.550000 3.730000 0.707079 0.080000 1.000000e-02 1.000000 0.080000 0.280792 0.080000 0 4.000000e-02 1.000000 RDX 5962 broad.mit.edu 37 11 110108333 110108333 + Nonsense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr11:110108333G>A ENST00000343115.4 - 11 1454 c.1135C>T c.(1135-1137)Cga>Tga p.R379* RDX_ENST00000544551.1_Nonsense_Mutation_p.R243*|RDX_ENST00000405097.1_Nonsense_Mutation_p.R379*|RDX_ENST00000528498.1_Nonsense_Mutation_p.R379*|RDX_ENST00000530301.1_Intron|RDX_ENST00000528900.1_Nonsense_Mutation_p.R32* NM_001260494.1|NM_002906.3 NP_001247423.1|NP_002897.1 P35241 RADI_HUMAN radixin 18 all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544) GCTCGTTTTCGTTCTTGATCC 0.423000 Esophageal Squamous(55;25 1062 11040 28755 44273) 0 SO:0001587 stop_gained ENST00000343115.4 0 1 hg19 CCDS8343.1 . . . . . . . . . . G 41 8.635797 0.98895 . . ENSG00000137710 ENST00000528498;ENST00000405097;ENST00000528900;ENST00000343115;ENST00000544551;ENST00000530085 . . . 5.78 3.73 0.42828 . 0.148841 0.44688 D 0.000430 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.07482 T 0.82 . 14.0536 0.64754 0.0:0.0:0.6747:0.3253 . . . . X 379;379;32;379;243;49 . ENSP00000342830:R379X R - 1 2 RDX 109613543 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 2.822000 0.48073 2.730000 0.93505 0.650000 0.86243 CGA TCGA-YY-A8LH-01A-11D-A36O-08 RDX-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000390535.2 1 0 0 51 576 0 177 0 1.379818e-01 0 8 0 177 2 0 0 0 0 0 2 1 1.000000 50 570 0 174 2 0 0 0 0 177 2 -12.955910 1 1 0 0 1 2 2 4 2.085219 0 0.550000 3.730000 0.708644 0.450000 3.400000e-01 0.590000 0.450000 0.464007 0.450000 0 3.900000e-01 0.530000 FAM160A2 84067 broad.mit.edu 37 11 6235766 6235766 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr11:6235766G>A ENST00000449352.2 - 11 2695 c.2432C>T c.(2431-2433)gCg>gTg p.A811V FAM160A2_ENST00000265978.4_Missense_Mutation_p.A825V|FAM160A2_ENST00000529360.1_5'UTR Q8N612 F16A2_HUMAN family with sequence similarity 160, member A2 42 CTGGGAAGCCGCAAAGTTCTC 0.532000 0 SO:0001583 missense ENST00000449352.2 0 1 hg19 CCDS44530.1 . . . . . . . . . . g 26.2 4.717264 0.89205 . . ENSG00000051009 ENST00000449352;ENST00000265978 T;T 0.11277 2.81;2.79 5.19 5.19 0.71726 . 0.000000 0.85682 D 0.000000 T 0.28001 0.0690 L 0.51914 1.62 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.991;0.996 T 0.00731 -1.1590 10 0.30078 T 0.28 -9.5991 17.6957 0.88281 0.0:0.0:1.0:0.0 . 811;825 Q8N612;Q8N612-2 F16A2_HUMAN;. V 811;825 ENSP00000416918:A811V;ENSP00000265978:A825V ENSP00000265978:A825V A - 2 0 FAM160A2 6192342 1.000000 0.71417 0.993000 0.49108 0.967000 0.64934 9.136000 0.94489 2.391000 0.81399 0.457000 0.33378 GCG TCGA-YY-A8LH-01A-11D-A36O-08 FAM160A2-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000383759.1 0 0 0 6 542 1 151 0 3.738182e-02 1 331 1 151 10 0 0 0 0 0 2 0 0.006521 6 540 2 148 19 0 0 0 1 151 2 -1.717238 0 1 0 0 1 2 4 6 2.051836 1 0.550000 3.730000 0.701195 0.070000 1.000000e-02 1.000000 0.070000 0.292879 0.070000 0 3.000000e-02 1.000000 PPFIA1 8500 broad.mit.edu 37 11 70171012 70171012 + Silent SNP C C A rs144282210 byFrequency TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr11:70171012C>A ENST00000253925.7 + 4 641 c.426C>A c.(424-426)acC>acA p.T142T AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Silent_p.T142T|CTA-797E19.2_ENST00000526017.1_RNA NM_003626.3 NP_003617.1 Q13136 LIPA1_HUMAN protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 p.T142T(1) 65 BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) TTAGGATGACCGTGGTGAAGA 0.473000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000253925.7 0 1 hg19 CCDS31627.1 TCGA-YY-A8LH-01A-11D-A36O-08 PPFIA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000393905.1 0 0 0 9 765 0 200 0 7.544369e-03 1 9 0 200 2 0 0 0 0 0 2 1 0.993928 8 757 0 198 2 0 0 0 0 200 2 -1.744953 0 1 0 0 1 2 2 4 2.108094 1 0.550000 3.730000 0.709677 0.060000 1.000000e-02 0.130000 0.080000 0.072539 0.060000 0 3.000000e-02 0.100000 KSR2 283455 broad.mit.edu 37 12 118405988 118405988 + Nonsense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:118405988C>A ENST00000339824.5 - 1 800 c.73G>T c.(73-75)Gaa>Taa p.E25* KSR2_ENST00000425217.1_5'UTR Q6VAB6 KSR2_HUMAN kinase suppressor of ras 2 67 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TGGACCAGTTCGCACTGCTGT 0.507000 0 SO:0001587 stop_gained ENST00000339824.5 0 1 hg19 . . . . . . . . . . C 46 12.515743 0.99674 . . ENSG00000171435 ENST00000339824 . . . 4.74 4.74 0.60224 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.40728 T 0.16 . 15.2228 0.73327 0.0:1.0:0.0:0.0 . . . . X 25 . ENSP00000339952:E25X E - 1 0 KSR2 116890371 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 6.802000 0.75175 2.158000 0.67659 0.491000 0.48974 GAA TCGA-YY-A8LH-01A-11D-A36O-08 KSR2-001 KNOWN non_canonical_conserved|not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000401987.2 0 0 0 10 633 0 152 0 0 0 1 0 152 2 0 0 0 0 0 2 1 0.996409 10 614 0 151 2 0 0 0 0 152 2 -2.273934 0 1 0 0 1 2 2 4 2.022142 0 0.550000 3.730000 0.698997 0.080000 3.000000e-02 1.000000 0.080000 0.166381 0.080000 0 5.000000e-02 0.140000 TMEM132D 121256 broad.mit.edu 37 12 129822360 129822360 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:129822360G>A ENST00000422113.2 - 4 1444 c.1118C>T c.(1117-1119)gCg>gTg p.A373V NM_133448.2 NP_597705.2 Q14C87 T132D_HUMAN transmembrane protein 132D 152 all_neural(191;0.101)|Medulloblastoma(191;0.163) all_epithelial(31;0.0934)|Breast(359;0.133) GGCGCCATCCGCACTGGAGAG 0.592000 0 SO:0001583 missense ENST00000422113.2 1 1 hg19 CCDS9266.1 . . . . . . . . . . G 7.293 0.611470 0.14066 . . ENSG00000151952 ENST00000422113 T 0.13657 2.57 5.15 -9.46 0.00597 . 1.098670 0.06965 N 0.817048 T 0.05547 0.0146 N 0.05230 -0.09 0.09310 N 1 B 0.06786 0.001 B 0.04013 0.001 T 0.44251 -0.9340 9 . . . -7.6336 13.872 0.63624 0.2209:0.0943:0.6848:0.0 . 373 Q14C87 T132D_HUMAN V 373 ENSP00000408581:A373V . A - 2 0 TMEM132D 128388313 0.000000 0.05858 0.000000 0.03702 0.012000 0.07955 -0.065000 0.11617 -2.151000 0.00795 -0.889000 0.02933 GCG TCGA-YY-A8LH-01A-11D-A36O-08 TMEM132D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399592.1 0 0 0 12 372 1 92 0 0 0 1 1 92 2 0 0 0 0 0 2 0 0.330087 12 366 1 91 15 0 0 0 1 92 2 -2.788778 1 1 0 0 1 2 2 4 2.022142 0 0.550000 3.730000 0.698997 0.170000 8.000000e-02 1.000000 0.160000 0.248988 0.170000 0 1.200000e-01 0.260000 FZD10 11211 broad.mit.edu 37 12 130648711 130648711 + Silent SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:130648711C>T ENST00000229030.4 + 1 1708 c.1224C>T c.(1222-1224)atC>atT p.I408I FZD10_ENST00000539839.1_Missense_Mutation_p.R376W|FZD10-AS1_ENST00000505807.2_RNA Q9ULW2 FZD10_HUMAN frizzled class receptor 10 35 all_neural(191;0.101)|Medulloblastoma(191;0.163) ACCTGGTCATCGGCACGTCCT 0.642000 0 SO:0001819 synonymous_variant ENST00000229030.4 1 1 hg19 CCDS9267.1 . . . . . . . . . . C 8.505 0.865101 0.17250 . . ENSG00000111432 ENST00000539839 . . . 5.21 -2.84 0.05751 . . . . . T 0.68888 0.3050 . . . 0.80722 D 1 . . . . . . T 0.72903 -0.4151 5 0.87932 D 0 . 12.273 0.54716 0.0:0.2908:0.5973:0.1119 . . . . W 376 . ENSP00000438460:R376W R + 1 2 FZD10 129214664 0.038000 0.19896 0.092000 0.20876 0.725000 0.41563 -0.798000 0.04565 -0.407000 0.07576 -0.305000 0.09177 CGG TCGA-YY-A8LH-01A-11D-A36O-08 FZD10-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 1 64 214 1 73 0 0 0 1 73 2 0 0 0 0 0 2 1 1.000000 64 210 1 73 14 0 0 0 1 73 2 -20.000000 1 1 0 0 1 2 2 4 2.022142 0 0.550000 3.730000 0.698997 0.990000 9.900000e-01 1.000000 1.000000 0.998965 0.990000 1 9.900000e-01 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-YY-A8LH-01A-11D-A36O-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 97 237 0 95 1 9.980131e-01 16 10 0 95 2 1 1 72 221 0 353 2 1 1.000000 96 235 0 93 2 1 1 3123 4899 0 95 2 -20.000000 1 1 0 0 1 2 2 4 2.022142 0 0.550000 3.730000 0.698997 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 LARP4 113251 broad.mit.edu 37 12 50847262 50847262 + Missense_Mutation SNP A A G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:50847262A>G ENST00000398473.2 + 9 936 c.824A>G c.(823-825)aAt>aGt p.N275S LARP4_ENST00000429001.3_Missense_Mutation_p.N281S|LARP4_ENST00000347328.5_Intron|LARP4_ENST00000293618.8_Missense_Mutation_p.N275S|LARP4_ENST00000518561.1_Missense_Mutation_p.N205S|LARP4_ENST00000522085.1_Missense_Mutation_p.N275S|LARP4_ENST00000518444.1_Missense_Mutation_p.N274S NM_052879.4|NM_199188.2 NP_443111.4|NP_954658.2 Q71RC2 LARP4_HUMAN La ribonucleoprotein domain family, member 4 23 AAAGCCATCAATACATTTTTT 0.308000 0 SO:0001583 missense ENST00000398473.2 1 1 hg19 CCDS41782.1 . . . . . . . . . . A 19.98 3.926632 0.73327 . . ENSG00000161813 ENST00000293618;ENST00000429001;ENST00000398473;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000518561;ENST00000520064 T;T;T;T;T;T 0.57595 1.24;0.94;0.92;0.39;0.89;0.5 3.89 3.89 0.44902 . 0.000000 0.85682 D 0.000000 T 0.70037 0.3178 M 0.74258 2.255 0.80722 D 1 D;D;D;D;P 0.69078 0.997;0.957;0.996;0.995;0.553 D;D;D;D;P 0.77557 0.985;0.914;0.99;0.956;0.627 T 0.72899 -0.4152 10 0.49607 T 0.09 . 13.3994 0.60874 1.0:0.0:0.0:0.0 . 176;274;275;275;281 Q71RC2-2;Q71RC2-3;G3XAA8;Q71RC2;Q71RC2-4 .;.;.;LARP4_HUMAN;. S 275;281;275;275;275;274;205;176 ENSP00000293618:N275S;ENSP00000415464:N281S;ENSP00000381490:N275S;ENSP00000429781:N275S;ENSP00000429077:N274S;ENSP00000430851:N205S ENSP00000293618:N275S N + 2 0 LARP4 49133529 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 8.707000 0.91367 1.724000 0.51502 0.260000 0.18958 AAT TCGA-YY-A8LH-01A-11D-A36O-08 LARP4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000374981.1 1 0 1 93 214 0 95 1 4.797068e-01 2 3 0 95 2 0 0 0 0 0 2 1 1.000000 93 211 0 95 2 0 0 0 0 95 2 -20.000000 1 1 0 0 1 2 2 4 2.022142 0 0.550000 3.730000 0.698997 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 RNF41 10193 broad.mit.edu 37 12 56600246 56600246 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:56600246G>A ENST00000345093.4 - 7 1308 c.939C>T c.(937-939)ggC>ggT p.G313G RNF41_ENST00000394013.2_Silent_p.G242G|RNF41_ENST00000552656.1_Silent_p.G313G NM_005785.3|NM_194359.2 NP_005776.1|NP_919340.1 Q9H4P4 RNF41_HUMAN ring finger protein 41, E3 ubiquitin protein ligase 11 TCTCTTCCACGCCATGCGCAA 0.522000 OREG0021921 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000345093.4 1 1 hg19 CCDS8909.1 TCGA-YY-A8LH-01A-11D-A36O-08 RNF41-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408525.1 0 0 0 53 692 0 226 1 9.525136e-01 5 62 0 226 2 0 0 0 0 0 2 1 1.000000 52 686 0 222 2 0 0 0 0 226 2 -10.535360 1 1 121412 4 42 1 2 2 4 2.022142 0 0.550000 3.730000 0.698997 0.390000 2.800000e-01 1.000000 0.380000 0.441890 0.390000 0 3.300000e-01 0.470000 ACRBP 84519 broad.mit.edu 37 12 6753307 6753307 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr12:6753307C>T ENST00000229243.2 - 5 1033 c.940G>A c.(940-942)Ggc>Agc p.G314S ACRBP_ENST00000414226.2_Missense_Mutation_p.G281S|ACRBP_ENST00000536350.1_Missense_Mutation_p.G314S|ACRBP_ENST00000542357.1_5'Flank NM_032489.2 NP_115878.2 acrosin binding protein 17 CTATACCTGCCAGGGTTTTGG 0.463000 0 SO:0001583 missense ENST00000229243.2 0 1 hg19 CCDS8554.1 . . . . . . . . . . C 14.70 2.612970 0.46631 . . ENSG00000111644 ENST00000229243;ENST00000414226;ENST00000536350 T;T 0.44881 0.92;0.91 4.25 2.41 0.29592 . 0.596770 0.15767 N 0.245645 T 0.29914 0.0748 L 0.50919 1.6 0.21325 N 0.999725 P;P 0.37525 0.598;0.598 B;B 0.31614 0.133;0.133 T 0.14504 -1.0470 10 0.41790 T 0.15 . 5.855 0.18714 0.0:0.767:0.0:0.233 . 281;314 E7EP66;Q8NEB7 .;ACRBP_HUMAN S 314;281;314 ENSP00000229243:G314S;ENSP00000402725:G281S ENSP00000229243:G314S G - 1 0 ACRBP 6623568 0.505000 0.26131 0.620000 0.29132 0.535000 0.34838 0.691000 0.25467 1.135000 0.42183 0.561000 0.74099 GGC TCGA-YY-A8LH-01A-11D-A36O-08 ACRBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400703.1 0 0 0 7 364 0 103 0 2.987832e-03 0 4 0 103 2 0 0 0 0 0 2 1 0.980661 7 363 0 102 2 0 0 0 0 103 2 -6.898041 1 1 0 0 1 2 2 4 2.040923 0 0.550000 3.730000 0.701195 0.110000 4.000000e-02 1.000000 0.110000 0.174193 0.110000 0 7.000000e-02 0.170000 COL4A1 1282 broad.mit.edu 37 13 110857736 110857736 + Silent SNP G G A rs138809869 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr13:110857736G>A ENST00000375820.4 - 17 1042 c.921C>T c.(919-921)ccC>ccT p.P307P COL4A1_ENST00000543140.1_Silent_p.P307P NM_001845.4 NP_001836.2 P02462 CO4A1_HUMAN collagen, type IV, alpha 1 105 all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604) Breast(118;0.2) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145) CTGGGTACCCGGGTTCACCAG 0.512000 0 SO:0001819 synonymous_variant ENST00000375820.4 1 1 hg19 CCDS9511.1 TCGA-YY-A8LH-01A-11D-A36O-08 COL4A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045759.3 1 0 1 96 318 0 119 1 9.999999e-01 8 71 0 119 2 0 0 0 0 0 2 1 1.000000 96 311 0 117 2 0 0 0 0 119 2 -3.752635 1 1 121412 2 36 1 2 2 4 2.108966 1 0.550000 3.730000 0.709677 0.990000 9.900000e-01 1.000000 1.000000 0.999923 0.990000 1 9.900000e-01 1.000000 FNDC3A 22862 broad.mit.edu 37 13 49775956 49775956 + Missense_Mutation SNP G G C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr13:49775956G>C ENST00000492622.2 + 24 3313 c.3008G>C c.(3007-3009)gGa>gCa p.G1003A FNDC3A_ENST00000398316.3_Missense_Mutation_p.G947A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.G1003A NM_001079673.1 NP_001073141.1 Q9Y2H6 FND3A_HUMAN fibronectin type III domain containing 3A 41 all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19) KIRC - Kidney renal clear cell carcinoma(9;0.206) CTATACAGAGGACCATGTCAT 0.328000 0 SO:0001583 missense ENST00000492622.2 0 1 hg19 CCDS41886.1 . . . . . . . . . . G 27.5 4.833531 0.91036 . . ENSG00000102531 ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316 T;T;T 0.56611 0.45;0.45;0.45 6.16 6.16 0.99307 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.64402 D 0.000003 T 0.78723 0.4328 M 0.90082 3.085 0.80722 D 1 D;P 0.89917 1.0;0.936 D;P 0.91635 0.999;0.908 T 0.76822 -0.2817 10 0.33141 T 0.24 -24.3933 19.848 0.96722 0.0:0.0:1.0:0.0 . 947;1003 Q9Y2H6-2;Q9Y2H6 .;FND3A_HUMAN A 1003;939;1003;947 ENSP00000417257:G1003A;ENSP00000441831:G1003A;ENSP00000381362:G947A ENSP00000338579:G939A G + 2 0 FNDC3A 48673957 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.414000 0.97362 2.937000 0.99478 0.650000 0.86243 GGA TCGA-YY-A8LH-01A-11D-A36O-08 FNDC3A-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354845.2 0 0 0 6 442 0 102 0 2.022002e-01 0 53 0 102 2 0 0 0 0 0 2 1 0.964476 6 439 0 102 2 0 0 0 0 102 2 -4.870415 1 1 0 0 1 2 2 4 2.108966 1 0.550000 3.730000 0.709677 0.070000 1.000000e-02 0.160000 0.080000 0.087277 0.070000 0 4.000000e-02 0.120000 CCDC70 83446 broad.mit.edu 37 13 52439534 52439534 + Missense_Mutation SNP G G T rs141731440 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr13:52439534G>T ENST00000242819.4 + 2 316 c.20G>T c.(19-21)cGg>cTg p.R7L NM_031290.2 NP_112580.2 Q6NSX1 CCD70_HUMAN coiled-coil domain containing 70 15 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19) CCGCCATTCCGGCTGATAAGG 0.577000 0 SO:0001583 missense ENST00000242819.4 0 1 hg19 CCDS9431.1 . . . . . . . . . . G 3.641 -0.073442 0.07184 . . ENSG00000123171 ENST00000242819 T 0.35789 1.29 4.67 1.94 0.25998 . 1.136360 0.06681 N 0.767977 T 0.25827 0.0629 N 0.24115 0.695 0.09310 N 1 B 0.23185 0.081 B 0.23275 0.045 T 0.29488 -1.0010 10 0.46703 T 0.11 -2.2162 6.8951 0.24251 0.2994:0.0:0.7006:0.0 . 7 Q6NSX1 CCD70_HUMAN L 7 ENSP00000242819:R7L ENSP00000242819:R7L R + 2 0 CCDC70 51337535 0.001000 0.12720 0.001000 0.08648 0.011000 0.07611 0.745000 0.26259 0.143000 0.18926 -0.672000 0.03802 CGG TCGA-YY-A8LH-01A-11D-A36O-08 CCDC70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045033.2 0 0 0 6 244 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 0.962808 6 238 0 52 2 0 0 0 0 54 2 -3.190722 1 1 0 0 1 2 2 4 2.108966 1 0.550000 3.730000 0.709677 0.140000 5.000000e-02 0.280000 0.130000 0.156340 0.140000 0 9.000000e-02 0.210000 ATP7B 540 broad.mit.edu 37 13 52585461 52585461 + Nonsense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr13:52585461C>A ENST00000242839.4 - 1 169 c.13G>T c.(13-15)Gag>Tag p.E5* ALG11_ENST00000521508.1_5'Flank|ATP7B_ENST00000448424.2_Nonsense_Mutation_p.E5*|ATP7B_ENST00000418097.2_Nonsense_Mutation_p.E5*|ATP7B_ENST00000400370.3_Nonsense_Mutation_p.E5*|ALG11_ENST00000523764.1_5'Flank|ATP7B_ENST00000400366.3_Nonsense_Mutation_p.E5*|ATP7B_ENST00000344297.5_Nonsense_Mutation_p.E5* NM_000053.3 NP_000044.2 P35670 ATP7B_HUMAN ATPase, Cu++ transporting, beta polypeptide 55 Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19) Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526) ATCTGTCTCTCCTGCTCAGGC 0.592000 Wilson disease 0 SO:0001587 stop_gained Familial Cancer Database ENST00000242839.4 0 1 hg19 CCDS41892.1 . . . . . . . . . . C 22.0 4.225575 0.79576 . . ENSG00000123191 ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000400370;ENST00000418097 . . . 3.89 1.0 0.19881 . 0.976046 0.08296 U 0.967727 . . . . . . 0.19945 N 0.999943 . . . . . . . . . . 0.45353 T 0.12 -0.074 2.4796 0.04584 0.1932:0.5103:0.1876:0.1088 . . . . X 5 . ENSP00000242839:E5X E - 1 0 ATP7B 51483462 0.002000 0.14202 0.001000 0.08648 0.037000 0.13140 0.524000 0.22940 0.051000 0.15978 -0.378000 0.06908 GAG TCGA-YY-A8LH-01A-11D-A36O-08 ATP7B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045981.1 1 0 0 64 239 0 82 0 2.888312e-01 0 5 0 82 2 0 0 0 0 0 2 1 1.000000 63 235 0 80 2 0 0 0 0 82 2 -20.000000 1 1 0 0 1 2 2 4 2.108966 1 0.550000 3.730000 0.709677 0.990000 9.400000e-01 1.000000 1.000000 0.996829 0.990000 1 9.900000e-01 1.000000 MDGA2 161357 broad.mit.edu 37 14 47426671 47426671 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr14:47426671G>A ENST00000399232.2 - 9 2152 c.1788C>T c.(1786-1788)taC>taT p.Y596Y MDGA2_ENST00000357362.3_Silent_p.Y367Y|MDGA2_ENST00000426342.1_Silent_p.Y367Y|MDGA2_ENST00000439988.3_Silent_p.Y665Y|SNORA25_ENST00000515926.1_RNA NM_001113498.2 NP_001106970.3 Q7Z553 MDGA2_HUMAN MAM domain containing glycosylphosphatidylinositol anchor 2 76 TCTTCACAGCGTACTCTGTGT 0.443000 0 SO:0001819 synonymous_variant ENST00000399232.2 1 1 hg19 TCGA-YY-A8LH-01A-11D-A36O-08 MDGA2-001 KNOWN upstream_ATG|basic|appris_principal protein_coding protein_coding OTTHUMT00000073352.5 0 0 0 13 376 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 0.999520 12 373 0 77 2 0 0 0 0 79 2 -3.687590 1 1 120838 10 42 1 2 2 4 2.105174 1 0.550000 3.730000 0.709677 0.190000 9.000000e-02 0.310000 0.200000 0.201607 0.190000 0 1.400000e-01 0.250000 RPS6KA5 9252 broad.mit.edu 37 14 91372565 91372565 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr14:91372565C>T ENST00000261991.3 - 8 1058 c.885G>A c.(883-885)atG>atA p.M295I RPS6KA5_ENST00000536315.2_Missense_Mutation_p.M216I|RPS6KA5_ENST00000556304.1_5'UTR|RPS6KA5_ENST00000418736.2_Missense_Mutation_p.M295I NM_004755.2 NP_004746.2 O75582 KS6A5_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 5 24 all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146) TGGGATCTTTCATCAAAAGAC 0.383000 0 SO:0001583 missense ENST00000261991.3 0 1 hg19 CCDS9893.1 . . . . . . . . . . C 12.75 2.031697 0.35797 . . ENSG00000100784 ENST00000261991;ENST00000536315;ENST00000418736 T;T;T 0.52983 0.64;0.64;0.64 5.33 5.33 0.75918 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.239079 0.49916 D 0.000136 T 0.24812 0.0602 N 0.03999 -0.3 0.41859 D 0.990216 B;B 0.02656 0.0;0.0 B;B 0.04013 0.0;0.001 T 0.09292 -1.0681 10 0.35671 T 0.21 . 9.9904 0.41868 0.0:0.8486:0.0:0.1514 . 295;295 O75582-2;O75582 .;KS6A5_HUMAN I 295;216;295 ENSP00000261991:M295I;ENSP00000442803:M216I;ENSP00000402787:M295I ENSP00000261991:M295I M - 3 0 RPS6KA5 90442318 1.000000 0.71417 1.000000 0.80357 0.956000 0.61745 1.240000 0.32731 2.640000 0.89533 0.585000 0.79938 ATG TCGA-YY-A8LH-01A-11D-A36O-08 RPS6KA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411442.2 0 0 0 6 409 0 105 0 0 0 1 0 105 2 0 0 0 0 0 2 1 0.963634 6 403 0 104 2 0 0 0 0 105 2 -3.031096 1 1 0 0 1 2 2 4 2.105174 1 0.550000 3.730000 0.709677 0.080000 1.000000e-02 0.170000 0.080000 0.094387 0.080000 0 5.000000e-02 0.130000 VRK1 7443 broad.mit.edu 37 14 97319216 97319216 + Missense_Mutation SNP A A G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr14:97319216A>G ENST00000216639.3 + 6 572 c.423A>G c.(421-423)atA>atG p.I141M NM_003384.2 NP_003375.1 Q99986 VRK1_HUMAN vaccinia related kinase 1 12 Melanoma(154;0.155) TTCAGAAAATATATGAAGCAA 0.328000 0 SO:0001583 missense ENST00000216639.3 1 1 hg19 CCDS9947.1 . . . . . . . . . . A 13.20 2.165260 0.38217 . . ENSG00000100749 ENST00000216639 T 0.21191 2.02 5.76 3.01 0.34805 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.418609 0.30446 N 0.009607 T 0.18509 0.0444 M 0.65498 2.005 0.41806 D 0.989943 P 0.44734 0.842 B 0.39876 0.312 T 0.07462 -1.0771 10 0.72032 D 0.01 -21.5458 1.8397 0.03147 0.4436:0.3034:0.106:0.1471 . 141 Q99986 VRK1_HUMAN M 141 ENSP00000216639:I141M ENSP00000216639:I141M I + 3 3 VRK1 96388969 0.957000 0.32711 1.000000 0.80357 0.997000 0.91878 0.138000 0.16016 0.978000 0.38470 0.482000 0.46254 ATA TCGA-YY-A8LH-01A-11D-A36O-08 VRK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413520.1 1 0 0 24 316 0 57 1 4.795262e-01 3 19 0 57 2 0 0 0 0 0 2 1 1.000000 24 313 0 55 2 0 0 0 0 57 2 -20.000000 1 1 0 0 1 2 2 4 2.105174 1 0.550000 3.730000 0.709677 0.400000 2.600000e-01 0.570000 0.400000 0.411529 0.400000 0 3.200000e-01 0.490000 NIPA1 123606 broad.mit.edu 37 15 23049053 23049053 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr15:23049053C>T ENST00000337435.4 - 5 790 c.766G>A c.(766-768)Gac>Aac p.D256N NIPA1_ENST00000437912.2_Missense_Mutation_p.D181N|NIPA1_ENST00000538684.1_Missense_Mutation_p.D86N|NIPA1_ENST00000561183.1_Missense_Mutation_p.D181N NM_001142275.1|NM_144599.4 NP_001135747.1|NP_653200.2 Q7RTP0 NIPA1_HUMAN non imprinted in Prader-Willi/Angelman syndrome 1 15 all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488) ACCGAGGAGTCGAAGCACTCC 0.612000 0 SO:0001583 missense ENST00000337435.4 1 1 hg19 CCDS10011.1 . . . . . . . . . . C 8.788 0.929927 0.18131 . . ENSG00000170113 ENST00000337435;ENST00000437912;ENST00000538684 D;D;D 0.87887 -2.31;-2.31;-2.31 5.46 5.46 0.80206 . 0.090329 0.85682 D 0.000000 T 0.78394 0.4276 N 0.04880 -0.145 0.47737 D 0.999502 D 0.67145 0.996 P 0.49561 0.615 T 0.76677 -0.2871 10 0.02654 T 1 -31.8615 19.2935 0.94112 0.0:1.0:0.0:0.0 . 256 Q7RTP0 NIPA1_HUMAN N 256;181;86 ENSP00000337452:D256N;ENSP00000393962:D181N;ENSP00000440957:D86N ENSP00000337452:D256N D - 1 0 NIPA1 20600494 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.979000 0.56888 2.572000 0.86782 0.591000 0.81541 GAC TCGA-YY-A8LH-01A-11D-A36O-08 NIPA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251135.2 1 0 0 8 164 0 54 1 3.115840e-01 4 18 0 54 2 0 0 0 0 0 2 1 0.989394 8 162 0 54 2 0 0 0 0 54 2 -10.684450 1 1 0 0 1 2 2 4 2.074351 0 0.550000 3.730000 0.707602 0.270000 1.200000e-01 0.530000 0.260000 0.295742 0.270000 0 1.900000e-01 0.390000 MYO9A 4649 broad.mit.edu 37 15 72300289 72300289 + Missense_Mutation SNP A A G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr15:72300289A>G ENST00000356056.5 - 8 1730 c.1258T>C c.(1258-1260)Ttc>Ctc p.F420L MYO9A_ENST00000444904.1_Missense_Mutation_p.F401L|MYO9A_ENST00000563542.1_5'UTR|RP11-390D11.1_ENST00000568391.1_RNA|MYO9A_ENST00000424560.1_Missense_Mutation_p.F420L|MYO9A_ENST00000564571.1_Missense_Mutation_p.F420L|MYO9A_ENST00000566885.1_Missense_Mutation_p.F15L NM_006901.3 NP_008832.2 B2RTY4 MYO9A_HUMAN myosin IXA 88 AGAAGAGAGAAAATCCTGGGA 0.343000 0 SO:0001583 missense ENST00000356056.5 0 1 hg19 CCDS10239.1 . . . . . . . . . . A 25.6 4.657601 0.88154 . . ENSG00000066933 ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448 D;D;D 0.87256 -2.23;-2.23;-2.23 5.28 5.28 0.74379 Myosin head, motor domain (2); . . . . D 0.89966 0.6868 L 0.59436 1.845 0.80722 D 1 D;P;P;P 0.69078 0.997;0.474;0.794;0.859 P;P;P;P 0.59643 0.861;0.523;0.523;0.781 D 0.90607 0.4549 9 0.72032 D 0.01 . 11.2077 0.48780 0.8465:0.1535:0.0:0.0 . 401;420;401;420 B2RTY4-2;B2RTY4-3;B7WP69;B2RTY4 .;.;.;MYO9A_HUMAN L 420;420;401;401;420 ENSP00000348349:F420L;ENSP00000399162:F420L;ENSP00000398250:F401L ENSP00000261864:F401L F - 1 0 MYO9A 70087343 1.000000 0.71417 1.000000 0.80357 0.971000 0.66376 6.834000 0.75339 2.107000 0.64212 0.460000 0.39030 TTC TCGA-YY-A8LH-01A-11D-A36O-08 MYO9A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257308.1 0 0 0 5 300 0 68 0 4.441812e-04 0 2 0 68 2 0 0 0 0 0 2 1 0.936960 5 298 0 67 2 0 0 0 0 68 2 -6.393507 1 1 0 0 1 2 2 4 2.138324 1 0.550000 3.730000 0.709677 0.090000 2.000000e-02 0.210000 0.080000 0.109849 0.090000 0 5.000000e-02 0.150000 BLM 641 broad.mit.edu 37 15 91303899 91303899 + Silent SNP T T C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr15:91303899T>C ENST00000355112.3 + 7 1414 c.1296T>C c.(1294-1296)ccT>ccC p.P432P BLM_ENST00000560509.1_Silent_p.P432P NM_000057.2 NP_000048.1 P54132 BLM_HUMAN Bloom syndrome, RecQ helicase-like 51 Lung NSC(78;0.0875)|all_lung(78;0.109) Lung(145;0.189) GATACAGGCCTGATTCACTTG 0.418000 Mis, N, F leukemia, lymphoma, skin squamous cell , other cancers Genes defective in diseases associated with sensitivity to DNA damaging agents Bloom syndrome yes Rec Bloom Syndrome 15 15q26.1 641 Bloom Syndrome L, E 0 SO:0001819 synonymous_variant Familial Cancer Database ENST00000355112.3 0 1 hg19 CCDS10363.1 TCGA-YY-A8LH-01A-11D-A36O-08 BLM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313495.1 0 0 0 7 856 0 213 0 0 0 0 213 2 0 0 0 0 0 2 1 0.980056 7 849 0 210 2 0 0 0 0 213 2 -2.454305 0 1 0 0 1 2 2 4 2.138324 1 0.550000 3.730000 0.709677 0.040000 0 0.100000 0.040000 0.049176 0.040000 0 2.000000e-02 0.070000 APRT 353 broad.mit.edu 37 16 88877975 88877975 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr16:88877975C>T ENST00000378364.3 - 2 214 c.170G>A c.(169-171)cGc>cAc p.R57H APRT_ENST00000426324.2_Missense_Mutation_p.R57H|APRT_ENST00000563655.1_Missense_Mutation_p.R57H NM_000485.2 NP_000476.1 P07741 APT_HUMAN adenine phosphoribosyltransferase 3 Adenine(DB00173)|Adenosine monophosphate(DB00131) GTAGTCGATGCGGCCCCCGTG 0.716000 0 SO:0001583 missense ENST00000378364.3 0 1 hg19 CCDS32511.1 . . . . . . . . . . C 14.69 2.610499 0.46527 . . ENSG00000198931 ENST00000378364;ENST00000426324 D;D 0.99369 -3.3;-5.78 4.63 -0.359 0.12571 Phosphoribosyltransferase (1); 0.950123 0.08812 N 0.890115 D 0.95510 0.8541 N 0.03891 -0.335 0.09310 N 1 B;B 0.06786 0.001;0.001 B;B 0.06405 0.002;0.001 D 0.90882 0.4754 10 0.72032 D 0.01 -3.3317 9.307 0.37881 0.0:0.5341:0.0:0.4659 . 57;57 G5E9J2;P07741 .;APT_HUMAN H 57 ENSP00000367615:R57H;ENSP00000397007:R57H ENSP00000367615:R57H R - 2 0 APRT 87405476 0.001000 0.12720 0.026000 0.17262 0.926000 0.56050 0.200000 0.17257 -0.387000 0.07809 0.313000 0.20887 CGC TCGA-YY-A8LH-01A-11D-A36O-08 APRT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000430000.2 0 0 0 4 51 0 17 0 9.999972e-01 1 945 0 17 2 0 0 0 0 0 2 1 0.884115 4 49 0 17 2 0 0 0 0 17 2 -8.347408 1 1 0 0 1 2 2 4 2.139844 1 0.550000 3.730000 0.709677 0.450000 1.500000e-01 0.920000 1.000000 0.488478 0.450000 0 2.800000e-01 0.690000 MYH4 4622 broad.mit.edu 37 17 10350494 10350494 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:10350494C>T ENST00000255381.2 - 35 5115 c.5005G>A c.(5005-5007)Gat>Aat p.D1669N RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA NM_017533.2 NP_060003.2 Q9Y623 MYH4_HUMAN myosin, heavy chain 4, skeletal muscle p.D1669N(1) 149 TTAAGGTCATCTTGGCCTCTG 0.478000 1 Substitution - Missense(1) SO:0001583 missense ENST00000255381.2 1 1 hg19 CCDS11154.1 . . . . . . . . . . C 33 5.200015 0.94997 . . ENSG00000141048 ENST00000255381 T 0.79845 -1.31 5.29 5.29 0.74685 Myosin tail (1); 0.189171 0.25052 U 0.033501 D 0.86226 0.5882 M 0.85197 2.74 0.52099 D 0.999943 P 0.37781 0.608 B 0.42462 0.388 D 0.88012 0.2763 10 0.72032 D 0.01 . 19.286 0.94069 0.0:1.0:0.0:0.0 . 1669 Q9Y623 MYH4_HUMAN N 1669 ENSP00000255381:D1669N ENSP00000255381:D1669N D - 1 0 MYH4 10291219 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 7.763000 0.85283 2.646000 0.89796 0.563000 0.77884 GAT TCGA-YY-A8LH-01A-11D-A36O-08 MYH4-001 KNOWN NAGNAG_splice_site|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252731.1 1 0 1 21 167 0 61 0 1.905298e-01 0 7 0 61 2 0 0 0 0 0 2 1 0.999998 21 167 0 60 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 2 2 1.436748 1 0.550000 3.730000 0.550000 0.400000 2.600000e-01 0.580000 0.400000 0.419218 0.400000 0 3.300000e-01 0.500000 MYO1D 4642 broad.mit.edu 37 17 31094737 31094737 + Missense_Mutation SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:31094737C>G ENST00000318217.5 - 7 1052 c.748G>C c.(748-750)Gtt>Ctt p.V250L MYO1D_ENST00000583621.1_Missense_Mutation_p.V250L|MYO1D_ENST00000394649.4_Missense_Mutation_p.V162L|MYO1D_ENST00000579584.1_Missense_Mutation_p.V250L NM_015194.1 NP_056009.1 O94832 MYO1D_HUMAN myosin ID 39 BRCA - Breast invasive adenocarcinoma(9;0.0362) GCATCAGCAACAACTCTGAAT 0.388000 0 SO:0001583 missense ENST00000318217.5 0 1 hg19 CCDS32615.1 . . . . . . . . . . C 33 5.288156 0.95517 . . ENSG00000176658 ENST00000318217 D 0.86627 -2.15 6.0 6.0 0.97389 Myosin head, motor domain (2); 0.000000 0.35646 U 0.003065 D 0.89329 0.6684 L 0.45698 1.435 0.58432 D 0.999999 P;P 0.51933 0.949;0.913 P;P 0.53760 0.734;0.649 D 0.89435 0.3719 10 0.62326 D 0.03 . 17.9887 0.89162 0.0:1.0:0.0:0.0 . 161;250 Q7Z3N6;O94832 .;MYO1D_HUMAN L 250 ENSP00000324527:V250L ENSP00000324527:V250L V - 1 0 MYO1D 28118850 1.000000 0.71417 0.994000 0.49952 0.984000 0.73092 7.487000 0.81328 2.848000 0.98002 0.655000 0.94253 GTT TCGA-YY-A8LH-01A-11D-A36O-08 MYO1D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447457.1 0 0 0 5 328 0 86 0 2.711816e-01 0 57 0 86 2 0 0 0 0 0 2 1 0.934451 5 321 0 85 2 0 0 0 0 86 2 -5.827601 1 1 0 0 1 2 2 4 2.137762 1 0.550000 3.730000 0.709677 0.090000 1.000000e-02 0.190000 0.080000 0.100544 0.090000 0 5.000000e-02 0.140000 CNTNAP1 8506 broad.mit.edu 37 17 40839935 40839935 + Silent SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:40839935C>A ENST00000264638.4 + 8 1459 c.1242C>A c.(1240-1242)ctC>ctA p.L414L CTD-3193K9.3_ENST00000592440.1_RNA NM_003632.2 NP_003623.1 P78357 CNTP1_HUMAN contactin associated protein 1 49 Breast(137;0.000143) AGCTGACGCTCAGCGAAGGGC 0.637000 0 SO:0001819 synonymous_variant ENST00000264638.4 0 1 hg19 CCDS11436.1 TCGA-YY-A8LH-01A-11D-A36O-08 CNTNAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452342.1 0 0 0 11 395 0 105 0 1.751589e-02 0 7 0 105 2 0 0 0 0 0 2 1 0.998194 11 387 0 104 2 0 0 0 0 105 2 -2.948390 1 1 0 0 1 3 4 7 2.171898 1 0.550000 3.730000 0.719626 0.180000 8.000000e-02 1.000000 0.170000 0.369384 0.180000 0 1.200000e-01 1.000000 RNF43 54894 broad.mit.edu 37 17 56434978 56434978 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:56434978G>A ENST00000584437.1 - 8 4114 c.2159C>T c.(2158-2160)tCa>tTa p.S720L RNF43_ENST00000407977.2_Missense_Mutation_p.S720L|RNF43_ENST00000583753.1_Missense_Mutation_p.S679L|RNF43_ENST00000500597.2_Missense_Mutation_p.S679L|RNF43_ENST00000581868.1_Missense_Mutation_p.S593L|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.S720L|RNF43_ENST00000577625.1_Missense_Mutation_p.S593L Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) CTGTGAATTTGAGTAACAGGG 0.592000 0 SO:0001583 missense ENST00000584437.1 1 1 hg19 CCDS11607.1 . . . . . . . . . . G 15.06 2.720039 0.48728 . . ENSG00000108375 ENST00000407977;ENST00000500597 T;T 0.08807 3.19;3.05 5.71 5.71 0.89125 . 0.652107 0.13771 N 0.363914 T 0.10337 0.0253 N 0.19112 0.55 0.25753 N 0.985036 B;P;B 0.41131 0.13;0.739;0.079 B;P;B 0.45232 0.149;0.474;0.071 T 0.20940 -1.0260 10 0.66056 D 0.02 -8.0908 15.33 0.74200 0.0:0.0:1.0:0.0 . 679;720;720 Q68DV7-2;Q68DV7-4;Q68DV7 .;.;RNF43_HUMAN L 720;679 ENSP00000385328:S720L;ENSP00000441969:S679L ENSP00000385328:S720L S - 2 0 RNF43 53789977 1.000000 0.71417 0.989000 0.46669 0.968000 0.65278 3.986000 0.56937 2.698000 0.92095 0.511000 0.50034 TCA TCGA-YY-A8LH-01A-11D-A36O-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 37 284 0 126 1 9.873056e-01 5 50 0 126 2 1 1 24 196 0 462 2 1 1.000000 37 282 0 126 2 0 0 0 0 126 2 -3.142717 1 1 0 0 1 0 3 3 1.475516 1 0.550000 3.730000 0.626091 0.520000 3.600000e-01 1.000000 0.500000 0.603510 0.520000 0 4.400000e-01 1.000000 RNF43 54894 broad.mit.edu 37 17 56435359 56435359 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:56435359G>A ENST00000584437.1 - 8 3733 c.1778C>T c.(1777-1779)tCt>tTt p.S593F RNF43_ENST00000407977.2_Missense_Mutation_p.S593F|RNF43_ENST00000583753.1_Missense_Mutation_p.S552F|RNF43_ENST00000500597.2_Missense_Mutation_p.S552F|RNF43_ENST00000581868.1_Missense_Mutation_p.S466F|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.S593F|RNF43_ENST00000577625.1_Missense_Mutation_p.S466F Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) CTGATCAGGAGAAGGTGGCTC 0.652000 0 SO:0001583 missense ENST00000584437.1 1 0 hg19 CCDS11607.1 . . . . . . . . . . G 5.168 0.216617 0.09810 . . ENSG00000108375 ENST00000407977;ENST00000500597 T;T 0.21031 2.03;2.03 4.66 3.65 0.41850 . 1.839710 0.02178 N 0.060263 T 0.17280 0.0415 N 0.24115 0.695 0.09310 N 1 B;B;B 0.14012 0.001;0.009;0.0 B;B;B 0.14023 0.005;0.01;0.002 T 0.19224 -1.0312 10 0.59425 D 0.04 -13.7741 5.2898 0.15721 0.1836:0.0:0.8164:0.0 . 552;593;593 Q68DV7-2;Q68DV7-4;Q68DV7 .;.;RNF43_HUMAN F 593;552 ENSP00000385328:S593F;ENSP00000441969:S552F ENSP00000385328:S593F S - 2 0 RNF43 53790358 0.633000 0.27181 0.009000 0.14445 0.257000 0.26127 3.840000 0.55843 1.049000 0.40321 0.205000 0.17691 TCT TCGA-YY-A8LH-01A-11D-A36O-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 0 51 381 0 143 1 9.872006e-01 3 50 0 143 2 1 1 29 236 1 513 4 1 1.000000 51 374 0 143 2 0 0 0 0 143 2 -18.988750 1 0 0 0 1 0 3 3 1.475516 1 0.550000 3.730000 0.626091 0.530000 3.900000e-01 1.000000 0.520000 0.611441 0.530000 0 4.500000e-01 1.000000 RNF43 54894 broad.mit.edu 37 17 56448366 56448366 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:56448366C>A ENST00000584437.1 - 2 2236 c.281G>T c.(280-282)aGt>aTt p.S94I RNF43_ENST00000407977.2_Missense_Mutation_p.S94I|RNF43_ENST00000583753.1_Intron|RNF43_ENST00000500597.2_Intron|RNF43_ENST00000581868.1_5'UTR|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.S94I|RNF43_ENST00000577625.1_5'UTR Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) GTCGTCATCACTGGCATTGCA 0.582000 0 SO:0001583 missense ENST00000584437.1 1 1 hg19 CCDS11607.1 . . . . . . . . . . C 29.4 5.006071 0.93287 . . ENSG00000108375 ENST00000407977 T 0.47177 0.85 5.45 5.45 0.79879 . 0.000000 0.85682 D 0.000000 T 0.52597 0.1744 L 0.27053 0.805 0.80722 D 1 D 0.57257 0.979 P 0.60415 0.874 T 0.41787 -0.9489 10 0.22706 T 0.39 -22.6639 18.2765 0.90085 0.0:1.0:0.0:0.0 . 94 Q68DV7 RNF43_HUMAN I 94 ENSP00000385328:S94I ENSP00000385328:S94I S - 2 0 RNF43 53803365 1.000000 0.71417 1.000000 0.80357 0.952000 0.60782 6.495000 0.73665 2.555000 0.86185 0.655000 0.94253 AGT TCGA-YY-A8LH-01A-11D-A36O-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 60 112 0 66 1 9.999600e-01 21 12 0 66 2 1 1 115 197 0 596 2 1 1.000000 59 111 0 65 2 0 0 0 0 66 2 -20.000000 1 1 0 0 1 0 3 3 1.475516 1 0.550000 3.730000 0.626091 0.990000 9.900000e-01 1.000000 1.000000 0.999996 0.990000 1 9.900000e-01 1.000000 HSF5 124535 broad.mit.edu 37 17 56557381 56557381 + Silent SNP G G A rs115372024 byFrequency TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:56557381G>A ENST00000323777.3 - 2 907 c.798C>T c.(796-798)acC>acT p.T266T NM_001080439.1 NP_001073908.1 Q4G112 HSF5_HUMAN heat shock transcription factor family member 5 16 Medulloblastoma(34;0.127)|all_neural(34;0.237) GCAGTGTATAGGTAACCTCAG 0.478000 0 SO:0001819 synonymous_variant ENST00000323777.3 1 1 hg19 CCDS32690.1 TCGA-YY-A8LH-01A-11D-A36O-08 HSF5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444719.1 1 0 1 135 277 0 185 0 0 0 0 185 2 0 0 0 0 0 2 1 1.000000 134 274 0 182 2 0 0 0 0 185 2 -2.920853 1 1 121412 104 55 1 0 3 3 1.475516 1 0.550000 3.730000 0.626091 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 POLR2A 5430 broad.mit.edu 37 17 7416998 7416998 + Silent SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:7416998C>T ENST00000322644.6 + 29 5814 c.5415C>T c.(5413-5415)tcC>tcT p.S1805S NM_000937.4 NP_000928 P24928 RPB1_HUMAN polymerase (RNA) II (DNA directed) polypeptide A, 220kDa 50 Prostate(122;0.173) CAAGTTACTCCCCTTCCAGCC 0.572000 0 SO:0001819 synonymous_variant ENST00000322644.6 1 1 hg19 CCDS32548.1 TCGA-YY-A8LH-01A-11D-A36O-08 POLR2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437967.1 1 0 1 113 761 0 429 1 1 59 253 0 429 2 0 0 0 0 0 2 1 1.000000 109 739 0 423 2 0 0 0 0 429 2 -20.000000 1 1 0 0 1 0 2 2 1.436748 1 0.550000 3.730000 0.550000 0.460000 3.800000e-01 0.550000 0.470000 0.472772 0.460000 0 4.200000e-01 0.510000 ARHGEF15 22899 broad.mit.edu 37 17 8216367 8216367 + Silent SNP G G A rs150417950 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr17:8216367G>A ENST00000361926.3 + 3 839 c.729G>A c.(727-729)ccG>ccA p.P243P ARHGEF15_ENST00000421050.1_Silent_p.P243P NM_173728.3 NP_776089.2 O94989 ARHGF_HUMAN Rho guanine nucleotide exchange factor (GEF) 15 37 GGGCCTCCCCGCTGCGGACCT 0.697000 0 SO:0001819 synonymous_variant ENST00000361926.3 1 1 hg19 CCDS11139.1 TCGA-YY-A8LH-01A-11D-A36O-08 ARHGEF15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000226993.2 0 0 0 12 271 0 137 0 6.465165e-03 0 3 0 137 2 0 0 0 0 0 2 1 0.999055 12 265 0 132 2 0 0 0 0 137 2 -3.273029 1 1 121406 1 33 1 0 2 2 1.436748 1 0.550000 3.730000 0.550000 0.150000 8.000000e-02 0.260000 0.160000 0.165375 0.150000 0 1.100000e-01 0.210000 LAMA3 3909 broad.mit.edu 37 18 21355821 21355821 + Missense_Mutation SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr18:21355821C>G ENST00000313654.9 + 10 1580 c.1339C>G c.(1339-1341)Cca>Gca p.P447A LAMA3_ENST00000399516.3_Missense_Mutation_p.P447A NM_198129.1 NP_937762.1 Q16787 LAMA3_HUMAN laminin, alpha 3 128 all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17) TCACTGCAAGCCAAATTTCCA 0.498000 0 SO:0001583 missense ENST00000313654.9 0 1 hg19 CCDS42419.1 . . . . . . . . . . C 7.523 0.657060 0.14580 . . ENSG00000053747 ENST00000313654;ENST00000399516;ENST00000416669;ENST00000538801 T;T 0.62105 0.05;0.05 4.76 1.88 0.25563 EGF-like, laminin (4);EGF-like region, conserved site (1); . . . . T 0.53158 0.1779 L 0.58510 1.815 0.48288 D 0.99962 B;B;B 0.34399 0.452;0.216;0.064 B;B;B 0.36567 0.228;0.069;0.069 T 0.37596 -0.9699 9 0.18710 T 0.47 . 7.7107 0.28675 0.0:0.7066:0.1346:0.1588 . 447;447;447 F5H8G3;Q6VU67;Q16787 .;.;LAMA3_HUMAN A 447;447;445;447 ENSP00000324532:P447A;ENSP00000382432:P447A ENSP00000324532:P447A P + 1 0 LAMA3 19609819 0.034000 0.19679 0.358000 0.25811 0.709000 0.40893 0.580000 0.23803 0.603000 0.29913 -0.186000 0.12905 CCA TCGA-YY-A8LH-01A-11D-A36O-08 LAMA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254824.3 0 0 0 6 371 0 89 0 7.547252e-03 0 7 0 89 2 0 0 0 0 0 2 1 0.963808 6 366 0 89 2 0 0 0 0 89 2 -4.506028 1 1 0 0 1 3 3 6 2.191191 1 0.550000 3.730000 0.721535 0.110000 2.000000e-02 1.000000 0.090000 0.321365 0.110000 0 6.000000e-02 1.000000 TCEB3B 51224 broad.mit.edu 37 18 44559687 44559687 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr18:44559687G>A ENST00000332567.4 - 1 2301 c.1949C>T c.(1948-1950)aCg>aTg p.T650M KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron NM_016427.2 NP_057511.2 Q8IYF1 ELOA2_HUMAN transcription elongation factor B polypeptide 3B (elongin A2) 58 ATCATAAGGCGTCTTGGCCAC 0.537000 0 SO:0001583 missense ENST00000332567.4 1 1 hg19 CCDS11932.1 . . . . . . . . . . G 10.28 1.307100 0.23821 . . ENSG00000206181 ENST00000332567 T 0.07216 3.21 1.4 -0.709 0.11237 . 0.754074 0.11156 U 0.593616 T 0.16471 0.0396 L 0.44542 1.39 0.09310 N 1 D 0.71674 0.998 D 0.71414 0.973 T 0.15636 -1.0430 10 0.62326 D 0.03 -1.8221 6.9376 0.24474 0.0:0.5733:0.4267:0.0 . 650 Q8IYF1 ELOA2_HUMAN M 650 ENSP00000331302:T650M ENSP00000331302:T650M T - 2 0 TCEB3B 42813685 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 0.276000 0.18716 -0.250000 0.09555 -0.222000 0.12452 ACG TCGA-YY-A8LH-01A-11D-A36O-08 TCEB3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255900.1 1 0 1 261 598 0 280 0 0 0 0 280 2 0 0 0 0 0 2 1 1.000000 259 585 0 279 2 0 0 0 0 280 2 -20.000000 1 1 0 0 1 3 4 7 2.256128 1 0.550000 3.730000 0.728916 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 ZNF709 163051 broad.mit.edu 37 19 12575884 12575884 + Silent SNP T T C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:12575884T>C ENST00000397732.3 - 4 1023 c.852A>G c.(850-852)caA>caG p.Q284Q ZNF709_ENST00000428311.1_Silent_p.Q284Q|CTD-3105H18.18_ENST00000598753.1_Intron NM_152601.3 NP_689814.1 Q8N972 ZN709_HUMAN zinc finger protein 709 6 CTTTACCACATTGCTTACACT 0.373000 GBM(33;565 669 12371 29134 51667) 0 SO:0001819 synonymous_variant ENST00000397732.3 1 1 hg19 CCDS42504.1 TCGA-YY-A8LH-01A-11D-A36O-08 ZNF709-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344088.1 1 0 0 142 268 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 140 266 0 104 2 0 0 0 0 108 2 -20.000000 1 1 121280 1 35 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 FARSA 2193 broad.mit.edu 37 19 13039582 13039582 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:13039582C>T ENST00000314606.4 - 5 601 c.583G>A c.(583-585)Gag>Aag p.E195K FARSA_ENST00000588025.1_Missense_Mutation_p.E235K|CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000423140.2_Intron NM_004461.2 NP_004452.1 Q9Y285 SYFA_HUMAN phenylalanyl-tRNA synthetase, alpha subunit 20 L-Phenylalanine(DB00120) GAGATCATCTCTGGGCTCAGC 0.627000 0 SO:0001583 missense ENST00000314606.4 1 1 hg19 CCDS12287.1 . . . . . . . . . . C 24.3 4.517058 0.85495 . . ENSG00000179115 ENST00000314606 T 0.68903 -0.36 4.94 4.94 0.65067 . 0.000000 0.85682 D 0.000000 D 0.82342 0.5016 M 0.91872 3.25 0.80722 D 1 D;D 0.57571 0.98;0.98 P;P 0.55222 0.771;0.771 D 0.87035 0.2137 10 0.87932 D 0 -15.1624 17.0788 0.86593 0.0:1.0:0.0:0.0 . 195;195 Q6IBR2;Q9Y285 .;SYFA_HUMAN K 195 ENSP00000320309:E195K ENSP00000320309:E195K E - 1 0 FARSA 12900582 1.000000 0.71417 1.000000 0.80357 0.944000 0.59088 6.952000 0.75989 2.563000 0.86464 0.563000 0.77884 GAG TCGA-YY-A8LH-01A-11D-A36O-08 FARSA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451935.1 1 0 1 61 231 0 91 1 1 80 135 0 91 2 0 0 0 0 0 2 1 1.000000 61 228 0 91 2 0 0 0 0 91 2 -3.497112 1 1 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.990000 9.200000e-01 1.000000 1.000000 0.995726 0.990000 1 9.900000e-01 1.000000 ZNF208 7757 broad.mit.edu 37 19 22171676 22171676 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:22171676G>T ENST00000397126.4 - 2 187 c.39C>A c.(37-39)ttC>ttA p.F13L ZNF208_ENST00000601773.1_Missense_Mutation_p.F13L|ZNF208_ENST00000599916.1_Missense_Mutation_p.F13L|ZNF208_ENST00000597040.1_5'UTR NM_007153.3 NP_009084.2 O43345 ZN208_HUMAN zinc finger protein 208 113 all_lung(12;0.0961)|Lung NSC(12;0.103) CCTCCAGAGAGAATTCTATGG 0.408000 0 SO:0001583 missense ENST00000397126.4 1 1 hg19 CCDS54240.1 . . . . . . . . . . G 12.00 1.805557 0.31961 . . ENSG00000160321 ENST00000397126;ENST00000428290 T 0.12879 2.64 1.32 -0.37 0.12530 Krueppel-associated box (4); . . . . T 0.22742 0.0549 . . . 0.09310 N 1 D;B 0.57571 0.98;0.087 P;B 0.60012 0.867;0.084 T 0.12785 -1.0534 8 0.72032 D 0.01 . 3.7697 0.08636 0.0:0.0:0.5735:0.4265 . 13;13 O43345;F8WEA0 ZN208_HUMAN;. L 13 ENSP00000380315:F13L ENSP00000380315:F13L F - 3 2 ZNF208 21963516 0.005000 0.15991 0.009000 0.14445 0.601000 0.36947 -0.135000 0.10420 0.636000 0.30508 0.281000 0.19383 TTC TCGA-YY-A8LH-01A-11D-A36O-08 ZNF208-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464302.1 0 0 0 23 875 0 237 0 0 0 1 0 237 2 0 0 0 0 0 2 1 0.999998 23 791 0 235 2 0 0 0 0 237 2 -3.006749 1 1 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.140000 8.000000e-02 0.220000 0.160000 0.150196 0.140000 0 1.000000e-01 0.180000 ZNF555 148254 broad.mit.edu 37 19 2852530 2852530 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:2852530G>A ENST00000334241.4 + 4 605 c.467G>A c.(466-468)cGc>cAc p.R156H ZNF555_ENST00000591539.1_Missense_Mutation_p.R155H|AC006130.3_ENST00000589365.1_RNA NM_001172775.1|NM_152791.4 NP_001166246.1|NP_690004.4 Q8NEP9 ZN555_HUMAN zinc finger protein 555 23 ATGCATCGCCGCACATCCCTC 0.468000 0 SO:0001583 missense ENST00000334241.4 0 1 hg19 CCDS12096.1 . . . . . . . . . . G 7.901 0.734449 0.15574 . . ENSG00000186300 ENST00000334241;ENST00000382127 T 0.76448 -1.02 3.4 -6.8 0.01709 Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.54062 0.1835 N 0.20685 0.6 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.42965 -0.9420 9 0.12430 T 0.62 . 7.4147 0.27038 0.2247:0.2852:0.4901:0.0 . 156;155 Q8NEP9;A8KA89 ZN555_HUMAN;. H 156;155 ENSP00000334853:R156H ENSP00000334853:R156H R + 2 0 ZNF555 2803530 0.002000 0.14202 0.000000 0.03702 0.002000 0.02628 0.082000 0.14847 -1.664000 0.01479 -1.567000 0.00876 CGC TCGA-YY-A8LH-01A-11D-A36O-08 ZNF555-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000451637.3 0 0 0 5 380 0 91 0 3.971434e-03 1 5 0 91 2 0 0 0 0 0 2 1 0.936204 5 376 0 91 2 0 0 0 0 91 2 -2.200178 0 1 121412 2 36 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.070000 1.000000e-02 0.170000 0.080000 0.086682 0.070000 0 4.000000e-02 0.120000 ZNF536 9745 broad.mit.edu 37 19 30936183 30936183 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:30936183G>T ENST00000355537.3 + 2 1861 c.1714G>T c.(1714-1716)Gat>Tat p.D572Y NM_014717.1 NP_055532.1 O15090 ZN536_HUMAN zinc finger protein 536 182 Esophageal squamous(110;0.0834) AGTGGGAGCAGATGGCTCCAA 0.527000 0 SO:0001583 missense ENST00000355537.3 1 1 hg19 CCDS32984.1 . . . . . . . . . . G 12.56 1.973891 0.34848 . . ENSG00000198597 ENST00000355537 T 0.46819 0.86 5.53 5.53 0.82687 . 0.000000 0.85682 D 0.000000 T 0.60894 0.2304 L 0.47716 1.5 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.998 T 0.51450 -0.8704 10 0.08599 T 0.76 -22.8705 19.4573 0.94900 0.0:0.0:1.0:0.0 . 572;572 A7E228;O15090 .;ZN536_HUMAN Y 572 ENSP00000347730:D572Y ENSP00000347730:D572Y D + 1 0 ZNF536 35628023 1.000000 0.71417 1.000000 0.80357 0.930000 0.56654 9.435000 0.97529 2.582000 0.87167 0.655000 0.94253 GAT TCGA-YY-A8LH-01A-11D-A36O-08 ZNF536-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459667.2 1 0 0 30 326 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 30 320 0 106 2 0 0 0 0 108 2 -20.000000 1 1 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.470000 3.200000e-01 0.650000 0.480000 0.487515 0.470000 0 3.900000e-01 0.570000 ZNF585B 92285 broad.mit.edu 37 19 37677796 37677796 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:37677796C>T ENST00000532828.2 - 5 894 c.643G>A c.(643-645)Gaa>Aaa p.E215K ZNF585B_ENST00000531805.1_Missense_Mutation_p.E160K|ZNF585B_ENST00000312908.5_5'UTR|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_Silent_p.*158* NM_152279.3 NP_689492.3 Q52M93 Z585B_HUMAN zinc finger protein 585B 29 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) TCACTACATTCATATAGTTTT 0.388000 Melanoma(93;882 1454 18863 28917 48427) 0 SO:0001583 missense ENST00000532828.2 0 1 hg19 CCDS12500.1 . . . . . . . . . . C 0.207 -1.040081 0.02013 . . ENSG00000245680 ENST00000531805;ENST00000532828 T;T 0.19250 2.16;2.16 2.78 0.507 0.16967 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.683944 0.12041 N 0.505100 T 0.06280 0.0162 N 0.04148 -0.265 0.09310 N 0.999998 B;B 0.14438 0.006;0.01 B;B 0.12156 0.007;0.007 T 0.37267 -0.9713 10 0.08599 T 0.76 . 0.6148 0.00767 0.1968:0.3698:0.1925:0.2409 . 160;215 E9PQH3;Q52M93 .;Z585B_HUMAN K 160;215 ENSP00000436774:E160K;ENSP00000433773:E215K ENSP00000436774:E160K E - 1 0 ZNF585B 42369636 0.000000 0.05858 0.080000 0.20451 0.159000 0.22180 -2.725000 0.00808 0.069000 0.16605 -0.384000 0.06662 GAA TCGA-YY-A8LH-01A-11D-A36O-08 ZNF585B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388272.2 0 0 0 8 600 0 171 0 2.329209e-03 0 5 0 171 2 0 0 0 0 0 2 1 0.988851 8 592 0 171 2 0 0 0 0 171 2 -3.077771 1 1 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.070000 1.000000e-02 0.150000 0.080000 0.083343 0.070000 0 4.000000e-02 0.110000 RYR1 6261 broad.mit.edu 37 19 39070714 39070714 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:39070714G>A ENST00000359596.3 + 100 14457 c.14457G>A c.(14455-14457)atG>atA p.M4819I RYR1_ENST00000360985.3_Missense_Mutation_p.M4814I|RYR1_ENST00000355481.4_Missense_Mutation_p.M4814I P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 285 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786) ACATCGCCATGGGGGTCAAGA 0.597000 0 SO:0001583 missense ENST00000359596.3 0 1 hg19 CCDS33011.1 . . . . . . . . . . G 15.88 2.962210 0.53400 . . ENSG00000196218 ENST00000359596;ENST00000355481;ENST00000360985 D;D;D 0.98400 -4.91;-4.91;-4.91 4.57 4.57 0.56435 Ion transport (1); 0.000000 0.85682 U 0.000000 D 0.98040 0.9354 L 0.38953 1.18 0.58432 D 0.999997 D;D 0.54964 0.962;0.969 D;D 0.70227 0.946;0.968 D 0.98600 1.0658 10 0.46703 T 0.11 . 17.129 0.86722 0.0:0.0:1.0:0.0 . 4814;4819 P21817-2;P21817 .;RYR1_HUMAN I 4819;4814;4814 ENSP00000352608:M4819I;ENSP00000347667:M4814I;ENSP00000354254:M4814I ENSP00000347667:M4814I M + 3 0 RYR1 43762554 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.612000 0.98347 2.357000 0.79964 0.462000 0.41574 ATG TCGA-YY-A8LH-01A-11D-A36O-08 RYR1-010 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000462137.1 0 0 0 5 314 0 80 0 0 0 1 0 80 2 0 0 0 0 0 2 1 0.934858 5 308 0 80 2 0 0 0 0 80 2 -2.795017 1 1 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.090000 2.000000e-02 0.200000 0.080000 0.105002 0.090000 0 5.000000e-02 0.150000 PSG6 5675 broad.mit.edu 37 19 43411250 43411250 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:43411250G>A ENST00000292125.2 - 5 1108 c.1064C>T c.(1063-1065)gCg>gTg p.A355V PSG6_ENST00000187910.2_Missense_Mutation_p.A355V|PSG6_ENST00000402603.4_Missense_Mutation_p.A262V NM_002782.4 NP_002773.1 Q00889 PSG6_HUMAN pregnancy specific beta-1-glycoprotein 6 44 Prostate(69;0.00899) GTTAGAGTCCGCAAAGCAGGA 0.448000 0 SO:0001583 missense ENST00000292125.2 0 1 hg19 CCDS12613.1 . . . . . . . . . . N 9.184 1.024244 0.19433 . . ENSG00000170848 ENST00000187910;ENST00000402603;ENST00000292125 T;T;T 0.14144 2.53;2.53;2.53 1.54 1.54 0.23209 Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1); . . . . T 0.13500 0.0327 L 0.50847 1.595 0.09310 N 0.999998 B;B;B 0.34372 0.132;0.292;0.451 B;B;B 0.36244 0.184;0.22;0.185 T 0.20840 -1.0263 9 0.59425 D 0.04 . 6.5495 0.22425 0.0:0.0:1.0:0.0 . 355;355;262 Q00889;Q00889-2;B5MCE1 PSG6_HUMAN;.;. V 355;262;355 ENSP00000187910:A355V;ENSP00000385736:A262V;ENSP00000292125:A355V ENSP00000187910:A355V A - 2 0 PSG6 48103090 0.001000 0.12720 0.002000 0.10522 0.014000 0.08584 0.729000 0.26028 0.854000 0.35336 0.134000 0.15878 GCG TCGA-YY-A8LH-01A-11D-A36O-08 PSG6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321436.1 0 0 0 8 1085 0 307 0 0 0 0 307 2 0 0 0 0 0 2 1 0.988613 7 1068 0 305 2 0 0 0 0 307 2 -1.713217 0 1 121350 3 44 1 3 3 6 2.212610 1 0.550000 3.730000 0.725275 0.040000 0 1.000000 0.040000 0.271785 0.040000 0 2.000000e-02 1.000000 GPR4 2828 broad.mit.edu 37 19 46094142 46094142 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:46094142G>T ENST00000323040.4 - 2 1927 c.983C>A c.(982-984)aCc>aAc p.T328N GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron NM_005282.2 NP_005273.1 P46093 GPR4_HUMAN G protein-coupled receptor 4 23 CCTCTTGGAGGTGAGTGGGGT 0.652000 Esophageal Squamous(117;181 1612 1673 14956 42937) 0 SO:0001583 missense ENST00000323040.4 1 1 hg19 CCDS12669.1 . . . . . . . . . . G 14.90 2.674372 0.47781 . . ENSG00000177464 ENST00000323040 T 0.61742 0.08 4.53 4.53 0.55603 . 0.190762 0.35378 N 0.003255 T 0.32133 0.0819 N 0.08118 0 0.30785 N 0.741534 B 0.34103 0.437 B 0.27500 0.08 T 0.28870 -1.0030 10 0.19147 T 0.46 . 12.6317 0.56661 0.0:0.0:1.0:0.0 . 328 P46093 GPR4_HUMAN N 328 ENSP00000319744:T328N ENSP00000319744:T328N T - 2 0 GPR4 50785982 0.977000 0.34250 0.425000 0.26659 0.971000 0.66376 6.583000 0.74053 2.356000 0.79943 0.455000 0.32223 ACC TCGA-YY-A8LH-01A-11D-A36O-08 GPR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459603.1 0 0 0 13 552 0 119 0 7.432037e-02 0 18 0 119 2 0 0 0 0 0 2 1 0.999494 13 544 0 118 2 0 0 0 0 119 2 -3.414721 1 1 0 0 1 3 6 9 2.722969 1 0.550000 3.730000 0.775112 0.190000 8.000000e-02 1.000000 0.170000 0.378109 0.190000 0 1.300000e-01 1.000000 NANOS2 339345 broad.mit.edu 37 19 46417571 46417571 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:46417571G>A ENST00000341294.2 - 1 465 c.381C>T c.(379-381)agC>agT p.S127S NM_001029861.2 NP_001025032.1 P60321 NANO2_HUMAN nanos homolog 2 (Drosophila) 6 Ovarian(192;0.0308)|all_neural(266;0.0476) AGTTGCGCCCGCTGCGGCGGT 0.667000 0 SO:0001819 synonymous_variant ENST00000341294.2 1 1 hg19 CCDS33056.1 TCGA-YY-A8LH-01A-11D-A36O-08 NANOS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461685.1 1 0 0 12 152 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.999137 11 150 0 34 2 0 0 0 0 34 2 -16.511560 1 1 0 0 1 3 6 9 2.722969 1 0.550000 3.730000 0.775112 0.610000 3.100000e-01 1.000000 0.520000 0.672828 0.610000 0 4.300000e-01 1.000000 ZNF350 59348 broad.mit.edu 37 19 52469393 52469393 + Nonsense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:52469393C>A ENST00000243644.4 - 5 540 c.313G>T c.(313-315)Gaa>Taa p.E105* HCCAT3_ENST00000600253.1_RNA|HCCAT3_ENST00000595010.1_RNA|ZNF350_ENST00000600703.1_5'Flank NM_021632.3 NP_067645.3 Q9GZX5 ZN350_HUMAN zinc finger protein 350 26 all_neural(266;0.0505) GCATCATGTTCATGACATGGT 0.363000 0 SO:0001587 stop_gained ENST00000243644.4 0 1 hg19 CCDS12845.1 . . . . . . . . . . C 16.19 3.054148 0.55218 . . ENSG00000256683 ENST00000243644 . . . 3.25 -3.54 0.04653 . 0.733993 0.11162 N 0.592957 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.18710 T 0.47 . 4.1621 0.10289 0.0:0.3024:0.19:0.5075 . . . . X 105 . ENSP00000243644:E105X E - 1 0 ZNF350 57161205 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -0.533000 0.06157 -0.395000 0.07715 -0.142000 0.14014 GAA TCGA-YY-A8LH-01A-11D-A36O-08 ZNF350-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462278.1 0 0 0 8 541 0 131 0 1.706219e-02 0 12 0 131 2 0 0 0 0 0 2 1 0.988890 7 536 0 130 2 0 0 0 0 131 2 -2.781414 1 1 0 0 1 2 2 4 2.155460 1 0.550000 3.730000 0.709677 0.080000 2.000000e-02 0.160000 0.080000 0.092338 0.080000 0 5.000000e-02 0.130000 PPP2R1A 5518 broad.mit.edu 37 19 52714630 52714630 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:52714630C>T ENST00000322088.6 + 4 446 c.388C>T c.(388-390)Ccg>Tcg p.P130S PPP2R1A_ENST00000462990.1_5'UTR|PPP2R1A_ENST00000473455.2_3'UTR|PPP2R1A_ENST00000444322.2_Missense_Mutation_p.P75S NM_014225.5 NP_055040.2 P30153 2AAA_HUMAN protein phosphatase 2, regulatory subunit A, alpha 135 GCACTTTGTGCCGCTAGTGAA 0.657000 Mis clear cell ovarian carcinoma Dom? yes 19 19q13.41 5518 protein phosphatase 2, regulatory subunit A, alpha E 0 SO:0001583 missense ENST00000322088.6 0 1 hg19 CCDS12849.1 . . . . . . . . . . C 14.74 2.624587 0.46840 . . ENSG00000105568 ENST00000423369;ENST00000322088;ENST00000444322 T;T 0.35973 1.28;1.28 4.46 4.46 0.54185 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.64402 D 0.000011 T 0.43897 0.1268 M 0.85373 2.75 0.58432 D 0.999999 P;P;P 0.37233 0.493;0.588;0.588 B;B;B 0.34301 0.179;0.102;0.102 T 0.56757 -0.7926 10 0.66056 D 0.02 -36.5931 15.0187 0.71609 0.0:1.0:0.0:0.0 . 75;130;130 F5H3X9;A8K7B7;P30153 .;.;2AAA_HUMAN S 120;130;75 ENSP00000324804:P130S;ENSP00000415067:P75S ENSP00000324804:P130S P + 1 0 PPP2R1A 57406442 1.000000 0.71417 0.994000 0.49952 0.038000 0.13279 6.787000 0.75099 2.482000 0.83794 0.655000 0.94253 CCG TCGA-YY-A8LH-01A-11D-A36O-08 PPP2R1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000267967.2 0 0 0 5 420 1 110 0 2.656785e-02 0 414 1 110 14 0 0 0 0 0 2 1 0.911943 5 365 0 80 2 0 0 0 1 110 2 -2.559621 1 1 0 0 1 2 2 4 2.155460 1 0.550000 3.730000 0.709677 0.070000 1.000000e-02 0.150000 0.080000 0.078196 0.070000 0 3.000000e-02 0.110000 RPL36 25873 broad.mit.edu 37 19 5691442 5691442 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:5691442C>T ENST00000577222.1 + 5 750 c.206C>T c.(205-207)gCc>gTc p.A69V RPL36_ENST00000579649.1_Missense_Mutation_p.A69V|RPL36_ENST00000394580.2_Missense_Mutation_p.A69V|RPL36_ENST00000579446.1_Missense_Mutation_p.A69V|RPL36_ENST00000347512.3_Missense_Mutation_p.A69V Q9Y3U8 RL36_HUMAN ribosomal protein L36 2 GACAAACGGGCCCTCAAATTT 0.642000 OREG0025183 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000577222.1 0 1 hg19 CCDS12147.1 . . . . . . . . . . C 22.6 4.311575 0.81358 . . ENSG00000130255 ENST00000347512;ENST00000394580 T;T 0.60920 0.15;0.15 4.21 4.21 0.49690 . 0.000000 0.85682 U 0.000000 T 0.77850 0.4192 H 0.95574 3.69 0.80722 D 1 P 0.48503 0.911 P 0.53360 0.724 D 0.85194 0.1011 10 0.72032 D 0.01 . 14.0553 0.64764 0.0:1.0:0.0:0.0 . 69 Q9Y3U8 RL36_HUMAN V 69 ENSP00000252543:A69V;ENSP00000378081:A69V ENSP00000252543:A69V A + 2 0 RPL36 5642442 1.000000 0.71417 0.959000 0.39883 0.303000 0.27691 7.568000 0.82369 1.881000 0.54492 0.467000 0.42956 GCC TCGA-YY-A8LH-01A-11D-A36O-08 RPL36-001 KNOWN alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000442561.1 0 0 0 7 383 0 106 1 1 85 6342 0 106 2 0 0 0 0 0 2 1 0.979350 7 376 0 105 2 0 0 0 0 106 2 -3.075512 1 0 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.100000 3.000000e-02 0.200000 0.110000 0.115033 0.100000 0 6.000000e-02 0.160000 MUC16 94025 broad.mit.edu 37 19 9058858 9058858 + Missense_Mutation SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr19:9058858C>G ENST00000397910.4 - 3 28791 c.28588G>C c.(28588-28590)Gag>Cag p.E9530Q NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TAGAGTTCCTCTGTAGCACTG 0.483000 0 SO:0001583 missense ENST00000397910.4 1 1 hg19 CCDS54212.1 . . . . . . . . . . c 5.207 0.223796 0.09863 . . ENSG00000181143 ENST00000397910 T 0.21734 1.99 2.3 -0.0756 0.13726 . . . . . T 0.10465 0.0256 N 0.08118 0 . . . B 0.16603 0.018 B 0.17979 0.02 T 0.16748 -1.0392 8 0.87932 D 0 . 8.0918 0.30805 0.0:0.5336:0.4664:0.0 . 9530 B5ME49 . Q 9530 ENSP00000381008:E9530Q ENSP00000381008:E9530Q E - 1 0 MUC16 8919858 0.000000 0.05858 0.000000 0.03702 0.064000 0.16182 -0.149000 0.10204 0.072000 0.16694 0.305000 0.20034 GAG TCGA-YY-A8LH-01A-11D-A36O-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 0 0 0 12 348 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 0.999108 11 346 0 95 2 0 0 0 0 95 2 -2.928019 1 1 0 0 1 2 2 4 2.124233 1 0.550000 3.730000 0.709677 0.190000 9.000000e-02 0.320000 0.200000 0.202186 0.190000 0 1.400000e-01 0.260000 COL11A1 1301 broad.mit.edu 37 1 103427802 103427802 + Missense_Mutation SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:103427802C>G ENST00000370096.3 - 40 3356 c.3044G>C c.(3043-3045)gGt>gCt p.G1015A COL11A1_ENST00000512756.1_Missense_Mutation_p.G899A|COL11A1_ENST00000358392.2_Missense_Mutation_p.G1027A|COL11A1_ENST00000353414.4_Missense_Mutation_p.G976A NM_001854.3 NP_001845.3 P12107 COBA1_HUMAN collagen, type XI, alpha 1 258 all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181) CCCTGAGATACCTTGAGGACC 0.383000 0 SO:0001583 missense ENST00000370096.3 1 1 hg19 CCDS778.1 . . . . . . . . . . C 19.41 3.822094 0.71028 . . ENSG00000060718 ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756 D;D;D;D 0.99607 -6.27;-6.27;-6.27;-6.27 5.37 5.37 0.77165 . 0.061018 0.64402 D 0.000003 D 0.99753 0.9901 M 0.92880 3.355 0.80722 D 1 D;D;D;D;D 0.76494 0.999;0.999;0.999;0.999;0.999 D;D;D;D;D 0.87578 0.997;0.998;0.998;0.995;0.994 D 0.97603 1.0124 10 0.59425 D 0.04 . 19.1062 0.93296 0.0:1.0:0.0:0.0 . 899;976;1027;1015;235 E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5 .;.;.;COBA1_HUMAN;. A 1015;1027;976;235;899 ENSP00000359114:G1015A;ENSP00000351163:G1027A;ENSP00000302551:G976A;ENSP00000426533:G899A ENSP00000302551:G976A G - 2 0 COL11A1 103200390 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.404000 0.79996 2.509000 0.84616 0.557000 0.71058 GGT TCGA-YY-A8LH-01A-11D-A36O-08 COL11A1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000029997.1 1 0 1 98 225 0 94 0 5.880410e-01 0 6 0 94 2 0 0 0 0 0 2 1 1.000000 98 221 0 94 2 0 0 0 0 94 2 -20.000000 1 1 0 0 1 0 4 4 1.660921 1 0.550000 3.730000 0.631148 0.990000 9.900000e-01 1.000000 1.000000 0.999988 0.990000 1 9.900000e-01 1.000000 PSMB4 5692 broad.mit.edu 37 1 151372581 151372581 + Nonsense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:151372581C>T ENST00000290541.6 + 2 319 c.265C>T c.(265-267)Cga>Tga p.R89* NM_002796.2 NP_002787.2 P28070 PSB4_HUMAN proteasome (prosome, macropain) subunit, beta type, 4 14 Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) TCGCATTATGCGAGTCAACAA 0.537000 0 SO:0001587 stop_gained ENST00000290541.6 0 1 hg19 CCDS996.1 . . . . . . . . . . C 23.8 4.459609 0.84317 . . ENSG00000159377 ENST00000290541 . . . 5.34 2.32 0.28847 . 0.261003 0.36703 N 0.002445 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.24483 T 0.36 -0.0211 13.7733 0.63038 0.6506:0.3494:0.0:0.0 . . . . X 89 . ENSP00000290541:R89X R + 1 2 PSMB4 149639205 0.998000 0.40836 0.954000 0.39281 0.610000 0.37248 0.845000 0.27668 0.197000 0.20387 -0.314000 0.08810 CGA TCGA-YY-A8LH-01A-11D-A36O-08 PSMB4-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034885.1 0 0 0 7 1111 0 263 1 9.915177e-01 3 1382 0 263 2 0 0 0 0 0 2 1 0.979696 7 1097 0 260 2 0 0 0 0 263 2 -1.724933 0 0 0 0 1 3 5 8 2.670671 1 0.550000 3.730000 0.773869 0.060000 0 1.000000 0.060000 0.276291 0.060000 0 3.000000e-02 1.000000 GATAD2B 57459 broad.mit.edu 37 1 153789912 153789912 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:153789912G>A ENST00000368655.4 - 6 1079 c.836C>T c.(835-837)cCg>cTg p.P279L NM_020699.2 NP_065750.1 Q8WXI9 P66B_HUMAN GATA zinc finger domain containing 2B 38 all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) AGGCTTAGGCGGGCCCCGCTG 0.527000 0 SO:0001583 missense ENST00000368655.4 1 1 hg19 CCDS1054.1 . . . . . . . . . . G 13.60 2.284508 0.40394 . . ENSG00000143614 ENST00000368655 T 0.35605 1.3 5.87 5.87 0.94306 . 0.054498 0.85682 D 0.000000 T 0.19248 0.0462 L 0.38175 1.15 0.80722 D 1 D 0.53619 0.961 B 0.36989 0.238 T 0.02126 -1.1209 10 0.40728 T 0.16 -4.5218 19.3531 0.94398 0.0:0.0:1.0:0.0 . 279 Q8WXI9 P66B_HUMAN L 279 ENSP00000357644:P279L ENSP00000357644:P279L P - 2 0 GATAD2B 152056536 1.000000 0.71417 0.931000 0.37212 0.149000 0.21700 6.016000 0.70798 2.941000 0.99782 0.655000 0.94253 CCG TCGA-YY-A8LH-01A-11D-A36O-08 GATAD2B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090305.1 1 0 1 103 284 0 79 1 6.720691e-01 2 6 0 79 2 0 0 0 0 0 2 1 1.000000 100 279 0 79 2 0 0 0 0 79 2 -6.151129 1 1 121412 6 39 1 3 5 8 2.670671 1 0.550000 3.730000 0.773869 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 ADAR 103 broad.mit.edu 37 1 154569625 154569625 + Missense_Mutation SNP T T C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:154569625T>C ENST00000368474.4 - 5 2252 c.2053A>G c.(2053-2055)Acc>Gcc p.T685A ADAR_ENST00000368471.3_Missense_Mutation_p.T390A|ADAR_ENST00000292205.5_Missense_Mutation_p.T728A NM_001111.4|NM_015840.3|NM_015841.3 NP_001102|NP_056655.2|NP_056656.2 P55265 DSRAD_HUMAN adenosine deaminase, RNA-specific 51 all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997) LUSC - Lung squamous cell carcinoma(543;0.185) ATGGAGTTGGTCGCCTCCCCA 0.522000 0 SO:0001583 missense ENST00000368474.4 0 1 hg19 CCDS1071.1 . . . . . . . . . . T 4.071 0.011032 0.07912 . . ENSG00000160710 ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168 T;T;T;T 0.14022 2.74;2.75;2.54;2.76 5.43 -3.95 0.04118 . 0.826008 0.10923 N 0.619176 T 0.01222 0.0040 N 0.08118 0 0.09310 N 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.06405 0.002;0.002;0.001 T 0.47837 -0.9086 10 0.06625 T 0.88 -5.3793 9.0032 0.36094 0.1254:0.5779:0.0:0.2967 . 685;685;685 P55265-3;P55265-2;P55265 .;.;DSRAD_HUMAN A 728;685;390;680 ENSP00000292205:T728A;ENSP00000357459:T685A;ENSP00000357456:T390A;ENSP00000431794:T680A ENSP00000292205:T728A T - 1 0 ADAR 152836249 0.001000 0.12720 0.000000 0.03702 0.428000 0.31595 0.036000 0.13819 -0.609000 0.05724 0.533000 0.62120 ACC TCGA-YY-A8LH-01A-11D-A36O-08 ADAR-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000090691.2 0 0 0 6 327 0 94 1 8.938192e-01 5 215 0 94 2 0 0 0 0 0 2 1 0.964349 6 324 0 94 2 0 0 0 0 94 2 -6.781585 1 1 0 0 1 3 5 8 2.670671 1 0.550000 3.730000 0.773869 0.160000 4.000000e-02 1.000000 0.120000 0.348384 0.160000 0 9.000000e-02 1.000000 LMNA 4000 broad.mit.edu 37 1 156105808 156105808 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:156105808G>A ENST00000368300.4 + 6 1265 c.1053G>A c.(1051-1053)agG>agA p.R351R LMNA_ENST00000368299.3_Silent_p.R351R|LMNA_ENST00000448611.2_Silent_p.R239R|LMNA_ENST00000392353.3_Silent_p.R270R|LMNA_ENST00000368297.1_Silent_p.R270R|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368301.2_Silent_p.R351R|LMNA_ENST00000473598.2_Silent_p.R252R|LMNA_ENST00000361308.4_Silent_p.R351R|LMNA_ENST00000347559.2_Silent_p.R351R NM_170707.3 NP_733821.1 P02545 LMNA_HUMAN lamin A/C 10 Hepatocellular(266;0.158) TGCGGGCAAGGATGCAGCAGC 0.647000 Werner syndrome;Hutchinson-Gilford Progeria Syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database WS, Adult Progeria;HGPS, Progeria ENST00000368300.4 1 0 hg19 CCDS1129.1 TCGA-YY-A8LH-01A-11D-A36O-08 LMNA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039200.2 1 0 0 12 232 0 74 1 1 98 1725 0 74 2 0 0 0 0 0 2 1 0.999026 12 225 0 73 2 0 0 0 0 74 2 -14.306460 1 1 0 0 1 3 5 8 2.670671 1 0.550000 3.730000 0.773869 0.410000 2.000000e-01 1.000000 0.340000 0.525588 0.410000 0 2.800000e-01 1.000000 INSRR 3645 broad.mit.edu 37 1 156824033 156824033 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:156824033C>T ENST00000368195.3 - 2 544 c.148G>A c.(148-150)Gtg>Atg p.V50M NTRK1_ENST00000392302.2_Intron NM_014215.2 NP_055030.1 P14616 INSRR_HUMAN insulin receptor-related receptor 42 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) CCCTCCACCACGCTGCAGTTC 0.627000 0 SO:0001583 missense ENST00000368195.3 1 1 hg19 CCDS1160.1 . . . . . . . . . . C 17.68 3.450024 0.63290 . . ENSG00000027644 ENST00000368195 D 0.82081 -1.57 5.06 4.15 0.48705 EGF receptor, L domain (1); 0.000000 0.41294 D 0.000916 D 0.87939 0.6304 . . . 0.48341 D 0.999632 D 0.89917 1.0 D 0.81914 0.995 D 0.89318 0.3638 9 0.72032 D 0.01 . 11.4951 0.50404 0.0:0.9113:0.0:0.0887 . 50 P14616 INSRR_HUMAN M 50 ENSP00000357178:V50M ENSP00000357178:V50M V - 1 0 INSRR 155090657 0.646000 0.27295 0.893000 0.35052 0.832000 0.47134 1.287000 0.33284 1.146000 0.42352 -0.252000 0.11476 GTG TCGA-YY-A8LH-01A-11D-A36O-08 INSRR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000098929.1 1 0 1 69 111 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 1.000000 69 109 0 42 2 0 0 0 0 42 2 -20.000000 1 1 121410 15 40 1 3 5 8 2.670671 1 0.550000 3.730000 0.773869 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 CLCNKA 1187 broad.mit.edu 37 1 16353850 16353850 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:16353850G>A ENST00000331433.4 + 8 720 c.701G>A c.(700-702)cGg>cAg p.R234Q CLCNKA_ENST00000420078.1_Missense_Mutation_p.R234Q|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R234Q|CLCNKA_ENST00000439316.2_Missense_Mutation_p.R191Q P51800 CLCKA_HUMAN chloride channel, voltage-sensitive Ka 19 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) Niflumic Acid(DB04552) TTCTCTGTCCGGGATTACTGG 0.637000 0 SO:0001583 missense ENST00000331433.4 0 1 hg19 CCDS167.1 . . . . . . . . . . G 17.47 3.397759 0.62177 . . ENSG00000186510 ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433 D;D;D;D 0.94758 -3.51;-3.51;-3.51;-3.51 3.02 3.02 0.34903 Chloride channel, core (2); 0.189554 0.45606 D 0.000349 D 0.94212 0.8142 M 0.68728 2.09 0.28863 N 0.895394 B;P;B 0.39480 0.364;0.675;0.364 B;P;B 0.46026 0.342;0.501;0.342 D 0.90856 0.4735 10 0.51188 T 0.08 . 13.4842 0.61355 0.0:0.0:1.0:0.0 . 191;234;234 E7EPH6;Q5T5Q4;P51800 .;.;CLCKA_HUMAN Q 234;234;191;234 ENSP00000364844:R234Q;ENSP00000410353:R234Q;ENSP00000414445:R191Q;ENSP00000332771:R234Q ENSP00000332771:R234Q R + 2 0 CLCNKA 16226437 1.000000 0.71417 1.000000 0.80357 0.945000 0.59286 5.291000 0.65667 1.674000 0.50907 0.313000 0.20887 CGG TCGA-YY-A8LH-01A-11D-A36O-08 CLCNKA-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000026326.1 0 0 0 12 593 0 215 0 0 0 1 0 215 2 0 0 0 0 0 2 1 0.998940 12 574 0 212 2 0 0 0 0 215 2 -2.080577 0 1 0 0 1 0 6 6 1.806204 1 0.550000 3.730000 0.661654 0.100000 4.000000e-02 1.000000 0.100000 0.284638 0.100000 0 7.000000e-02 1.000000 F5 2153 broad.mit.edu 37 1 169519117 169519117 + Missense_Mutation SNP G G C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:169519117G>C ENST00000367797.3 - 10 1734 c.1533C>G c.(1531-1533)atC>atG p.I511M F5_ENST00000367796.3_Missense_Mutation_p.I511M|F5_ENST00000546081.1_3'UTR NM_000130.4 NP_000121 P12259 FA5_HUMAN coagulation factor V (proaccelerin, labile factor) 128 all_hematologic(923;0.208) ART-123(DB05777)|Drotrecogin alfa(DB00055) TGTCTCTCATGATGTCCACGT 0.433000 0 SO:0001583 missense ENST00000367797.3 0 1 hg19 CCDS1281.1 . . . . . . . . . . G 9.285 1.049094 0.19827 . . ENSG00000198734 ENST00000367797;ENST00000367796 D;D 0.98602 -5.02;-5.02 5.71 0.262 0.15597 Cupredoxin (2); 0.596635 0.18720 N 0.133041 D 0.85600 0.5734 N 0.11064 0.09 0.25005 N 0.991444 B 0.26195 0.144 B 0.18263 0.021 T 0.74819 -0.3535 9 0.15066 T 0.55 -0.6017 7.1569 0.25643 0.2659:0.4684:0.2657:0.0 . 511 P12259 FA5_HUMAN M 511 ENSP00000356771:I511M;ENSP00000356770:I511M ENSP00000356770:I511M I - 3 3 F5 167785741 0.072000 0.21174 0.226000 0.23910 0.924000 0.55760 -0.367000 0.07553 0.060000 0.16281 -0.175000 0.13238 ATC TCGA-YY-A8LH-01A-11D-A36O-08 F5-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000083712.1 0 0 0 8 479 0 102 0 3.654612e-02 0 16 0 102 2 0 0 0 0 0 2 1 0.988842 8 472 0 100 2 0 0 0 0 102 2 -3.240787 1 1 0 0 1 3 6 9 2.666250 1 0.550000 3.730000 0.770701 0.140000 4.000000e-02 1.000000 0.110000 0.342269 0.140000 0 8.000000e-02 1.000000 MRPS14 63931 broad.mit.edu 37 1 174983906 174983906 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:174983906G>A ENST00000476371.1 - 3 302 c.286C>T c.(286-288)Cgt>Tgt p.R96C MRPS14_ENST00000498253.1_5'UTR NM_022100.2 NP_071383.1 mitochondrial ribosomal protein S14 p.R96S(1) 10 CCACGCGGACGGGACGTCATA 0.522000 1 Substitution - Missense(1) SO:0001583 missense ENST00000476371.1 0 1 hg19 CCDS1316.1 . . . . . . . . . . G 28.2 4.899841 0.91962 . . ENSG00000120333 ENST00000476371 . . . 6.07 6.07 0.98685 . 0.000000 0.85682 D 0.000000 D 0.91653 0.7362 H 0.98738 4.315 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.94083 0.7346 9 0.87932 D 0 -16.0916 20.6593 0.99626 0.0:0.0:1.0:0.0 . 96 O60783 RT14_HUMAN C 96 . ENSP00000420714:R96C R - 1 0 MRPS14 173250529 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 6.365000 0.73090 2.885000 0.99019 0.655000 0.94253 CGT TCGA-YY-A8LH-01A-11D-A36O-08 MRPS14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084416.2 0 0 0 9 540 1 133 0 8.914797e-02 4 187 1 133 7 0 0 0 0 0 2 0 0.134414 8 526 1 130 15 0 0 0 1 133 2 -1.977340 0 1 0 0 1 3 6 9 2.666250 1 0.550000 3.730000 0.770701 0.140000 4.000000e-02 1.000000 0.110000 0.341029 0.140000 0 8.000000e-02 1.000000 CFHR1 3078 broad.mit.edu 37 1 196797211 196797211 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:196797211G>T ENST00000320493.5 + 4 530 c.442G>T c.(442-444)Gtg>Ttg p.V148L CFHR1_ENST00000367424.4_Intron|CFHR2_ENST00000367421.3_Intron NM_002113.2 NP_002104.2 Q03591 FHR1_HUMAN complement factor H-related 1 11 CACTTCCTGTGTGAATCCGCC 0.383000 0 SO:0001583 missense ENST00000320493.5 0 1 hg19 CCDS1386.1 . . . . . . . . . . . 6.008 0.369878 0.11352 . . ENSG00000244414 ENST00000320493 T 0.64260 -0.09 2.89 1.95 0.26073 Complement control module (2);Sushi/SCR/CCP (3); . . . . T 0.55561 0.1928 L 0.37466 1.105 0.80722 D 1 B;D 0.54047 0.387;0.964 B;P 0.52554 0.326;0.702 T 0.47995 -0.9073 9 0.28530 T 0.3 . 6.0102 0.19571 0.1541:0.0:0.8459:0.0 . 148;1049 Q03591;A8K5T0 FHR1_HUMAN;. L 148 ENSP00000314299:V148L ENSP00000314299:V148L V + 1 0 CFHR1 195063834 0.321000 0.24625 0.995000 0.50966 0.022000 0.10575 0.327000 0.19663 0.520000 0.28426 0.398000 0.26397 GTG TCGA-YY-A8LH-01A-11D-A36O-08 CFHR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000088251.2 0 0 0 8 579 0 135 0 0 0 0 135 2 0 0 0 0 0 2 1 0.988836 8 571 0 133 2 0 0 0 0 135 2 -6.444139 1 1 0 0 1 3 6 9 2.666250 1 0.550000 3.730000 0.770701 0.110000 2.000000e-02 1.000000 0.110000 0.325133 0.110000 0 6.000000e-02 1.000000 ANGEL2 90806 broad.mit.edu 37 1 213178772 213178772 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:213178772C>A ENST00000366962.3 - 5 891 c.737G>T c.(736-738)cGg>cTg p.R246L ANGEL2_ENST00000535388.1_Missense_Mutation_p.R77L|ANGEL2_ENST00000544555.1_Missense_Mutation_p.R77L|ANGEL2_ENST00000540642.1_Missense_Mutation_p.R120L|ANGEL2_ENST00000360506.2_Missense_Mutation_p.R77L NM_144567.3 NP_653168.2 Q5VTE6 ANGE2_HUMAN angel homolog 2 (Drosophila) p.R246L(1) 24 CCTTCCTGTCCGCATCTTATA 0.363000 1 Substitution - Missense(1) SO:0001583 missense ENST00000366962.3 0 1 hg19 CCDS1512.1 . . . . . . . . . . C 25.1 4.606850 0.87157 . . ENSG00000174606 ENST00000366962;ENST00000360506;ENST00000544555;ENST00000540642;ENST00000535388 D;D;D;D;D 0.95622 -3.76;-3.16;-3.16;-3.76;-3.16 5.45 4.53 0.55603 Endonuclease/exonuclease/phosphatase (2); 0.060391 0.64402 D 0.000003 D 0.98137 0.9385 M 0.93420 3.415 0.58432 D 0.999999 D;D 0.76494 0.996;0.999 D;D 0.77557 0.959;0.99 D 0.99007 1.0813 10 0.87932 D 0 -10.8417 13.6511 0.62312 0.0:0.9244:0.0:0.0756 . 120;246 F5H476;Q5VTE6 .;ANGE2_HUMAN L 246;77;77;120;77 ENSP00000355929:R246L;ENSP00000353696:R77L;ENSP00000443193:R77L;ENSP00000446124:R120L;ENSP00000438141:R77L ENSP00000353696:R77L R - 2 0 ANGEL2 211245395 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.604000 0.67626 1.398000 0.46701 0.650000 0.86243 CGG TCGA-YY-A8LH-01A-11D-A36O-08 ANGEL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000089693.1 0 0 0 10 586 0 120 0 4.477750e-02 0 18 0 120 2 0 0 0 0 0 2 1 0.996730 9 580 0 120 2 0 0 0 0 120 2 -2.102206 0 1 0 0 1 3 6 9 2.666250 1 0.550000 3.730000 0.770701 0.140000 5.000000e-02 1.000000 0.110000 0.342352 0.140000 0 9.000000e-02 1.000000 RAB3GAP2 25782 broad.mit.edu 37 1 220364491 220364491 + Missense_Mutation SNP G G A rs151225064 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:220364491G>A ENST00000358951.2 - 14 1522 c.1406C>T c.(1405-1407)gCg>gTg p.A469V NM_012414.3 NP_036546.2 Q9H2M9 RBGPR_HUMAN RAB3 GTPase activating protein subunit 2 (non-catalytic) p.A469V(1) 39 CCTTCTTGGCGCATAGATCAC 0.493000 1 Substitution - Missense(1) SO:0001583 missense ENST00000358951.2 0 1 hg19 CCDS31028.1 . . . . . . . . . . G 35 5.508939 0.96386 0.0 2.33E-4 ENSG00000118873 ENST00000358951 D 0.90444 -2.67 5.65 5.65 0.86999 . 0.000000 0.85682 D 0.000000 D 0.94925 0.8359 M 0.65975 2.015 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 D 0.94568 0.7768 10 0.56958 D 0.05 . 19.7176 0.96129 0.0:0.0:1.0:0.0 . 469 Q9H2M9 RBGPR_HUMAN V 469 ENSP00000351832:A469V ENSP00000351832:A469V A - 2 0 RAB3GAP2 218431114 1.000000 0.71417 0.907000 0.35723 0.936000 0.57629 9.090000 0.94144 2.670000 0.90874 0.563000 0.77884 GCG TCGA-YY-A8LH-01A-11D-A36O-08 RAB3GAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090205.2 0 0 0 6 611 0 125 0 8.721834e-03 0 12 0 125 2 0 0 0 0 0 2 1 0.964035 6 606 0 124 2 0 0 0 0 125 2 -1.721084 0 1 121410 19 47 1 3 6 9 2.666250 1 0.550000 3.730000 0.770701 0.080000 1.000000e-02 1.000000 0.060000 0.301197 0.080000 0 4.000000e-02 1.000000 TRIM67 440730 broad.mit.edu 37 1 231339749 231339749 + Silent SNP A A G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:231339749A>G ENST00000366653.5 + 6 1671 c.1671A>G c.(1669-1671)ggA>ggG p.G557G TRIM67_ENST00000449018.3_Silent_p.G495G|TRIM67_ENST00000366652.2_Silent_p.G557G|TRIM67_ENST00000444294.3_Silent_p.G555G Q6ZTA4 TRI67_HUMAN tripartite motif containing 67 29 Breast(184;0.0871) all_cancers(173;0.189)|Prostate(94;0.167) GTGCCGGGGGACAGTTCCGGG 0.637000 0 SO:0001819 synonymous_variant ENST00000366653.5 1 1 hg19 CCDS44333.1 TCGA-YY-A8LH-01A-11D-A36O-08 TRIM67-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000092649.3 1 0 1 37 200 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 1.000000 37 196 0 37 2 0 0 0 0 37 2 -20.000000 1 1 0 0 1 3 6 9 2.666250 1 0.550000 3.730000 0.770701 0.990000 8.300000e-01 1.000000 1.000000 0.985346 0.990000 1 9.800000e-01 1.000000 ARID1A 8289 broad.mit.edu 37 1 27099950 27099950 + Nonsense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:27099950C>T ENST00000324856.7 + 15 4200 c.3829C>T c.(3829-3831)Cag>Tag p.Q1277* ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q894*|ARID1A_ENST00000540690.1_5'UTR|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q1277* NM_006015.4 NP_006006.3 O14497 ARI1A_HUMAN AT rich interactive domain 1A (SWI-like) p.G1274fs*7(2)|p.M1273fs(1) ARID1A/MAST2_ENST00000361297(2) 411 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) GGGACCACGACAGCACTATCC 0.602000 Mis, N, F, S, D clear cell ovarian carcinoma, RCC Rec yes 1 1p35.3 8289 AT rich interactive domain 1A (SWI-like) E 3 Deletion - Frameshift(2)|Complex(1) SO:0001587 stop_gained ENST00000324856.7 0 1 hg19 CCDS285.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 42|42 9.172493|9.172493 0.99089|0.99089 .|. .|. ENSG00000117713|ENSG00000117713 ENST00000324856;ENST00000457599;ENST00000374152|ENST00000430799 .|. .|. .|. 4.72|4.72 4.72|4.72 0.59763|0.59763 .|. 0.053822|. 0.85682|. D|. 0.000000|. .|T .|0.73938 .|0.3651 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.72997 .|-0.4121 .|4 0.09843|. T|. 0.71|. -1.2962|-1.2962 18.2413|18.2413 0.89968|0.89968 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|. .|. .|. X|I 1277;1277;894|173 .|. ENSP00000320485:Q1277X|. Q|T +|+ 1|2 0|0 ARID1A|ARID1A 26972537|26972537 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 7.231000|7.231000 0.78106|0.78106 2.627000|2.627000 0.88993|0.88993 0.655000|0.655000 0.94253|0.94253 CAG|ACA TCGA-YY-A8LH-01A-11D-A36O-08 ARID1A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000011437.2 1 0 1 48 62 0 34 1 9.999679e-01 10 16 0 34 2 1 1 268 416 0 900 2 1 1.000000 47 62 0 33 2 0 0 0 0 34 2 -20.000000 1 1 0 0 1 0 5 5 1.780378 1 0.550000 3.730000 0.653045 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 BSND 7809 broad.mit.edu 37 1 55470697 55470697 + Silent SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr1:55470697C>T ENST00000371265.4 + 2 434 c.180C>T c.(178-180)atC>atT p.I60I NM_057176.2 NP_476517.1 Q8WZ55 BSND_HUMAN barttin CLCNK-type chloride channel accessory beta subunit 17 GCTTGCAGATCACCTTCGTCC 0.577000 Ovarian(191;1657 2078 22894 42033 48899) 0 SO:0001819 synonymous_variant ENST00000371265.4 1 1 hg19 CCDS602.1 TCGA-YY-A8LH-01A-11D-A36O-08 BSND-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000022213.4 1 0 1 61 85 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 60 84 0 53 2 0 0 0 0 53 2 -20.000000 1 1 121412 1 33 1 0 5 5 1.780378 1 0.550000 3.730000 0.653045 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 ZHX3 23051 broad.mit.edu 37 20 39832133 39832133 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr20:39832133G>A ENST00000309060.3 - 4 1839 c.1424C>T c.(1423-1425)gCg>gTg p.A475V ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000560361.1_Missense_Mutation_p.A475V|ZHX3_ENST00000432768.2_Missense_Mutation_p.A475V|ZHX3_ENST00000544979.2_Missense_Mutation_p.A475V|ZHX3_ENST00000559234.1_Missense_Mutation_p.A475V|ZHX3_ENST00000540170.1_Missense_Mutation_p.A475V|ZHX3_ENST00000558993.1_Intron Q9H4I2 ZHX3_HUMAN zinc fingers and homeoboxes 3 p.A475V(1) 31 Myeloproliferative disorder(115;0.00425) CGACTGGGCCGCATTGACCAC 0.537000 1 Substitution - Missense(1) SO:0001583 missense ENST00000309060.3 0 1 hg19 CCDS13315.1 . . . . . . . . . . G 12.63 1.997092 0.35226 . . ENSG00000174306 ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262;ENST00000432768 T;T;T;T;T 0.34859 1.34;2.8;2.8;2.59;1.34 5.93 5.93 0.95920 . 0.242897 0.40469 N 0.001094 T 0.32645 0.0836 L 0.40543 1.245 0.18873 N 0.999981 P;B;P 0.41673 0.532;0.348;0.759 B;B;B 0.37480 0.251;0.102;0.176 T 0.38394 -0.9663 10 0.72032 D 0.01 -9.9771 16.3863 0.83505 0.0:0.1314:0.8686:0.0 . 475;475;475 A8K8Q0;Q9H4I2;F5H820 .;ZHX3_HUMAN;. V 475;475;475;475;253;475 ENSP00000312222:A475V;ENSP00000362360:A475V;ENSP00000442290:A475V;ENSP00000443783:A475V;ENSP00000415498:A475V ENSP00000312222:A475V A - 2 0 ZHX3 39265547 0.534000 0.26362 0.181000 0.23098 0.707000 0.40811 2.718000 0.47236 2.815000 0.96918 0.561000 0.74099 GCG TCGA-YY-A8LH-01A-11D-A36O-08 ZHX3-010 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079262.3 0 0 0 5 180 0 50 0 1.097081e-02 0 5 0 50 2 0 0 0 0 0 2 1 0.934761 5 176 0 50 2 0 0 0 0 50 2 -2.799494 1 1 121412 5 36 1 3 3 6 2.220022 1 0.550000 3.730000 0.725275 0.200000 6.000000e-02 1.000000 0.170000 0.381746 0.200000 0 1.200000e-01 1.000000 DIDO1 11083 broad.mit.edu 37 20 61538515 61538515 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr20:61538515G>T ENST00000266070.4 - 5 1683 c.1358C>A c.(1357-1359)cCg>cAg p.P453Q DIDO1_ENST00000395340.1_Missense_Mutation_p.P453Q|DIDO1_ENST00000395335.2_Missense_Mutation_p.P453Q|DIDO1_ENST00000370371.4_Missense_Mutation_p.P453Q|DIDO1_ENST00000354665.4_Missense_Mutation_p.P453Q|DIDO1_ENST00000370366.1_Missense_Mutation_p.P453Q|DIDO1_ENST00000266071.5_Missense_Mutation_p.P453Q|DIDO1_ENST00000395343.1_Missense_Mutation_p.P453Q|DIDO1_ENST00000370368.1_Missense_Mutation_p.P453Q NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 p.P453L(1) 99 Breast(26;5.68e-08) ACCGCATTTCGGAAGACTGGG 0.527000 Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095) 1 Substitution - Missense(1) SO:0001583 missense ENST00000266070.4 0 1 hg19 CCDS33506.1 . . . . . . . . . . G 1.689 -0.504488 0.04261 . . ENSG00000101191 ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335;ENST00000370371;ENST00000370368;ENST00000354665;ENST00000370366;ENST00000266071 T;T;T;T;T;T;T;T;T 0.18338 3.06;3.06;2.72;2.72;2.22;2.22;2.22;2.23;2.23 4.91 1.78 0.24846 . 0.173706 0.27622 N 0.018547 T 0.11793 0.0287 L 0.41236 1.265 0.09310 N 1 B;B;B;B 0.33494 0.239;0.414;0.203;0.128 B;B;B;B 0.28991 0.097;0.097;0.034;0.026 T 0.17258 -1.0375 10 0.36615 T 0.2 -8.571 8.456 0.32899 0.0737:0.0:0.6357:0.2906 . 453;453;453;453 Q9BTC0-2;Q9BTC0-3;Q9BTC0-1;Q9BTC0 .;.;.;DIDO1_HUMAN Q 453 ENSP00000266070:P453Q;ENSP00000378752:P453Q;ENSP00000378749:P453Q;ENSP00000378744:P453Q;ENSP00000359397:P453Q;ENSP00000359394:P453Q;ENSP00000346692:P453Q;ENSP00000359391:P453Q;ENSP00000266071:P453Q ENSP00000266070:P453Q P - 2 0 DIDO1 61008960 0.105000 0.21958 0.097000 0.21041 0.010000 0.07245 0.494000 0.22467 0.557000 0.29117 0.561000 0.74099 CCG TCGA-YY-A8LH-01A-11D-A36O-08 DIDO1-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080091.2 0 0 0 9 846 0 240 0 3.417694e-01 0 105 0 240 2 0 0 0 0 0 2 1 0.993916 8 836 0 236 2 0 0 0 0 240 2 -1.887496 0 1 0 0 1 3 3 6 2.220022 1 0.550000 3.730000 0.725275 0.070000 1.000000e-02 1.000000 0.070000 0.287662 0.070000 0 3.000000e-02 1.000000 CCT8L2 150160 broad.mit.edu 37 22 17072527 17072527 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr22:17072527G>T ENST00000359963.3 - 1 1173 c.914C>A c.(913-915)aCa>aAa p.T305K NM_014406.4 NP_055221.1 Q96SF2 TCPQM_HUMAN chaperonin containing TCP1, subunit 8 (theta)-like 2 67 all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977) all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175) GTCCGCCAGTGTGAGGGTCTC 0.517000 0 SO:0001583 missense ENST00000359963.3 0 1 hg19 CCDS13738.1 . . . . . . . . . . g 6.540 0.467967 0.12402 . . ENSG00000198445 ENST00000359963 T 0.74526 -0.85 1.98 -1.43 0.08884 . 1.219940 0.06186 U 0.680487 T 0.64327 0.2588 L 0.44542 1.39 0.09310 N 1 B 0.15141 0.012 B 0.14578 0.011 T 0.53954 -0.8365 10 0.87932 D 0 -0.7241 5.2737 0.15638 0.5034:0.0:0.4966:0.0 . 305 Q96SF2 TCPQM_HUMAN K 305 ENSP00000353048:T305K ENSP00000353048:T305K T - 2 0 CCT8L2 15452527 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -0.513000 0.06305 -0.295000 0.08960 -1.325000 0.01285 ACA TCGA-YY-A8LH-01A-11D-A36O-08 CCT8L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000280580.1 0 0 0 9 478 0 200 0 0 0 0 200 2 0 0 0 0 0 2 1 0.991874 9 441 0 204 2 0 0 0 0 200 2 -3.002451 1 1 0 0 1 0 3 3 1.756595 1 0.550000 3.730000 0.647059 0.080000 3.000000e-02 0.160000 0.090000 0.094718 0.080000 0 5.000000e-02 0.130000 DGCR2 9993 broad.mit.edu 37 22 19035956 19035956 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr22:19035956G>A ENST00000263196.7 - 7 1250 c.1003C>T c.(1003-1005)Cca>Tca p.P335S DGCR11_ENST00000609958.1_RNA|DGCR2_ENST00000545799.1_3'UTR|DGCR2_ENST00000537045.1_Missense_Mutation_p.P294S NM_001184781.1|NM_005137.2 NP_001171710.1|NP_005128.1 P98153 IDD_HUMAN DiGeorge syndrome critical region gene 2 18 Colorectal(54;0.0993) GTCTCACCTGGGTCCAGACAC 0.587000 0 SO:0001583 missense ENST00000263196.7 1 1 hg19 CCDS33598.1 . . . . . . . . . . G 18.85 3.711467 0.68730 . . ENSG00000070413 ENST00000537045;ENST00000263196 T;D 0.97114 0.87;-4.25 5.8 5.8 0.92144 . 0.100398 0.64402 D 0.000001 D 0.95338 0.8487 L 0.46157 1.445 0.80722 D 1 P;P 0.41232 0.743;0.485 B;B 0.38755 0.281;0.146 D 0.94464 0.7679 10 0.34782 T 0.22 . 19.6734 0.95921 0.0:0.0:1.0:0.0 . 291;335 B7Z3T5;P98153 .;IDD_HUMAN S 294;335 ENSP00000440062:P294S;ENSP00000263196:P335S ENSP00000263196:P335S P - 1 0 DGCR2 17415956 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.485000 0.73625 2.735000 0.93741 0.655000 0.94253 CCA TCGA-YY-A8LH-01A-11D-A36O-08 DGCR2-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316504.1 0 0 0 14 421 0 212 1 6.531106e-01 5 62 0 212 2 0 0 0 0 0 2 1 0.999734 13 415 0 210 2 0 0 0 0 212 2 -3.002296 1 1 0 0 1 0 3 3 1.489688 1 0.550000 3.730000 0.618240 0.150000 7.000000e-02 1.000000 0.130000 0.334407 0.150000 0 1.000000e-01 1.000000 GNB1L 54584 broad.mit.edu 37 22 19794255 19794255 + Missense_Mutation SNP T T A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr22:19794255T>A ENST00000329517.6 - 6 679 c.443A>T c.(442-444)aAg>aTg p.K148M GNB1L_ENST00000405009.1_Missense_Mutation_p.K148M|GNB1L_ENST00000403325.1_Missense_Mutation_p.K148M|GNB1L_ENST00000460402.1_5'UTR NM_053004.2 NP_443730.1 Q9BYB4 GNB1L_HUMAN guanine nucleotide binding protein (G protein), beta polypeptide 1-like 12 Colorectal(54;0.0993) CACTGACGTCTTGGAGGGCAT 0.572000 0 SO:0001583 missense ENST00000329517.6 1 1 hg19 CCDS13768.1 . . . . . . . . . . T 25.5 4.640031 0.87760 . . ENSG00000185838 ENST00000329517;ENST00000403325;ENST00000405009 T;T;T 0.40756 1.02;1.02;5.0 5.21 4.16 0.48862 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.128959 0.50627 U 0.000116 T 0.52273 0.1724 M 0.77103 2.36 0.49299 D 0.999779 D 0.56746 0.977 P 0.49887 0.625 T 0.57774 -0.7753 10 0.87932 D 0 -3.2795 11.353 0.49598 0.1361:0.0:0.0:0.8639 . 148 Q9BYB4 GNB1L_HUMAN M 148 ENSP00000331313:K148M;ENSP00000385154:K148M;ENSP00000384626:K148M ENSP00000331313:K148M K - 2 0 GNB1L 18174255 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 5.204000 0.65180 0.798000 0.33994 -0.333000 0.08304 AAG TCGA-YY-A8LH-01A-11D-A36O-08 GNB1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075202.1 0 0 1 5 70 0 30 0 7.843762e-01 1 41 0 30 2 0 0 0 0 0 2 1 0.935284 5 68 0 30 2 0 0 0 0 30 2 -9.538021 1 1 0 0 1 0 3 3 1.489688 1 0.550000 3.730000 0.618240 0.350000 1.200000e-01 1.000000 0.290000 0.478250 0.350000 0 2.100000e-01 1.000000 SGSM3 27352 broad.mit.edu 37 22 40797636 40797636 + Missense_Mutation SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr22:40797636C>G ENST00000248929.9 + 3 236 c.47C>G c.(46-48)aCt>aGt p.T16S SGSM3_ENST00000454798.2_Intron NM_015705.4 NP_056520.2 small G protein signaling modulator 3 19 TCAGCCCTGACTCCGAGCATA 0.567000 0 SO:0001583 missense ENST00000248929.9 1 1 hg19 CCDS14002.1 . . . . . . . . . . C 27.3 4.814574 0.90790 . . ENSG00000100359 ENST00000248929 T 0.13901 2.55 5.45 5.45 0.79879 . 0.000000 0.85682 D 0.000000 T 0.31482 0.0798 M 0.71581 2.175 0.80722 D 1 P;P;P 0.48230 0.887;0.907;0.907 P;B;B 0.52217 0.693;0.437;0.437 T 0.01045 -1.1470 10 0.54805 T 0.06 . 19.6801 0.95958 0.0:1.0:0.0:0.0 . 16;16;16 Q96HU1-2;B9A6J5;Q96HU1 .;.;SGSM3_HUMAN S 16 ENSP00000248929:T16S ENSP00000248929:T16S T + 2 0 SGSM3 39127582 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 6.973000 0.76116 2.749000 0.94314 0.655000 0.94253 ACT TCGA-YY-A8LH-01A-11D-A36O-08 SGSM3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321504.2 1 0 1 109 227 0 164 1 1 37 34 0 164 2 0 0 0 0 0 2 1 1.000000 106 224 0 164 2 0 0 0 0 164 2 -20.000000 1 1 0 0 1 0 3 3 1.503948 1 0.550000 3.730000 0.620013 0.990000 9.900000e-01 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1.000000 TTN 7273 broad.mit.edu 37 2 179433869 179433869 + Missense_Mutation SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr2:179433869G>T ENST00000591111.1 - 276 72291 c.72067C>A c.(72067-72069)Cag>Aag p.Q24023K TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q23096K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q16599K|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Q25664K|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q16791K|TTN_ENST00000359218.5_Missense_Mutation_p.Q16724K|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCTTGGAGCTGATCGATTTTC 0.388000 0 SO:0001583 missense ENST00000591111.1 0 1 hg19 . . . . . . . . . . G 2.557 -0.302746 0.05495 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.52526 0.66;0.66;0.66;0.66 5.93 3.1 0.35709 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.26048 0.0635 N 0.02266 -0.62 0.33359 D 0.572126 B;B;B;B 0.14012 0.009;0.009;0.009;0.002 B;B;B;B 0.14023 0.005;0.005;0.005;0.01 T 0.16808 -1.0390 9 0.87932 D 0 . 14.5358 0.67960 0.0589:0.212:0.7291:0.0 . 16599;16724;16791;24023 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN K 23096;16599;16791;16724;16597 ENSP00000343764:Q23096K;ENSP00000434586:Q16599K;ENSP00000340554:Q16791K;ENSP00000352154:Q16724K ENSP00000340554:Q16791K Q - 1 0 TTN 179142115 1.000000 0.71417 0.163000 0.22734 0.218000 0.24690 4.194000 0.58393 0.087000 0.17167 -0.810000 0.03169 CAG TCGA-YY-A8LH-01A-11D-A36O-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 12 887 0 249 0 0 0 0 249 2 0 0 0 0 0 2 1 0.999088 11 884 0 248 2 0 0 0 0 249 2 -2.277787 0 1 0 0 1 2 2 4 2.110673 1 0.550000 3.730000 0.709677 0.070000 2.000000e-02 0.140000 0.080000 0.082724 0.070000 0 5.000000e-02 0.110000 TTN 7273 broad.mit.edu 37 2 179434141 179434141 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr2:179434141C>A ENST00000591111.1 - 276 72019 c.71795G>T c.(71794-71796)cGa>cTa p.R23932L TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R23005L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R16508L|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R25573L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R16700L|TTN_ENST00000359218.5_Missense_Mutation_p.R16633L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ACTATCATATCGGTTGACATT 0.423000 0 SO:0001583 missense ENST00000591111.1 0 1 hg19 . . . . . . . . . . C 14.92 2.679673 0.47886 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.39997 1.05;1.05;1.05;1.05 5.71 5.71 0.89125 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.65913 0.2737 M 0.68593 2.085 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.999;0.999;0.999 T 0.67114 -0.5752 9 0.87932 D 0 . 19.8644 0.96799 0.0:1.0:0.0:0.0 . 16508;16633;16700;23932 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN L 23005;16508;16700;16633;16506 ENSP00000343764:R23005L;ENSP00000434586:R16508L;ENSP00000340554:R16700L;ENSP00000352154:R16633L ENSP00000340554:R16700L R - 2 0 TTN 179142387 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.818000 0.86416 2.691000 0.91804 0.655000 0.94253 CGA TCGA-YY-A8LH-01A-11D-A36O-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 5 347 0 106 0 0 0 0 106 2 0 0 0 0 0 2 1 0.934621 5 340 0 105 2 0 0 0 0 106 2 -2.924756 1 1 0 0 1 2 2 4 2.110673 1 0.550000 3.730000 0.709677 0.080000 1.000000e-02 0.180000 0.080000 0.095034 0.080000 0 4.000000e-02 0.130000 TTN 7273 broad.mit.edu 37 2 179440550 179440550 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr2:179440550C>T ENST00000591111.1 - 276 65610 c.65386G>A c.(65386-65388)Ggc>Agc p.G21796S RP11-171I2.2_ENST00000603521.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G20869S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G14372S|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G23437S|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G14564S|TTN_ENST00000359218.5_Missense_Mutation_p.G14497S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin p.G14372C(1)|p.G20867C(1) 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGGACTGGGCCTGGCGTGTCC 0.493000 2 Substitution - Missense(2) SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 16.49 3.138080 0.56936 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.51574 0.7;0.7;0.7;0.7 5.67 5.67 0.87782 Fibronectin, type III (3);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.70298 0.3208 M 0.72479 2.2 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;1.0;1.0;1.0 T 0.72124 -0.4385 9 0.87932 D 0 . 19.7429 0.96238 0.0:1.0:0.0:0.0 . 14372;14497;14564;21796 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN S 20869;14372;14564;14497;14370 ENSP00000343764:G20869S;ENSP00000434586:G14372S;ENSP00000340554:G14564S;ENSP00000352154:G14497S ENSP00000340554:G14564S G - 1 0 TTN 179148796 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 7.818000 0.86416 2.685000 0.91497 0.655000 0.94253 GGC TCGA-YY-A8LH-01A-11D-A36O-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 31 571 0 179 0 0 0 0 179 2 0 0 0 0 0 2 1 1.000000 32 566 0 177 2 0 0 0 0 179 2 -5.622918 1 1 0 0 1 2 2 4 2.110673 1 0.550000 3.730000 0.709677 0.290000 1.900000e-01 0.400000 0.280000 0.298419 0.290000 0 2.300000e-01 0.350000 DNER 92737 broad.mit.edu 37 2 230377562 230377562 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr2:230377562C>T ENST00000341772.4 - 6 1218 c.1084G>A c.(1084-1086)Gcg>Acg p.A362T NM_139072.3 NP_620711.3 Q8NFT8 DNER_HUMAN delta/notch-like EGF repeat containing 63 all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175) ATACAGCTCGCGTTGTTTTGG 0.438000 0 SO:0001583 missense ENST00000341772.4 1 1 hg19 CCDS33390.1 . . . . . . . . . . C 17.02 3.281809 0.59758 . . ENSG00000187957 ENST00000341772;ENST00000543700 D 0.94232 -3.38 5.76 5.76 0.90799 EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1); 0.221819 0.45867 D 0.000328 D 0.95082 0.8407 M 0.77486 2.375 0.27064 N 0.963488 D 0.57899 0.981 P 0.50049 0.629 D 0.91199 0.4990 10 0.72032 D 0.01 . 18.7207 0.91692 0.0:1.0:0.0:0.0 . 362 Q8NFT8 DNER_HUMAN T 362;90 ENSP00000345229:A362T ENSP00000345229:A362T A - 1 0 DNER 230085806 0.921000 0.31238 0.021000 0.16686 0.046000 0.14306 5.864000 0.69575 2.724000 0.93272 0.591000 0.81541 GCG TCGA-YY-A8LH-01A-11D-A36O-08 DNER-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331902.1 1 0 0 31 392 0 93 0 1.656908e-02 0 3 0 93 2 0 0 0 0 0 2 1 1.000000 31 391 0 93 2 0 0 0 0 93 2 -8.468063 1 1 121412 7 39 1 2 2 4 2.110673 1 0.550000 3.730000 0.709677 0.410000 2.800000e-01 0.570000 0.400000 0.423984 0.410000 0 3.400000e-01 0.490000 VAX2 25806 broad.mit.edu 37 2 71148347 71148347 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr2:71148347C>T ENST00000234392.2 + 2 399 c.367C>T c.(367-369)Cgc>Tgc p.R123C NM_012476.2 NP_036608.1 Q9UIW0 VAX2_HUMAN ventral anterior homeobox 2 p.R123S(1) 7 GGAGTTCCAGCGCTGCCAGTA 0.637000 1 Substitution - Missense(1) SO:0001583 missense ENST00000234392.2 1 1 hg19 CCDS1911.1 . . . . . . . . . . C 20.3 3.967070 0.74131 . . ENSG00000116035 ENST00000234392 D 0.96365 -3.99 5.43 4.47 0.54385 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.059173 0.64402 D 0.000005 D 0.96632 0.8901 L 0.52905 1.665 0.80722 D 1 D 0.76494 0.999 P 0.61722 0.893 D 0.96374 0.9276 10 0.72032 D 0.01 -14.5215 12.2143 0.54398 0.2453:0.7547:0.0:0.0 . 123 Q9UIW0 VAX2_HUMAN C 123 ENSP00000234392:R123C ENSP00000234392:R123C R + 1 0 VAX2 71001855 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 2.230000 0.42999 2.547000 0.85894 0.655000 0.94253 CGC TCGA-YY-A8LH-01A-11D-A36O-08 VAX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251923.1 1 0 0 25 241 0 69 0 2.518388e-01 0 10 0 69 2 0 0 0 0 0 2 1 1.000000 24 241 0 66 2 0 0 0 0 69 2 -10.026350 1 0 0 0 1 2 2 4 2.110673 1 0.550000 3.730000 0.709677 0.530000 3.500000e-01 0.740000 0.520000 0.545981 0.530000 0 4.300000e-01 0.640000 SEMA4C 54910 broad.mit.edu 37 2 97527586 97527586 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr2:97527586C>T ENST00000305476.5 - 13 1621 c.1489G>A c.(1489-1491)Gtg>Atg p.V497M NM_017789.4 NP_060259.4 Q9C0C4 SEM4C_HUMAN sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C 17 CAGTCGGCCACGGGCAGCTGC 0.682000 0 SO:0001583 missense ENST00000305476.5 1 1 hg19 CCDS2029.1 . . . . . . . . . . C 12.33 1.906697 0.33628 . . ENSG00000168758 ENST00000305476 T 0.36340 1.26 4.93 1.01 0.19927 WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2); 0.261632 0.33075 N 0.005317 T 0.22085 0.0532 L 0.28649 0.875 0.20489 N 0.999892 B;B 0.09022 0.002;0.002 B;B 0.06405 0.002;0.002 T 0.14868 -1.0457 10 0.52906 T 0.07 . 5.9613 0.19301 0.2318:0.4117:0.3565:0.0 . 497;207 Q9C0C4;Q6P5A5 SEM4C_HUMAN;. M 497 ENSP00000306844:V497M ENSP00000306844:V497M V - 1 0 SEMA4C 96891313 1.000000 0.71417 0.960000 0.40013 0.749000 0.42624 0.770000 0.26618 0.274000 0.22072 -0.232000 0.12228 GTG TCGA-YY-A8LH-01A-11D-A36O-08 SEMA4C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252957.1 1 0 0 7 120 0 36 1 9.181122e-01 8 71 0 36 2 0 0 0 0 0 2 1 0.980486 7 118 0 36 2 0 0 0 0 36 2 -11.131590 1 1 121222 1 19 1 2 2 4 2.110673 1 0.550000 3.730000 0.709677 0.320000 1.400000e-01 0.590000 0.320000 0.348430 0.320000 0 2.200000e-01 0.460000 SLC6A1 6529 broad.mit.edu 37 3 11058924 11058924 + Silent SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:11058924C>T ENST00000287766.4 + 3 448 c.27C>T c.(25-27)gcC>gcT p.A9A SLC6A1_ENST00000536032.1_5'UTR|SLC6A1-AS1_ENST00000414969.2_RNA|SLC6A1_ENST00000462473.1_3'UTR NM_003042.3 NP_003033.3 P30531 SC6A1_HUMAN solute carrier family 6 (neurotransmitter transporter), member 1 26 Ovarian(110;0.0392) Clobazam(DB00349)|Tiagabine(DB00906) GCAAGGTGGCCGACGGGCAGA 0.632000 0 SO:0001819 synonymous_variant ENST00000287766.4 1 1 hg19 CCDS2603.1 TCGA-YY-A8LH-01A-11D-A36O-08 SLC6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102767.2 0 0 0 7 150 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 0.980480 7 148 0 56 2 0 0 0 0 56 2 -3.269789 1 1 0 0 1 1 2 3 1.724728 1 0.550000 3.730000 0.645530 0.210000 9.000000e-02 0.430000 0.210000 0.238991 0.210000 0 1.400000e-01 0.310000 FBXO40 51725 broad.mit.edu 37 3 121340995 121340995 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:121340995G>A ENST00000338040.4 + 3 1133 c.719G>A c.(718-720)aGc>aAc p.S240N NM_016298.3 NP_057382.2 Q9UH90 FBX40_HUMAN F-box protein 40 46 AGCTGTGAGAGCAAGAACAAG 0.458000 0 SO:0001583 missense ENST00000338040.4 0 1 hg19 CCDS33835.1 . . . . . . . . . . G 0.205 -1.041439 0.02013 . . ENSG00000163833 ENST00000338040 T 0.43688 0.94 5.64 2.3 0.28687 . 1.305700 0.04337 N 0.353342 T 0.22475 0.0542 N 0.08118 0 0.09310 N 0.999999 B 0.02656 0.0 B 0.04013 0.001 T 0.19647 -1.0299 10 0.17832 T 0.49 -0.1509 4.5317 0.12008 0.3425:0.1562:0.5013:0.0 . 240 Q9UH90 FBX40_HUMAN N 240 ENSP00000337510:S240N ENSP00000337510:S240N S + 2 0 FBXO40 122823685 0.057000 0.20700 0.014000 0.15608 0.512000 0.34134 0.903000 0.28475 0.121000 0.18284 0.591000 0.81541 AGC TCGA-YY-A8LH-01A-11D-A36O-08 FBXO40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355158.1 0 0 0 4 134 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 0.888040 4 132 0 38 2 0 0 0 0 39 2 -6.571600 1 1 0 0 1 1 2 3 1.690063 1 0.550000 3.730000 0.636877 0.150000 4.000000e-02 1.000000 0.140000 0.247795 0.150000 0 9.000000e-02 0.280000 OSBPL11 114885 broad.mit.edu 37 3 125279224 125279224 + Splice_Site SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:125279224C>A ENST00000296220.5 - 8 1443 c.1154G>T c.(1153-1155)aGa>aTa p.R385I NM_022776.4 NP_073613.2 Q9BXB4 OSB11_HUMAN oxysterol binding protein-like 11 27 ATTACTTACTCTTGTTAAATC 0.383000 0 SO:0001630 splice_region_variant ENST00000296220.5 1 0 hg19 CCDS3033.1 . . . . . . . . . . C 20.4 3.977820 0.74360 . . ENSG00000144909 ENST00000296220 T 0.34072 1.38 5.04 5.04 0.67666 . 0.000000 0.85682 D 0.000000 T 0.68796 0.3040 M 0.91196 3.185 0.80722 D 1 D 0.76494 0.999 D 0.71184 0.972 T 0.76451 -0.2954 10 0.87932 D 0 -26.5516 18.9367 0.92589 0.0:1.0:0.0:0.0 . 385 Q9BXB4 OSB11_HUMAN I 385 ENSP00000296220:R385I ENSP00000296220:R385I R - 2 0 OSBPL11 126761914 1.000000 0.71417 0.922000 0.36590 0.516000 0.34256 7.555000 0.82223 2.776000 0.95493 0.655000 0.94253 AGA TCGA-YY-A8LH-01A-11D-A36O-08 OSBPL11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356295.1 1 0 0 32 375 0 135 0 7.970774e-02 0 6 0 135 2 0 0 0 0 0 2 1 1.000000 32 367 0 134 2 0 0 0 0 135 2 -2.879461 1 1 0 0 1 1 2 3 1.720110 1 0.550000 3.730000 0.643987 0.360000 2.500000e-01 1.000000 0.360000 0.388478 0.360000 0 3.000000e-01 0.440000 ABCC5 10057 broad.mit.edu 37 3 183663704 183663704 + Silent SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:183663704C>A ENST00000334444.6 - 24 3678 c.3438G>T c.(3436-3438)acG>acT p.T1146T ABCC5_ENST00000265586.6_Silent_p.T1103T NM_005688.2 NP_005679.2 O15440 MRP5_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 5 62 all_cancers(143;1.85e-10)|Ovarian(172;0.0303) Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22) Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495) CCAGTCTGACCGTAAACTGGA 0.448000 0 SO:0001819 synonymous_variant ENST00000334444.6 0 1 hg19 CCDS43176.1 TCGA-YY-A8LH-01A-11D-A36O-08 ABCC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346350.1 0 0 0 8 837 0 278 0 5.348054e-02 0 34 0 278 2 0 0 0 0 0 2 1 0.988967 8 829 0 275 2 0 0 0 0 278 2 -1.730994 0 1 0 0 1 1 2 3 1.720110 1 0.550000 3.730000 0.643987 0.040000 0 1.000000 0.050000 0.075009 0.040000 0 2.000000e-02 0.070000 EHHADH 1962 broad.mit.edu 37 3 184910478 184910478 + Nonsense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:184910478G>A ENST00000231887.3 - 7 1783 c.1708C>T c.(1708-1710)Cga>Tga p.R570* EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Nonsense_Mutation_p.R474* NM_001166415.1|NM_001966.3 NP_001159887.1|NP_001957.2 Q08426 ECHP_HUMAN enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase 24 all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247) Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21) TGGCCAAATCGTCCTAATTCA 0.473000 0 SO:0001587 stop_gained ENST00000231887.3 0 1 hg19 CCDS33901.1 . . . . . . . . . . G 39 7.633440 0.98403 . . ENSG00000113790 ENST00000231887;ENST00000456310 . . . 5.91 -0.0269 0.13928 . 0.058373 0.64402 D 0.000003 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -13.3739 17.2992 0.87177 0.0:0.0:0.3145:0.6855 . . . . X 570;474 . ENSP00000231887:R570X R - 1 2 EHHADH 186393172 1.000000 0.71417 0.893000 0.35052 0.999000 0.98932 1.576000 0.36504 0.050000 0.15949 0.655000 0.94253 CGA TCGA-YY-A8LH-01A-11D-A36O-08 EHHADH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345326.1 0 0 0 9 369 0 133 0 7.132423e-03 0 5 0 133 2 0 0 0 0 0 2 1 0.993616 9 359 0 132 2 0 0 0 0 133 2 -3.747530 1 1 121412 2 31 1 1 2 3 1.720110 1 0.550000 3.730000 0.643987 0.110000 4.000000e-02 1.000000 0.120000 0.146087 0.110000 0 7.000000e-02 0.160000 LRRFIP2 9209 broad.mit.edu 37 3 37154441 37154441 + Missense_Mutation SNP T T C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:37154441T>C ENST00000336686.4 - 8 483 c.403A>G c.(403-405)Aag>Gag p.K135E LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.K104E|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.K135E|LRRFIP2_ENST00000354379.4_Intron Q9Y608 LRRF2_HUMAN leucine rich repeat (in FLII) interacting protein 2 p.0?(1) 22 GACCTCTTCTTCATTCCATGA 0.328000 1 Whole gene deletion(1) SO:0001583 missense ENST00000336686.4 1 1 hg19 CCDS2664.1 . . . . . . . . . . T 15.62 2.886492 0.51908 . . ENSG00000093167 ENST00000421307;ENST00000336686;ENST00000396428 T;T;T 0.46063 0.88;0.88;1.21 5.31 5.31 0.75309 . 0.394787 0.25872 N 0.027745 T 0.30355 0.0762 N 0.14661 0.345 0.32566 N 0.530498 P;P 0.45348 0.762;0.856 B;B 0.42738 0.303;0.396 T 0.40794 -0.9544 10 0.40728 T 0.16 -25.7202 14.3757 0.66874 0.0:0.0:0.0:1.0 . 104;135 A8MXR0;Q9Y608 .;LRRF2_HUMAN E 135;135;104 ENSP00000392217:K135E;ENSP00000338727:K135E;ENSP00000379705:K104E ENSP00000338727:K135E K - 1 0 LRRFIP2 37129445 1.000000 0.71417 0.998000 0.56505 0.982000 0.71751 5.517000 0.67061 2.145000 0.66743 0.482000 0.46254 AAG TCGA-YY-A8LH-01A-11D-A36O-08 LRRFIP2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000253335.3 1 0 1 202 535 0 219 0 0 0 0 219 2 0 0 0 0 0 2 1 1.000000 199 528 0 218 2 0 0 0 0 219 2 -20.000000 1 1 0 0 1 1 2 3 1.724728 1 0.550000 3.730000 0.645530 0.990000 9.900000e-01 1.000000 1.000000 0.999998 0.990000 1 9.900000e-01 1.000000 ZNF502 91392 broad.mit.edu 37 3 44763222 44763222 + Silent SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:44763222C>A ENST00000296091.4 + 4 1169 c.913C>A c.(913-915)Cga>Aga p.R305R ZNF502_ENST00000449836.1_Silent_p.R305R|ZNF502_ENST00000436624.2_Silent_p.R305R NM_001134440.1|NM_001282880.1|NM_033210.4 NP_001127912.1|NP_001269809.1|NP_149987.2 Q8TBZ5 ZN502_HUMAN zinc finger protein 502 19 CTCTTCTTTTCGAAAACACTC 0.408000 0 SO:0001819 synonymous_variant ENST00000296091.4 0 1 hg19 CCDS2719.1 . . . . . . . . . . C 4.294 0.053853 0.08291 . . ENSG00000196653 ENST00000427783 . . . 4.27 -0.248 0.13015 . . . . . T 0.39545 0.1082 . . . 0.09310 N 0.999997 . . . . . . T 0.40478 -0.9561 5 0.87932 D 0 -0.978 6.8198 0.23851 0.4135:0.3026:0.2839:0.0 . . . . L 304 . ENSP00000397812:F304L F + 3 2 ZNF502 44738226 0.547000 0.26465 0.305000 0.25099 0.935000 0.57460 2.045000 0.41250 0.132000 0.18615 0.655000 0.94253 TTC TCGA-YY-A8LH-01A-11D-A36O-08 ZNF502-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256744.4 0 0 0 9 714 0 246 0 1.226507e-03 0 4 0 246 2 0 0 0 0 0 2 1 0.994066 11 707 0 245 2 0 0 0 0 246 2 -2.319485 0 1 0 0 1 1 2 3 1.724728 1 0.550000 3.730000 0.645530 0.050000 1.000000e-02 0.120000 0.060000 0.073238 0.050000 0 3.000000e-02 0.090000 CXCR6 10663 broad.mit.edu 37 3 45988477 45988477 + Silent SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr3:45988477C>A ENST00000458629.1 + 1 1967 c.504C>A c.(502-504)atC>atA p.I168I CXCR6_ENST00000457814.1_Silent_p.I168I|FYCO1_ENST00000296137.2_Intron|FYCO1_ENST00000535325.1_Intron|CXCR6_ENST00000438735.1_Silent_p.I168I|FYCO1_ENST00000438446.1_Intron|CXCR6_ENST00000304552.4_Silent_p.I168I O00574 CXCR6_HUMAN chemokine (C-X-C motif) receptor 6 8 CCCAAATTATCTATGGCAATG 0.502000 Esophageal Squamous(63;1005 1117 15521 45762 47089) 0 SO:0001819 synonymous_variant ENST00000458629.1 0 1 hg19 CCDS2735.1 TCGA-YY-A8LH-01A-11D-A36O-08 CXCR6-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344395.1 0 0 0 8 360 0 132 0 6.521172e-04 0 2 0 132 2 0 0 0 0 0 2 1 0.988955 8 355 0 129 2 0 0 0 0 132 2 -3.126642 1 1 0 0 1 1 2 3 1.724728 1 0.550000 3.730000 0.645530 0.100000 4.000000e-02 0.210000 0.100000 0.120831 0.100000 0 6.000000e-02 0.150000 PCDH10 57575 broad.mit.edu 37 4 134073128 134073128 + Silent SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr4:134073128C>T ENST00000264360.5 + 1 2659 c.1833C>T c.(1831-1833)ggC>ggT p.G611G RP11-9G1.3_ENST00000505289.1_lincRNA NM_032961.1 NP_116586.1 Q9P2E7 PCD10_HUMAN protocadherin 10 136 CGGACGACGGCGAGAACGCCC 0.692000 0 SO:0001819 synonymous_variant ENST00000264360.5 0 1 hg19 CCDS34063.1 TCGA-YY-A8LH-01A-11D-A36O-08 PCDH10-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000364457.2 0 0 0 5 214 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 0.936747 5 212 0 72 2 0 0 0 0 74 2 -6.531740 1 1 0 0 1 2 2 4 2.111114 1 0.550000 3.730000 0.709677 0.130000 4.000000e-02 0.280000 0.120000 0.152737 0.130000 0 8.000000e-02 0.210000 ZFYVE28 57732 broad.mit.edu 37 4 2355738 2355738 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr4:2355738G>A ENST00000290974.2 - 2 441 c.102C>T c.(100-102)gcC>gcT p.A34A ZFYVE28_ENST00000509171.1_Intron|ZFYVE28_ENST00000515312.1_5'UTR|ZFYVE28_ENST00000503000.1_Silent_p.A34A|ZFYVE28_ENST00000515169.1_5'UTR|ZFYVE28_ENST00000511071.1_Silent_p.A34A NM_020972.2 NP_066023.2 Q9HCC9 LST2_HUMAN zinc finger, FYVE domain containing 28 31 CCAGCTCCGCGGCCACCTGGT 0.677000 0 SO:0001819 synonymous_variant ENST00000290974.2 0 1 hg19 CCDS33942.1 TCGA-YY-A8LH-01A-11D-A36O-08 ZFYVE28-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000360078.1 1 0 1 7 37 0 14 1 6.893196e-01 5 9 0 14 2 0 0 0 0 0 2 1 0.982226 7 36 0 14 2 0 0 0 0 14 2 -14.381540 1 1 121166 36 38 1 2 2 4 2.111114 1 0.550000 3.730000 0.709677 0.930000 4.400000e-01 1.000000 1.000000 0.860893 0.930000 1 6.500000e-01 1.000000 FAM193A 8603 broad.mit.edu 37 4 2691390 2691390 + Missense_Mutation SNP A A T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr4:2691390A>T ENST00000324666.5 + 12 1967 c.1616A>T c.(1615-1617)aAg>aTg p.K539M FAM193A_ENST00000545951.1_Missense_Mutation_p.K539M|FAM193A_ENST00000382839.3_Missense_Mutation_p.K539M|FAM193A_ENST00000505311.1_Missense_Mutation_p.K539M|FAM193A_ENST00000502458.1_Missense_Mutation_p.K561M NM_001256666.1 NP_001243595.1 P78312 F193A_HUMAN family with sequence similarity 193, member A 40 ATGAATGATAAGAACTGGAAT 0.353000 0 SO:0001583 missense ENST00000324666.5 0 1 hg19 CCDS58875.1 . . . . . . . . . . A 20.3 3.973078 0.74246 . . ENSG00000125386 ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350 T;T;T;T;T 0.26223 1.75;1.75;1.75;1.75;1.75 5.38 5.38 0.77491 . 0.000000 0.85682 D 0.000000 T 0.47728 0.1461 L 0.59436 1.845 0.58432 D 0.999999 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.87578 0.998;0.997;0.998;0.997;0.998 T 0.47724 -0.9095 10 0.72032 D 0.01 -39.2116 14.6205 0.68582 1.0:0.0:0.0:0.0 . 539;561;539;561;539 B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2 .;.;F193A_HUMAN;.;. M 539;539;539;561;393 ENSP00000372290:K539M;ENSP00000324587:K539M;ENSP00000443617:K539M;ENSP00000427505:K561M;ENSP00000427260:K393M ENSP00000324587:K539M K + 2 0 FAM193A 2661188 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.217000 0.72218 2.048000 0.60808 0.456000 0.33151 AAG TCGA-YY-A8LH-01A-11D-A36O-08 FAM193A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000360903.1 0 0 0 8 374 0 88 0 4.424851e-02 0 14 0 88 2 0 0 0 0 0 2 1 0.989201 8 371 0 88 2 0 0 0 0 88 2 -8.269270 1 1 0 0 1 2 2 4 2.111114 1 0.550000 3.730000 0.709677 0.120000 4.000000e-02 0.220000 0.120000 0.132008 0.120000 0 8.000000e-02 0.180000 UGDH 7358 broad.mit.edu 37 4 39512385 39512385 + Missense_Mutation SNP T T C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr4:39512385T>C ENST00000316423.6 - 4 703 c.361A>G c.(361-363)Aat>Gat p.N121D UGDH_ENST00000507089.1_Missense_Mutation_p.N24D|UGDH_ENST00000506179.1_Missense_Mutation_p.N121D|UGDH_ENST00000501493.2_Intron|UGDH_ENST00000515398.1_5'Flank NM_001184701.1|NM_003359.3 NP_001171630.1|NP_003350.1 O60701 UGDH_HUMAN UDP-glucose 6-dehydrogenase 27 TTGTACCCATTTGAGTTTTGC 0.433000 0 SO:0001583 missense ENST00000316423.6 1 1 hg19 CCDS3455.1 . . . . . . . . . . T 14.53 2.563464 0.45694 . . ENSG00000109814 ENST00000316423;ENST00000506179;ENST00000507089;ENST00000515021;ENST00000514106;ENST00000509391 T;T;T;T;T;T 0.75938 -0.98;-0.98;-0.98;-0.98;-0.98;-0.98 5.95 -0.408 0.12381 UDP-glucose/GDP-mannose dehydrogenase, N-terminal (1);NAD(P)-binding domain (1); 0.233858 0.49916 D 0.000133 T 0.53238 0.1784 N 0.17922 0.545 0.37435 D 0.914199 B 0.02656 0.0 B 0.06405 0.002 T 0.41998 -0.9477 10 0.12430 T 0.62 0.1388 11.693 0.51527 0.0828:0.0:0.1465:0.7707 . 121 O60701 UGDH_HUMAN D 121;121;24;134;121;121 ENSP00000319501:N121D;ENSP00000421757:N121D;ENSP00000426560:N24D;ENSP00000421954:N134D;ENSP00000425834:N121D;ENSP00000422603:N121D ENSP00000319501:N121D N - 1 0 UGDH 39188780 0.994000 0.37717 0.980000 0.43619 0.998000 0.95712 1.356000 0.34079 0.011000 0.14865 0.528000 0.53228 AAT TCGA-YY-A8LH-01A-11D-A36O-08 UGDH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216818.3 1 0 1 207 466 0 162 1 1 22 57 0 162 2 0 0 0 0 0 2 1 1.000000 205 463 0 162 2 0 0 0 0 162 2 -20.000000 1 1 121410 4 42 1 2 2 4 2.111114 1 0.550000 3.730000 0.709677 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 HERC5 51191 broad.mit.edu 37 4 89414249 89414249 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr4:89414249G>A ENST00000264350.3 + 17 2373 c.2220G>A c.(2218-2220)ccG>ccA p.P740P AC083829.1_ENST00000408152.2_RNA|HERC5_ENST00000508159.1_Silent_p.P378P NM_016323.3 NP_057407.2 Q9UII4 HERC5_HUMAN HECT and RLD domain containing E3 ubiquitin protein ligase 5 53 Hepatocellular(203;0.114) TGATCCAGCCGGAATATGGGA 0.443000 Esophageal Squamous(39;887 1012 34045 50514) 0 SO:0001819 synonymous_variant ENST00000264350.3 1 1 hg19 CCDS3630.1 TCGA-YY-A8LH-01A-11D-A36O-08 HERC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253554.2 0 0 0 28 338 1 83 0 5.338351e-01 1 48 1 83 4 0 0 0 0 0 2 1 0.975938 28 333 1 82 16 0 0 0 1 83 2 -2.665581 1 1 121412 3 37 1 2 2 4 2.111114 1 0.550000 3.730000 0.709677 0.430000 2.900000e-01 0.600000 0.440000 0.443684 0.430000 0 3.500000e-01 0.520000 CTNND2 1501 broad.mit.edu 37 5 11364949 11364949 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:11364949G>A ENST00000304623.8 - 8 1420 c.1231C>T c.(1231-1233)Cgg>Tgg p.R411W CTNND2_ENST00000503622.1_Missense_Mutation_p.R74W|CTNND2_ENST00000458100.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.R320W|CTNND2_ENST00000359640.2_Missense_Mutation_p.R411W|CTNND2_ENST00000495388.2_5'UTR NM_001332.2 NP_001323.1 Q9UQB3 CTND2_HUMAN catenin (cadherin-associated protein), delta 2 136 TGCAGGGCCCGCAACTCTGGG 0.577000 0 SO:0001583 missense ENST00000304623.8 1 1 hg19 CCDS3881.1 . . . . . . . . . . G 24.2 4.504805 0.85176 . . ENSG00000169862 ENST00000304623;ENST00000359640;ENST00000511377;ENST00000503622;ENST00000502551 D;D;D;T 0.83419 -1.6;-1.72;-1.6;-1.41 5.47 4.52 0.55395 . 0.000000 0.64402 D 0.000019 D 0.88097 0.6345 L 0.57536 1.79 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.87578 0.99;0.998 D 0.88375 0.2997 10 0.87932 D 0 -20.37 10.9741 0.47456 0.0:0.0:0.5842:0.4157 . 74;411 B4DRK2;Q9UQB3 .;CTND2_HUMAN W 411;411;320;74;151 ENSP00000307134:R411W;ENSP00000352661:R411W;ENSP00000426510:R320W;ENSP00000426887:R74W ENSP00000307134:R411W R - 1 2 CTNND2 11417949 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 3.008000 0.49544 2.581000 0.87130 0.655000 0.94253 CGG TCGA-YY-A8LH-01A-11D-A36O-08 CTNND2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206999.1 1 0 1 29 109 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 1.000000 28 105 0 28 2 0 0 0 0 28 2 -3.771706 1 1 0 0 1 2 2 4 1.978537 0 0.550000 3.730000 0.692202 0.990000 8.000000e-01 1.000000 1.000000 0.979939 0.990000 1 9.600000e-01 1.000000 FBN2 2201 broad.mit.edu 37 5 127624885 127624885 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:127624885C>T ENST00000508053.1 - 58 7545 c.6571G>A c.(6571-6573)Gac>Aac p.D2191N FBN2_ENST00000262464.4_Missense_Mutation_p.D2191N P35556 FBN2_HUMAN fibrillin 2 197 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) AAAGATCCGTCGGTGTTGATA 0.413000 0 SO:0001583 missense ENST00000508053.1 1 1 hg19 CCDS34222.1 . . . . . . . . . . C 26.2 4.715887 0.89112 . . ENSG00000138829 ENST00000262464;ENST00000508053 D;D 0.92299 -3.01;-3.01 5.76 4.88 0.63580 EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.090325 0.48286 D 0.000191 D 0.87087 0.6090 L 0.46885 1.475 0.51233 D 0.999917 P 0.51933 0.949 B 0.35470 0.203 D 0.86989 0.2109 10 0.34782 T 0.22 . 15.7202 0.77705 0.0:0.9314:0.0:0.0686 . 2191 P35556 FBN2_HUMAN N 2191 ENSP00000262464:D2191N;ENSP00000424571:D2191N ENSP00000262464:D2191N D - 1 0 FBN2 127652784 1.000000 0.71417 0.702000 0.30337 0.730000 0.41778 5.939000 0.70179 2.882000 0.98803 0.655000 0.94253 GAC TCGA-YY-A8LH-01A-11D-A36O-08 FBN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371618.2 1 0 0 22 504 0 137 0 0 0 0 137 2 0 0 0 0 0 2 1 0.999999 22 497 0 134 2 0 0 0 0 137 2 -3.292531 1 1 0 0 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.230000 1.400000e-01 0.350000 0.240000 0.244462 0.230000 0 1.800000e-01 0.300000 TRPC7 57113 broad.mit.edu 37 5 135692940 135692940 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:135692940G>A ENST00000513104.1 - 2 418 c.136C>T c.(136-138)Cgc>Tgc p.R46C TRPC7_ENST00000355180.3_Missense_Mutation_p.R46C|TRPC7_ENST00000426057.2_Missense_Mutation_p.R46C NM_020389.2 NP_065122.1 Q9HCX4 TRPC7_HUMAN transient receptor potential cation channel, subfamily C, member 7 46 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) TCCAGGAAGCGCTCCTCCTCG 0.612000 0 SO:0001583 missense ENST00000513104.1 1 1 hg19 CCDS47267.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 27.2|27.2 4.814083|4.814083 0.90790|0.90790 .|. .|. ENSG00000069018|ENSG00000069018 ENST00000352189;ENST00000378459;ENST00000502753|ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193 .|T;T;T .|0.79247 .|-1.09;-1.25;-1.21 5.2|5.2 5.2|5.2 0.72013|0.72013 .|. .|0.000000 .|0.85682 .|D .|0.000000 D|D 0.85327|0.85327 0.5671|0.5671 L|L 0.55990|0.55990 1.75|1.75 0.58432|0.58432 D|D 0.999993|0.999993 .|P;D;D;D .|0.89917 .|0.916;1.0;0.999;0.999 .|B;D;P;P .|0.65010 .|0.232;0.931;0.899;0.899 D|D 0.86290|0.86290 0.1673|0.1673 5|10 .|0.72032 .|D .|0.01 -15.4883|-15.4883 18.9316|18.9316 0.92568|0.92568 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|46;46;46;46 .|Q8IWP7;F5H5U9;Q70T25;Q9HCX4 .|.;.;.;TRPC7_HUMAN V|C 45|46 .|ENSP00000347312:R46C;ENSP00000441628:R46C;ENSP00000426070:R46C .|ENSP00000265193:R46C A|R -|- 2|1 0|0 TRPC7|TRPC7 135720839|135720839 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.972000|0.972000 0.66771|0.66771 7.761000|7.761000 0.85260|0.85260 2.691000|2.691000 0.91804|0.91804 0.655000|0.655000 0.94253|0.94253 GCG|CGC TCGA-YY-A8LH-01A-11D-A36O-08 TRPC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366975.1 0 0 0 22 636 0 184 0 0 0 0 184 2 0 0 0 0 0 2 1 0.999999 22 629 0 184 2 0 0 0 0 184 2 -3.276538 1 1 0 0 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.180000 1.100000e-01 0.290000 0.200000 0.195600 0.180000 0 1.400000e-01 0.240000 PCDHA9 9752 broad.mit.edu 37 5 140229544 140229544 + Silent SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:140229544C>G ENST00000532602.1 + 1 2497 c.1464C>G c.(1462-1464)gcC>gcG p.A488A PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.A488A|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron NM_031857.1 NP_114063.1 Q9Y5H5 PCDA9_HUMAN protocadherin alpha 9 59 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AGGAGAACGCCCTGGTGTCCT 0.667000 Melanoma(55;1800 1972 14909) 0 SO:0001819 synonymous_variant ENST00000532602.1 1 1 hg19 CCDS54920.1 TCGA-YY-A8LH-01A-11D-A36O-08 PCDHA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372896.2 1 0 1 129 409 0 175 0 0 0 0 175 2 0 0 0 0 0 2 1 1.000000 109 397 0 178 2 0 0 0 0 175 2 -4.882734 1 0 120800 8 41 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.990000 9.900000e-01 1.000000 1.000000 0.999996 0.990000 1 9.900000e-01 1.000000 TCERG1 10915 broad.mit.edu 37 5 145851118 145851118 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:145851118C>A ENST00000296702.5 + 9 1618 c.1580C>A c.(1579-1581)gCt>gAt p.A527D TCERG1_ENST00000394421.2_Missense_Mutation_p.A506D NM_006706.3 NP_006697.2 O14776 TCRG1_HUMAN transcription elongation regulator 1 46 Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) GTTGCTACTGCTCCTATTCCT 0.423000 0 SO:0001583 missense ENST00000296702.5 0 1 hg19 CCDS4282.1 . . . . . . . . . . C 16.34 3.095411 0.56075 . . ENSG00000113649 ENST00000296702;ENST00000394421 T;T 0.44482 0.92;0.92 5.63 5.63 0.86233 . 0.094736 0.64402 D 0.000001 T 0.30978 0.0782 N 0.08118 0 0.31301 N 0.688266 P;P;B 0.42649 0.786;0.762;0.041 B;B;B 0.43082 0.407;0.242;0.003 T 0.15263 -1.0443 10 0.30078 T 0.28 -8.6494 19.6756 0.95930 0.0:1.0:0.0:0.0 . 506;506;527 B7Z921;O14776-2;O14776 .;.;TCRG1_HUMAN D 527;506 ENSP00000296702:A527D;ENSP00000377943:A506D ENSP00000296702:A527D A + 2 0 TCERG1 145831311 1.000000 0.71417 0.998000 0.56505 0.751000 0.42716 4.739000 0.62080 2.664000 0.90586 0.313000 0.20887 GCT TCGA-YY-A8LH-01A-11D-A36O-08 TCERG1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251886.1 0 0 0 5 526 0 105 0 3.286819e-02 0 24 0 105 2 0 0 0 0 0 2 1 0.933653 4 514 0 105 2 0 0 0 0 105 2 -4.486774 1 0 0 0 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.050000 0 0.130000 0.040000 0.061583 0.050000 0 2.000000e-02 0.090000 GABRG2 2566 broad.mit.edu 37 5 161580182 161580182 + Silent SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:161580182C>T ENST00000361925.4 + 9 1432 c.1212C>T c.(1210-1212)taC>taT p.Y404Y GABRG2_ENST00000393933.4_Silent_p.Y309Y|GABRG2_ENST00000414552.2_Silent_p.Y452Y|GABRG2_ENST00000356592.3_Silent_p.Y412Y P18507 GBRG2_HUMAN gamma-aminobutyric acid (GABA) A receptor, gamma 2 62 Renal(175;0.000319) Medulloblastoma(196;0.0208)|all_neural(177;0.0672) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) ATGAAGAGTACGGCTATGAGT 0.488000 0 SO:0001819 synonymous_variant ENST00000361925.4 0 1 hg19 CCDS4358.1 TCGA-YY-A8LH-01A-11D-A36O-08 GABRG2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000252706.1 0 0 0 6 318 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 0.963989 6 314 0 88 2 0 0 0 0 88 2 -2.841467 1 1 121410 17 44 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.110000 3.000000e-02 0.230000 0.120000 0.120489 0.110000 0 6.000000e-02 0.170000 NKX2-5 1482 broad.mit.edu 37 5 172660081 172660081 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:172660081G>A ENST00000329198.4 - 2 739 c.466C>T c.(466-468)Cgc>Tgc p.R156C NKX2-5_ENST00000424406.2_3'UTR|NKX2-5_ENST00000521848.1_3'UTR NM_001166175.1|NM_001166176.1|NM_004387.3 NP_001159647.1|NP_001159648.1|NP_004378.1 P52952 NKX25_HUMAN NK2 homeobox 5 12 Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183) TGCTTGAAGCGCCGCTCCAGC 0.677000 Esophageal Squamous(72;810 1219 2387 13420 44943) 0 SO:0001583 missense ENST00000329198.4 0 1 hg19 CCDS4387.1 . . . . . . . . . . G 20.7 4.038907 0.75617 . . ENSG00000183072 ENST00000329198 D 0.96136 -3.92 4.12 3.16 0.36331 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.000000 0.52532 D 0.000063 D 0.96589 0.8887 M 0.64997 1.995 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.96214 0.9155 10 0.87932 D 0 . 11.6702 0.51396 0.0:0.0:0.7125:0.2875 . 156 P52952 NKX25_HUMAN C 156 ENSP00000327758:R156C ENSP00000327758:R156C R - 1 0 NKX2-5 172592687 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 3.303000 0.51858 2.307000 0.77673 0.462000 0.41574 CGC TCGA-YY-A8LH-01A-11D-A36O-08 NKX2-5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252942.2 0 0 1 8 61 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 0.990252 7 61 0 24 2 0 0 0 0 24 2 -14.680890 1 1 0 0 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.680000 3.300000e-01 1.000000 1.000000 0.694449 0.680000 0 4.800000e-01 0.920000 MRPS27 23107 broad.mit.edu 37 5 71533926 71533926 + Missense_Mutation SNP A A G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr5:71533926A>G ENST00000261413.5 - 5 350 c.311T>C c.(310-312)cTg>cCg p.L104P MRPS27_ENST00000522562.1_5'UTR|MRPS27_ENST00000513900.1_Missense_Mutation_p.L118P|MRPS27_ENST00000457646.4_Missense_Mutation_p.L48P|MRPS27_ENST00000515404.1_Missense_Mutation_p.L48P NM_015084.2 NP_055899.2 Q92552 RT27_HUMAN mitochondrial ribosomal protein S27 6 Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198) CCAGTTTCTCAGGTACCAGCA 0.413000 0 SO:0001583 missense ENST00000261413.5 0 1 hg19 CCDS4013.1 . . . . . . . . . . A 24.3 4.518352 0.85495 . . ENSG00000113048 ENST00000261413;ENST00000457646;ENST00000513900;ENST00000508863;ENST00000515404 T;T;T;T;T 0.59364 0.27;0.27;0.27;0.27;0.27 5.22 5.22 0.72569 . 0.000000 0.64402 D 0.000001 T 0.75657 0.3879 M 0.75264 2.295 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.998;0.998 T 0.79317 -0.1853 10 0.87932 D 0 -18.2091 15.0979 0.72250 1.0:0.0:0.0:0.0 . 118;48;104 B4DRT2;D6RJC7;Q92552 .;.;RT27_HUMAN P 104;48;118;48;48 ENSP00000261413:L104P;ENSP00000428120:L48P;ENSP00000426941:L118P;ENSP00000426176:L48P;ENSP00000427237:L48P ENSP00000261413:L104P L - 2 0 MRPS27 71569682 1.000000 0.71417 1.000000 0.80357 0.968000 0.65278 8.771000 0.91751 1.970000 0.57323 0.374000 0.22700 CTG TCGA-YY-A8LH-01A-11D-A36O-08 MRPS27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000218560.2 0 0 0 6 664 0 157 1 6.069618e-02 2 35 0 157 2 0 0 0 0 0 2 1 0.963426 6 654 0 157 2 0 0 0 0 157 2 -2.999378 1 0 0 0 1 2 2 4 2.090344 0 0.550000 3.730000 0.708644 0.040000 0 0.110000 0.040000 0.056180 0.040000 0 2.000000e-02 0.090000 GRIK2 2898 broad.mit.edu 37 6 102266347 102266347 + Missense_Mutation SNP A A T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr6:102266347A>T ENST00000421544.1 + 9 1796 c.1306A>T c.(1306-1308)Acc>Tcc p.T436S GRIK2_ENST00000369138.1_Missense_Mutation_p.T436S|GRIK2_ENST00000413795.1_Missense_Mutation_p.T436S|GRIK2_ENST00000318991.6_Missense_Mutation_p.T436S|GRIK2_ENST00000369137.3_Missense_Mutation_p.T436S|GRIK2_ENST00000369134.4_Missense_Mutation_p.T387S NM_021956.4 NP_068775.1 Q13002 GRIK2_HUMAN glutamate receptor, ionotropic, kainate 2 83 all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599) TTTGATTGTTACCACCATTTT 0.383000 0 SO:0001583 missense ENST00000421544.1 1 1 hg19 CCDS5048.1 . . . . . . . . . . A 14.46 2.541984 0.45280 . . ENSG00000164418 ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076;ENST00000455610;ENST00000436862 T;T;T;T;T;T;T;T 0.35973 2.79;2.79;2.79;2.79;2.79;2.79;1.28;2.79 5.81 5.81 0.92471 Ionotropic glutamate receptor (1); 0.053012 0.85682 D 0.000000 T 0.28830 0.0715 L 0.61218 1.895 0.43226 D 0.995116 B;B;B 0.18863 0.031;0.002;0.007 B;B;B 0.27380 0.079;0.022;0.049 T 0.15723 -1.0427 10 0.72032 D 0.01 . 16.151 0.81622 1.0:0.0:0.0:0.0 . 436;436;436 Q13002-5;Q13002;Q13002-2 .;GRIK2_HUMAN;. S 436;436;436;436;436;436;387;398;149;35 ENSP00000397026:T436S;ENSP00000405596:T436S;ENSP00000358134:T436S;ENSP00000358133:T436S;ENSP00000313276:T436S;ENSP00000358130:T387S;ENSP00000391988:T149S;ENSP00000407140:T35S ENSP00000313276:T436S T + 1 0 GRIK2 102373040 1.000000 0.71417 1.000000 0.80357 0.940000 0.58332 5.412000 0.66392 2.221000 0.72209 0.523000 0.50628 ACC TCGA-YY-A8LH-01A-11D-A36O-08 GRIK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043718.1 1 0 0 6 114 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 0.964399 6 112 0 38 2 0 0 0 0 38 2 -4.280973 1 1 0 0 1 0 2 2 1.454667 1 0.550000 3.730000 0.550000 0.190000 7.000000e-02 1.000000 0.180000 0.244449 0.190000 0 1.200000e-01 0.300000 GRIK2 2898 broad.mit.edu 37 6 102266348 102266348 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr6:102266348C>T ENST00000421544.1 + 9 1797 c.1307C>T c.(1306-1308)aCc>aTc p.T436I GRIK2_ENST00000369138.1_Missense_Mutation_p.T436I|GRIK2_ENST00000413795.1_Missense_Mutation_p.T436I|GRIK2_ENST00000318991.6_Missense_Mutation_p.T436I|GRIK2_ENST00000369137.3_Missense_Mutation_p.T436I|GRIK2_ENST00000369134.4_Missense_Mutation_p.T387I NM_021956.4 NP_068775.1 Q13002 GRIK2_HUMAN glutamate receptor, ionotropic, kainate 2 83 all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599) TTGATTGTTACCACCATTTTG 0.383000 0 SO:0001583 missense ENST00000421544.1 1 1 hg19 CCDS5048.1 . . . . . . . . . . C 20.1 3.935787 0.73442 . . ENSG00000164418 ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076;ENST00000455610;ENST00000436862 T;T;T;T;T;T;T;T 0.35789 2.8;2.8;2.8;2.8;2.8;2.8;1.29;2.8 5.81 5.81 0.92471 Ionotropic glutamate receptor (1); 0.053012 0.85682 D 0.000000 T 0.56673 0.2001 M 0.77406 2.37 0.54753 D 0.999982 D;P;D 0.58970 0.984;0.932;0.984 D;P;P 0.65573 0.936;0.794;0.899 T 0.57665 -0.7772 10 0.59425 D 0.04 . 20.064 0.97700 0.0:1.0:0.0:0.0 . 436;436;436 Q13002-5;Q13002;Q13002-2 .;GRIK2_HUMAN;. I 436;436;436;436;436;436;387;398;149;35 ENSP00000397026:T436I;ENSP00000405596:T436I;ENSP00000358134:T436I;ENSP00000358133:T436I;ENSP00000313276:T436I;ENSP00000358130:T387I;ENSP00000391988:T149I;ENSP00000407140:T35I ENSP00000313276:T436I T + 2 0 GRIK2 102373041 1.000000 0.71417 1.000000 0.80357 0.946000 0.59487 7.487000 0.81328 2.753000 0.94483 0.643000 0.83706 ACC TCGA-YY-A8LH-01A-11D-A36O-08 GRIK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043718.1 0 0 0 6 113 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 0.964395 6 111 0 39 2 0 0 0 0 39 2 -4.229092 1 1 0 0 1 0 2 2 1.454667 1 0.550000 3.730000 0.550000 0.190000 8.000000e-02 1.000000 0.180000 0.246070 0.190000 0 1.300000e-01 0.300000 LPA 4018 broad.mit.edu 37 6 161020546 161020546 + Missense_Mutation SNP T T G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr6:161020546T>G ENST00000316300.5 - 20 3317 c.3273A>C c.(3271-3273)gaA>gaC p.E1091D LPA_ENST00000447678.1_Missense_Mutation_p.E1091D P08519 APOA_HUMAN lipoprotein, Lp(a) 107 Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965) Aminocaproic Acid(DB00513) TTGGGTAGTTTTCTGGGGTCC 0.483000 0 SO:0001583 missense ENST00000316300.5 0 1 hg19 CCDS43523.1 . . . . . . . . . . t 8.354 0.831520 0.16820 . . ENSG00000198670 ENST00000316300;ENST00000447678 T;T 0.68025 -0.3;-0.3 2.48 -2.05 0.07321 Kringle (4);Kringle-like fold (1); . . . . T 0.31009 0.0783 L 0.41824 1.3 0.09310 N 1 B 0.15141 0.012 B 0.31751 0.135 T 0.39683 -0.9602 9 0.30078 T 0.28 . 2.9399 0.05826 0.0:0.3134:0.2443:0.4423 . 3599 P08519 APOA_HUMAN D 1091 ENSP00000321334:E1091D;ENSP00000395608:E1091D ENSP00000321334:E1091D E - 3 2 LPA 160940536 0.000000 0.05858 0.013000 0.15412 0.003000 0.03518 -0.976000 0.03786 -0.618000 0.05656 -0.782000 0.03352 GAA TCGA-YY-A8LH-01A-11D-A36O-08 LPA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042957.1 0 0 0 8 1211 0 638 0 0 0 0 638 2 0 0 0 0 0 2 1 0.988449 7 1188 0 626 2 0 0 0 0 638 2 -7.885989 1 0 0 0 1 0 2 2 1.454667 1 0.550000 3.730000 0.550000 0.010000 0 1.000000 0.020000 0.070741 0.010000 0 0 0.040000 PHIP 55023 broad.mit.edu 37 6 79711802 79711802 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr6:79711802G>A ENST00000275034.4 - 17 1860 c.1693C>T c.(1693-1695)Ctt>Ttt p.L565F NM_017934.5 NP_060404 Q8WWQ0 PHIP_HUMAN pleckstrin homology domain interacting protein 68 all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219) TCACGAATAAGTGGCCGATAA 0.358000 0 SO:0001583 missense ENST00000275034.4 1 1 hg19 CCDS4987.1 . . . . . . . . . . G 20.2 3.950918 0.73787 . . ENSG00000146247 ENST00000275034 T 0.61392 0.11 5.63 4.75 0.60458 . 0.088632 0.45867 D 0.000337 T 0.77890 0.4198 M 0.92604 3.325 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.80764 0.994;0.994 T 0.82327 -0.0512 9 . . . -16.7819 14.5837 0.68310 0.074:0.0:0.926:0.0 . 565;565 A7J992;Q8WWQ0 .;PHIP_HUMAN F 565 ENSP00000275034:L565F . L - 1 0 PHIP 79768521 1.000000 0.71417 1.000000 0.80357 0.442000 0.32017 6.205000 0.72148 2.799000 0.96334 0.650000 0.86243 CTT TCGA-YY-A8LH-01A-11D-A36O-08 PHIP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041297.2 1 0 0 16 173 0 55 0 8.344241e-03 0 2 0 55 2 0 0 0 0 0 2 1 0.999946 16 173 0 55 2 0 0 0 0 55 2 -19.995470 1 1 0 0 1 0 2 2 1.454667 1 0.550000 3.730000 0.550000 0.310000 1.800000e-01 1.000000 0.300000 0.354078 0.310000 0 2.400000e-01 0.410000 GNB2 2783 broad.mit.edu 37 7 100276124 100276124 + Missense_Mutation SNP A A T rs147810006 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:100276124A>T ENST00000303210.4 + 9 1285 c.803A>T c.(802-804)aAc>aTc p.N268I GNB2_ENST00000393926.1_Missense_Mutation_p.N268I|GNB2_ENST00000427895.1_Missense_Mutation_p.N168I|GNB2_ENST00000436220.1_Missense_Mutation_p.N224I|GNB2_ENST00000393924.1_Missense_Mutation_p.N268I|GNB2_ENST00000424361.1_Missense_Mutation_p.N224I|GNB2_ENST00000419828.1_Missense_Mutation_p.N168I NM_005273.3 NP_005264.2 P62879 GBB2_HUMAN guanine nucleotide binding protein (G protein), beta polypeptide 2 7 Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817) Ovarian(593;0.238) TCCCATGACAACATCATCTGT 0.607000 0 SO:0001583 missense ENST00000303210.4 1 1 hg19 CCDS5703.1 . . . . . . . . . . . 21.3 4.125242 0.77436 0.0 2.33E-4 ENSG00000172354 ENST00000303210;ENST00000436220;ENST00000424361;ENST00000419828;ENST00000427895;ENST00000393926;ENST00000393924 T;D;D;D;D;T;T 0.82619 5.0;-1.63;-1.63;-1.63;-1.63;5.0;5.0 5.67 4.45 0.53987 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 D 0.85952 0.5817 M 0.75264 2.295 0.58432 D 0.999996 B 0.32409 0.37 P 0.44732 0.459 D 0.86865 0.2032 10 0.72032 D 0.01 -11.881 10.667 0.45736 0.8397:0.1603:0.0:0.0 . 268 P62879 GBB2_HUMAN I 268;224;224;168;168;268;268 ENSP00000305260:N268I;ENSP00000401873:N224I;ENSP00000389391:N224I;ENSP00000390543:N168I;ENSP00000400286:N168I;ENSP00000377503:N268I;ENSP00000377501:N268I ENSP00000305260:N268I N + 2 0 GNB2 100114060 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 1.846000 0.39289 2.174000 0.68829 0.454000 0.30748 AAC TCGA-YY-A8LH-01A-11D-A36O-08 GNB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268391.2 1 0 1 43 144 0 48 1 1 291 857 0 48 2 0 0 0 0 0 2 1 1.000000 41 143 0 47 2 0 0 0 0 48 2 -20.000000 1 1 121412 2 38 1 2 2 4 2.097417 0 0.550000 3.730000 0.709677 0.990000 9.700000e-01 1.000000 1.000000 0.998207 0.990000 1 9.900000e-01 1.000000 NDUFA4 4697 broad.mit.edu 37 7 10979646 10979646 + Silent SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:10979646C>A ENST00000339600.5 - 1 237 c.39G>T c.(37-39)ccG>ccT p.P13P RP5-855F16.1_ENST00000604183.1_lincRNA|NDUFA4_ENST00000492822.1_5'UTR NM_002489.3 NP_002480.1 O00483 NDUA4_HUMAN NDUFA4, mitochondrial complex associated 3 AACTTACGCTCGGATGCTTCT 0.567000 0 SO:0001819 synonymous_variant ENST00000339600.5 0 1 hg19 CCDS5357.1 TCGA-YY-A8LH-01A-11D-A36O-08 NDUFA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207507.3 0 0 0 11 915 0 156 0 9.999990e-01 1 2601 0 156 2 0 0 0 0 0 2 1 0.998195 11 903 0 153 2 0 0 0 0 156 2 -2.028848 0 1 0 0 1 2 5 7 3.090611 1 0.550000 3.730000 0.801325 0.100000 1.000000e-02 1.000000 0.130000 0.162449 0.100000 0 5.000000e-02 0.160000 SSPO 23145 broad.mit.edu 37 7 149503953 149503953 + RNA SNP G G T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:149503953G>T ENST00000378016.2 + 0 8777 A2VEC9 SSPO_HUMAN SCO-spondin Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) GCCCCCGGCTGCACCTGCCCC 0.657000 0 ENST00000378016.2 0 1 hg19 TCGA-YY-A8LH-01A-11D-A36O-08 SSPO-202 KNOWN basic processed_transcript processed_transcript 0 0 0 20 74 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 0.999997 18 74 0 20 2 0 0 0 0 21 2 -20.000000 1 1 0 0 1 2 2 4 2.097417 0 0.550000 3.730000 0.709677 0.990000 7.900000e-01 1.000000 1.000000 0.981714 0.990000 1 9.800000e-01 1.000000 HDAC9 9734 broad.mit.edu 37 7 18767353 18767353 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:18767353C>A ENST00000432645.2 + 12 1873 c.1873C>A c.(1873-1875)Cgc>Agc p.R625S HDAC9_ENST00000441542.2_Missense_Mutation_p.R628S|HDAC9_ENST00000401921.1_Missense_Mutation_p.R584S|HDAC9_ENST00000406451.4_Missense_Mutation_p.R625S NM_058176.2 NP_478056.1 Q9UKV0 HDAC9_HUMAN histone deacetylase 9 82 all_lung(11;0.187) Valproic Acid(DB00313) AGCAATGGACCGCCCCCTCCA 0.527000 0 SO:0001583 missense ENST00000432645.2 0 1 hg19 CCDS47555.1 . . . . . . . . . . C 5.499 0.276989 0.10403 . . ENSG00000048052 ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009 T;T;T;T 0.57107 0.43;0.42;0.42;0.43 4.87 1.44 0.22558 . 0.387462 0.22358 N 0.061105 T 0.35537 0.0935 L 0.36672 1.1 0.80722 D 1 B;B;B;B;B;B;B 0.19817 0.001;0.01;0.034;0.01;0.02;0.01;0.039 B;B;B;B;B;B;B 0.17979 0.003;0.01;0.018;0.018;0.008;0.018;0.02 T 0.10337 -1.0634 10 0.09338 T 0.73 -24.6513 9.38 0.38306 0.0:0.7311:0.0:0.2689 . 625;537;584;628;625;625;603 Q9UKV0-4;Q9UKV0-2;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5;Q8N879 .;.;.;.;HDAC9_HUMAN;.;. S 625;584;625;628;537 ENSP00000384657:R625S;ENSP00000383912:R584S;ENSP00000410337:R625S;ENSP00000408617:R628S ENSP00000339165:R537S R + 1 0 HDAC9 18733878 1.000000 0.71417 0.829000 0.32907 0.991000 0.79684 1.096000 0.30976 0.150000 0.19136 0.557000 0.71058 CGC TCGA-YY-A8LH-01A-11D-A36O-08 HDAC9-023 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000376176.1 0 0 0 5 135 0 23 0 0 0 1 0 23 2 0 0 0 0 0 2 1 0.938689 5 135 0 22 2 0 0 0 0 23 2 -3.346692 1 1 0 0 1 2 5 7 3.090611 1 0.550000 3.730000 0.801325 0.330000 1.100000e-01 1.000000 0.270000 0.389371 0.330000 0 2.000000e-01 0.530000 FAM188B 84182 broad.mit.edu 37 7 30825421 30825421 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:30825421C>A ENST00000265299.6 + 4 553 c.476C>A c.(475-477)cCg>cAg p.P159Q INMT-FAM188B_ENST00000458257.1_3'UTR NM_032222.2 NP_115598.2 Q4G0A6 F188B_HUMAN family with sequence similarity 188, member B 29 AAAAGGCCCCCGCACAAAAGT 0.448000 0 SO:0001583 missense ENST00000265299.6 0 1 hg19 CCDS43565.1 . . . . . . . . . . C 2.790 -0.251521 0.05867 . . ENSG00000106125 ENST00000265299 T 0.23552 1.9 5.19 2.32 0.28847 . 0.790451 0.11983 N 0.510580 T 0.16642 0.0400 L 0.41236 1.265 0.09310 N 1 P 0.34955 0.477 B 0.24701 0.055 T 0.19943 -1.0290 10 0.87932 D 0 -7.9428 4.8572 0.13564 0.1701:0.6496:0.0:0.1803 . 159 Q4G0A6 F188B_HUMAN Q 159 ENSP00000265299:P159Q ENSP00000265299:P159Q P + 2 0 FAM188B 30791946 0.001000 0.12720 0.104000 0.21259 0.172000 0.22775 1.070000 0.30653 0.762000 0.33152 0.650000 0.86243 CCG TCGA-YY-A8LH-01A-11D-A36O-08 FAM188B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000327962.1 0 0 0 9 683 0 100 0 6.828432e-02 0 29 0 100 2 0 0 0 0 0 2 1 0.993943 9 675 0 99 2 0 0 0 0 100 2 -2.063888 0 1 0 0 1 2 5 7 3.090611 1 0.550000 3.730000 0.801325 0.110000 2.000000e-02 1.000000 0.130000 0.175118 0.110000 0 6.000000e-02 0.180000 GLI3 2737 broad.mit.edu 37 7 42116379 42116379 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:42116379C>T ENST00000395925.3 - 4 529 c.445G>A c.(445-447)Gat>Aat p.D149N GLI3_ENST00000479210.1_5'UTR NM_000168.5 NP_000159.3 P10071 GLI3_HUMAN GLI family zinc finger 3 112 GGAGATGGATCGTAATGGTAA 0.433000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 0 SO:0001583 missense Familial Cancer Database ; ENST00000395925.3 0 1 hg19 CCDS5465.1 . . . . . . . . . . C 31 5.070585 0.93950 . . ENSG00000106571 ENST00000395925;ENST00000448703 T;T 0.69561 -0.41;-0.41 5.65 5.65 0.86999 . 0.099090 0.64402 D 0.000003 T 0.72510 0.3469 L 0.34521 1.04 0.80722 D 1 D 0.67145 0.996 P 0.57960 0.83 T 0.74411 -0.3674 10 0.72032 D 0.01 . 20.0781 0.97751 0.0:1.0:0.0:0.0 . 149 P10071 GLI3_HUMAN N 149 ENSP00000379258:D149N;ENSP00000406135:D149N ENSP00000379258:D149N D - 1 0 GLI3 42082904 1.000000 0.71417 0.966000 0.40874 0.990000 0.78478 7.252000 0.78309 2.817000 0.96982 0.563000 0.77884 GAT TCGA-YY-A8LH-01A-11D-A36O-08 GLI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250806.3 0 0 0 8 360 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 0.989319 8 358 0 46 2 0 0 0 0 47 2 -2.849615 1 1 0 0 1 2 5 7 3.090611 1 0.550000 3.730000 0.801325 0.190000 7.000000e-02 1.000000 0.200000 0.251803 0.190000 0 1.200000e-01 0.290000 ABCA13 154664 broad.mit.edu 37 7 48317894 48317894 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:48317894C>T ENST00000435803.1 + 18 7127 c.7103C>T c.(7102-7104)gCc>gTc p.A2368V NM_152701.3 NP_689914.2 Q86UQ4 ABCAD_HUMAN ATP-binding cassette, sub-family A (ABC1), member 13 270 TTATTTAATGCCCTTCTCAGG 0.308000 0 SO:0001583 missense ENST00000435803.1 1 1 hg19 CCDS47584.1 . . . . . . . . . . C 4.546 0.101394 0.08731 . . ENSG00000179869 ENST00000435803 T 0.55760 0.5 4.75 1.32 0.21799 . 1.533400 0.04221 N 0.333578 T 0.38480 0.1042 L 0.28274 0.84 0.09310 N 1 B 0.02656 0.0 B 0.06405 0.002 T 0.34675 -0.9819 10 0.72032 D 0.01 . 2.659 0.05020 0.2212:0.501:0.0:0.2778 . 2368 Q86UQ4 ABCAD_HUMAN V 2368 ENSP00000411096:A2368V ENSP00000411096:A2368V A + 2 0 ABCA13 48288440 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.498000 0.06420 0.517000 0.28361 0.561000 0.74099 GCC TCGA-YY-A8LH-01A-11D-A36O-08 ABCA13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341964.2 1 0 1 28 154 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 1.000000 28 150 0 23 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 2 5 7 3.105492 1 0.550000 3.730000 0.802523 0.990000 8.900000e-01 1.000000 1.000000 0.993708 0.990000 1 9.900000e-01 1.000000 KCTD7 154881 broad.mit.edu 37 7 66103879 66103879 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:66103879G>A ENST00000275532.3 + 4 714 c.530G>A c.(529-531)cGt>cAt p.R177H KCTD7_ENST00000443322.1_Missense_Mutation_p.R177H NM_001167961.2|NM_153033.4 NP_001161433.1|NP_694578.1 Q96MP8 KCTD7_HUMAN potassium channel tetramerization domain containing 7 p.R177H(1) 16 GCCCGGCTGCGTGCGGTCCAG 0.577000 1 Substitution - Missense(1) SO:0001583 missense ENST00000275532.3 0 1 hg19 CCDS5534.1 . . . . . . . . . . g 34 5.320885 0.95682 . . ENSG00000243335 ENST00000275532;ENST00000443322 T;T 0.79033 -1.23;-1.23 5.36 5.36 0.76844 . . . . . T 0.79411 0.4441 L 0.43152 1.355 0.80722 D 1 D 0.67145 0.996 P 0.51170 0.661 T 0.80476 -0.1366 9 0.52906 T 0.07 . 18.4294 0.90620 0.0:0.0:1.0:0.0 . 177 Q96MP8 KCTD7_HUMAN H 177 ENSP00000275532:R177H;ENSP00000411624:R177H ENSP00000275532:R177H R + 2 0 KCTD7 65741314 1.000000 0.71417 0.993000 0.49108 0.978000 0.69477 9.097000 0.94193 2.675000 0.91044 0.655000 0.94253 CGT TCGA-YY-A8LH-01A-11D-A36O-08 KCTD7-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000251733.2 0 0 0 5 250 0 82 0 5.908465e-03 0 5 0 82 2 0 0 0 0 0 2 1 0.936200 5 248 0 81 2 0 0 0 0 82 2 -3.977127 1 1 0 0 1 2 2 4 2.097417 0 0.550000 3.730000 0.709677 0.110000 3.000000e-02 0.250000 0.120000 0.131341 0.110000 0 7.000000e-02 0.180000 SAMD9L 219285 broad.mit.edu 37 7 92764937 92764937 + Silent SNP T T C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:92764937T>C ENST00000318238.4 - 5 1564 c.348A>G c.(346-348)tcA>tcG p.S116S SAMD9L_ENST00000437805.1_Silent_p.S116S|SAMD9L_ENST00000411955.1_Silent_p.S116S NM_152703.2 NP_689916.2 Q8IVG5 SAM9L_HUMAN sterile alpha motif domain containing 9-like 88 all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989) STAD - Stomach adenocarcinoma(171;0.000302) CAATATTAGATGACATTGAAT 0.323000 0 SO:0001819 synonymous_variant ENST00000318238.4 1 1 hg19 CCDS34681.1 TCGA-YY-A8LH-01A-11D-A36O-08 SAMD9L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341730.1 1 0 1 131 286 0 98 1 9.605059e-01 6 8 0 98 2 0 0 0 0 0 2 1 1.000000 130 283 0 98 2 0 0 0 0 98 2 -20.000000 1 1 0 0 1 2 2 4 2.097417 0 0.550000 3.730000 0.709677 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 COL1A2 1278 broad.mit.edu 37 7 94039063 94039063 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr7:94039063G>A ENST00000297268.6 + 19 1436 c.965G>A c.(964-966)gGc>gAc p.G322D NM_000089.3 NP_000080.2 P08123 CO1A2_HUMAN collagen, type I, alpha 2 COL1A2/PLAG1(3) 115 all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08) STAD - Stomach adenocarcinoma(171;0.0031) Collagenase(DB00048) GGGGCTCCCGGCCTCCCTGGA 0.577000 HNSCC(75;0.22) 0 SO:0001583 missense ENST00000297268.6 1 1 hg19 CCDS34682.1 . . . . . . . . . . G 22.8 4.335985 0.81801 . . ENSG00000164692 ENST00000297268;ENST00000545487 D 0.99619 -6.28 5.58 5.58 0.84498 . 0.000000 0.85682 D 0.000000 D 0.99796 0.9913 H 0.96365 3.81 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.97235 0.9887 10 0.87932 D 0 . 19.966 0.97266 0.0:0.0:1.0:0.0 . 322 P08123 CO1A2_HUMAN D 322;323 ENSP00000297268:G322D ENSP00000297268:G322D G + 2 0 COL1A2 93876999 1.000000 0.71417 0.985000 0.45067 0.772000 0.43724 9.439000 0.97543 2.802000 0.96397 0.655000 0.94253 GGC TCGA-YY-A8LH-01A-11D-A36O-08 COL1A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000309045.2 1 0 0 25 302 0 74 0 9.999997e-01 0 311 0 74 2 0 0 0 0 0 2 1 1.000000 26 301 0 74 2 0 0 0 0 74 2 -8.187247 1 1 0 0 1 2 2 4 2.097417 0 0.550000 3.730000 0.709677 0.430000 2.800000e-01 0.610000 0.440000 0.444880 0.430000 0 3.500000e-01 0.530000 USP17L2 377630 broad.mit.edu 37 8 11995011 11995011 + Nonsense_Mutation SNP A A T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr8:11995011A>T ENST00000333796.3 - 1 1575 c.1259T>A c.(1258-1260)tTg>tAg p.L420* FAM66D_ENST00000434078.2_RNA NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2 NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2 Q6R6M4 U17L2_HUMAN ubiquitin specific peptidase 17-like family member 2 29 GCGCTCGTCCAACTCGGGTGC 0.567000 0 SO:0001587 stop_gained ENST00000333796.3 0 1 hg19 CCDS43713.1 . . . . . . . . . . A 19.49 3.836544 0.71373 . . ENSG00000223443 ENST00000333796 . . . 0.36 -0.721 0.11189 . 0.944627 0.08527 U 0.932543 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.14252 T 0.57 . . . . . . . . X 420 . ENSP00000333329:L420X L - 2 0 USP17L2 12032420 0.001000 0.12720 0.001000 0.08648 0.001000 0.01503 -0.011000 0.12721 -0.718000 0.04949 -0.731000 0.03576 TTG TCGA-YY-A8LH-01A-11D-A36O-08 USP17L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383303.2 1 0 0 23 409 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 0.999999 23 385 0 121 2 0 0 0 0 121 2 -19.999990 1 1 0 0 1 3 3 6 2.162354 1 0.550000 3.730000 0.717691 0.330000 2.000000e-01 1.000000 0.310000 0.483988 0.330000 0 2.600000e-01 1.000000 CYP11B1 1584 broad.mit.edu 37 8 143957228 143957228 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr8:143957228G>A ENST00000292427.4 - 6 1053 c.1021C>T c.(1021-1023)Cgc>Tgc p.R341C CYP11B1_ENST00000377675.3_Missense_Mutation_p.R412C|CYP11B1_ENST00000517471.1_Missense_Mutation_p.R341C NM_000497.3 NP_000488.3 P15538 C11B1_HUMAN cytochrome P450, family 11, subfamily B, polypeptide 1 67 all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155) Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421) CTCTCCTGGCGCAGGGCCTGC 0.642000 Familial Hyperaldosteronism type I 0 GRCh37 HM972176 CYP11B1 M SO:0001583 missense Familial Cancer Database Dexamethasone Sensitive Aldosteronism, FH-I ENST00000292427.4 1 1 hg19 CCDS6392.1 . . . . . . . . . . . 17.71 3.456204 0.63401 0.0 1.16E-4 ENSG00000160882 ENST00000292427;ENST00000517471;ENST00000377675 T;T;T 0.73152 -0.72;2.31;-0.72 4.42 2.16 0.27623 . 0.126247 0.31963 N 0.006789 D 0.85652 0.5746 M 0.93854 3.465 0.58432 D 0.999996 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.998;0.997;0.997;0.976;0.999 D 0.86599 0.1865 10 0.66056 D 0.02 . 9.7347 0.40382 0.0:0.0:0.4473:0.5527 . 412;341;341;341;57 Q4VAR0;Q8TDD0;Q4VAQ9;P15538;Q8N9P8 .;.;.;C11B1_HUMAN;. C 341;341;412 ENSP00000292427:R341C;ENSP00000428043:R341C;ENSP00000366903:R412C ENSP00000292427:R341C R - 1 0 CYP11B1 143954230 0.011000 0.17503 0.991000 0.47740 0.808000 0.45660 0.560000 0.23500 0.949000 0.37715 0.555000 0.69702 CGC TCGA-YY-A8LH-01A-11D-A36O-08 CYP11B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379475.2 1 0 0 44 524 0 178 0 0 0 0 178 2 0 0 0 0 0 2 1 1.000000 43 516 0 176 2 0 0 0 0 178 2 -10.672130 1 1 121408 12 43 1 3 3 6 2.162354 1 0.550000 3.730000 0.717691 0.470000 3.300000e-01 1.000000 0.460000 0.588020 0.470000 0 3.900000e-01 1.000000 PLEC 5339 broad.mit.edu 37 8 144994985 144994985 + Nonsense_Mutation SNP G G A rs137853161 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr8:144994985G>A ENST00000322810.4 - 32 9584 c.9415C>T c.(9415-9417)Cga>Tga p.R3139* PLEC_ENST00000436759.2_Nonsense_Mutation_p.R3029*|PLEC_ENST00000354589.3_Nonsense_Mutation_p.R3002*|PLEC_ENST00000527096.1_Nonsense_Mutation_p.R3025*|PLEC_ENST00000357649.2_Nonsense_Mutation_p.R3006*|PLEC_ENST00000354958.2_Nonsense_Mutation_p.R2980*|PLEC_ENST00000345136.3_Nonsense_Mutation_p.R3002*|PLEC_ENST00000356346.3_Nonsense_Mutation_p.R2988*|PLEC_ENST00000398774.2_Nonsense_Mutation_p.R2970* NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 137 CGCTCACCTCGCTGCAGCTGC 0.687000 0 GRCh37 CM050309 PLEC M rs137853161 SO:0001587 stop_gained ENST00000322810.4 0 1 hg19 CCDS43772.1 . . . . . . . . . . G 49 15.377758 0.99832 . . ENSG00000178209 ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096 . . . 4.6 3.71 0.42584 . 0.750881 0.11464 U 0.561429 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.05620 T 0.96 . 13.7863 0.63112 0.0:0.1557:0.8443:0.0 . . . . X 3002;3006;3002;2970;3139;2980;2988;3029;3025 . ENSP00000323856:R3139X R - 1 2 PLEC 145066973 0.864000 0.29904 0.748000 0.31131 0.005000 0.04900 2.894000 0.48640 1.042000 0.40150 0.448000 0.29417 CGA TCGA-YY-A8LH-01A-11D-A36O-08 PLEC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383281.1 1 0 0 13 209 0 50 1 9.998292e-01 20 233 0 50 2 0 0 0 0 0 2 1 0.999555 14 206 0 47 2 0 0 0 0 50 2 -16.106850 1 1 0 0 1 3 3 6 2.162354 1 0.550000 3.730000 0.717691 0.380000 2.000000e-01 1.000000 0.330000 0.515406 0.380000 0 2.700000e-01 1.000000 BMP1 649 broad.mit.edu 37 8 22054897 22054897 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr8:22054897G>A ENST00000306385.5 + 15 2741 c.2071G>A c.(2071-2073)Gtg>Atg p.V691M BMP1_ENST00000397816.3_Missense_Mutation_p.V691M|BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000306349.8_Missense_Mutation_p.V691M NM_006129.4 NP_006120.1 P13497 BMP1_HUMAN bone morphogenetic protein 1 30 CGACAACACCGTGTCCAAAAA 0.567000 0 SO:0001583 missense ENST00000306385.5 1 1 hg19 CCDS6026.1 . . . . . . . . . . G 28.2 4.895680 0.91962 0.0 1.16E-4 ENSG00000168487 ENST00000306385;ENST00000397816;ENST00000306349 T;T;T 0.30981 1.51;1.51;1.51 5.29 5.29 0.74685 CUB (5); 0.000000 0.34853 U 0.003625 T 0.58836 0.2150 M 0.79343 2.45 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.999;1.0;0.999;0.993 T 0.63346 -0.6658 10 0.72032 D 0.01 . 17.6986 0.88289 0.0:0.0:1.0:0.0 . 691;764;691;691 P13497;Q59F71;P13497-2;P13497-6 BMP1_HUMAN;.;.;. M 691 ENSP00000305714:V691M;ENSP00000380917:V691M;ENSP00000306121:V691M ENSP00000306121:V691M V + 1 0 BMP1 22110842 1.000000 0.71417 0.998000 0.56505 0.994000 0.84299 9.869000 0.99810 2.451000 0.82905 0.563000 0.77884 GTG TCGA-YY-A8LH-01A-11D-A36O-08 BMP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214995.2 0 0 0 22 676 0 213 0 7.014472e-01 1 74 0 213 2 0 0 0 0 0 2 1 0.999998 22 660 0 210 2 0 0 0 0 213 2 -3.047490 1 1 121412 4 42 1 3 3 6 2.162354 1 0.550000 3.730000 0.717691 0.200000 1.100000e-01 1.000000 0.170000 0.385379 0.200000 0 1.500000e-01 1.000000 OPRK1 4986 broad.mit.edu 37 8 54142191 54142191 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr8:54142191C>T ENST00000265572.3 - 4 1106 c.809G>A c.(808-810)cGt>cAt p.R270H RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Missense_Mutation_p.R270H|OPRK1_ENST00000524278.1_Missense_Mutation_p.R181H NM_000912.3 NP_000903.2 P41145 OPRK_HUMAN opioid receptor, kappa 1 43 all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136) Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193) GGTGATCCTACGCAGGTTGCG 0.572000 0 SO:0001583 missense ENST00000265572.3 0 1 hg19 CCDS6152.1 . . . . . . . . . . C 16.06 3.017222 0.54576 . . ENSG00000082556 ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798 T;T;T 0.73681 -0.77;-0.77;-0.77 5.8 4.91 0.64330 GPCR, rhodopsin-like superfamily (1); 0.047781 0.85682 D 0.000000 D 0.87176 0.6112 M 0.83118 2.625 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.89336 0.3650 10 0.87932 D 0 . 16.2563 0.82519 0.1338:0.8662:0.0:0.0 . 270 P41145 OPRK_HUMAN H 270;181;270;256 ENSP00000265572:R270H;ENSP00000430923:R181H;ENSP00000429706:R270H ENSP00000265572:R270H R - 2 0 OPRK1 54304744 1.000000 0.71417 0.055000 0.19348 0.004000 0.04260 7.818000 0.86416 1.433000 0.47394 -0.188000 0.12872 CGT TCGA-YY-A8LH-01A-11D-A36O-08 OPRK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378048.1 0 0 0 7 179 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.979295 6 175 0 51 2 0 0 0 0 52 2 -9.099499 1 1 121412 2 35 1 3 3 6 2.162354 1 0.550000 3.730000 0.717691 0.260000 1.000000e-01 1.000000 0.210000 0.427731 0.260000 0 1.600000e-01 1.000000 OR2K2 26248 broad.mit.edu 37 9 114090184 114090184 + Missense_Mutation SNP G G A rs137871340 by1000genomes TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr9:114090184G>A ENST00000374428.1 - 1 616 c.617C>T c.(616-618)aCg>aTg p.T206M OR2K2_ENST00000302681.1_Missense_Mutation_p.T177M Q8NGT1 OR2K2_HUMAN olfactory receptor, family 2, subfamily K, member 2 20 AATTTCACACGTGAAGTGATC 0.517000 0 SO:0001583 missense ENST00000374428.1 1 1 hg19 3 0.0013736263736263737 0 0.0 0 0.0 3 0.005244755244755245 0 0.0 G 7.211 0.595400 0.13875 . . ENSG00000171133 ENST00000302681;ENST00000374428 T;T 0.00084 8.75;8.75 4.92 1.0 0.19881 GPCR, rhodopsin-like superfamily (1); 0.000000 0.41712 U 0.000834 T 0.00144 0.0004 L 0.31926 0.97 0.18873 N 0.999982 D 0.89917 1.0 D 0.70716 0.97 T 0.52975 -0.8503 10 0.62326 D 0.03 . 3.5372 0.07798 0.2438:0.0:0.4545:0.3016 . 206 Q8NGT1 OR2K2_HUMAN M 177;206 ENSP00000305055:T177M;ENSP00000363550:T206M ENSP00000305055:T177M T - 2 0 OR2K2 113130005 0.000000 0.05858 0.023000 0.16930 0.086000 0.17979 0.148000 0.16224 0.096000 0.17463 -0.194000 0.12790 ACG TCGA-YY-A8LH-01A-11D-A36O-08 OR2K2-201 KNOWN basic protein_coding protein_coding 1 0 0 9 207 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 0.993885 9 202 0 84 2 0 0 0 0 84 2 -3.277497 1 1 121410 35 46 1 1 2 3 1.623441 1 0.550000 3.730000 0.626943 0.200000 9.000000e-02 1.000000 0.190000 0.344041 0.200000 0 1.400000e-01 1.000000 ASS1 445 broad.mit.edu 37 9 133355188 133355188 + Splice_Site SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr9:133355188G>A ENST00000372394.1 + 11 1254 c.e11+1 ASS1_ENST00000493984.2_Splice_Site|ASS1_ENST00000372393.3_Splice_Site|ASS1_ENST00000352480.5_Splice_Site P00966 ASSY_HUMAN argininosuccinate synthase 1 17 Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155) ACGAAGTCGCGTGAGTGTCTG 0.617000 0 SO:0001630 splice_region_variant ENST00000372394.1 1 1 hg19 CCDS6933.1 . . . . . . . . . . G 7.670 0.686809 0.14973 . . ENSG00000130707 ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393 . . . 4.91 4.91 0.64330 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.0774 0.86590 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . ASS1 132345009 1.000000 0.71417 0.999000 0.59377 0.096000 0.18686 8.569000 0.90744 2.270000 0.75569 0.467000 0.42956 . TCGA-YY-A8LH-01A-11D-A36O-08 ASS1-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054652.1 1 0 0 16 179 0 89 1 4.325148e-01 3 14 0 89 2 0 0 0 0 0 2 1 0.946225 15 177 1 88 9 0 0 0 0 89 2 -19.980240 1 1 0 0 1 1 2 3 1.664950 1 0.550000 3.730000 0.635258 0.390000 2.200000e-01 1.000000 0.370000 0.458941 0.390000 0 2.900000e-01 0.550000 C9orf72 203228 broad.mit.edu 37 9 27567059 27567059 + Missense_Mutation SNP A A T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chr9:27567059A>T ENST00000380003.3 - 2 123 c.60T>A c.(58-60)agT>agA p.S20R C9orf72_ENST00000488117.1_5'UTR|C9orf72_ENST00000379997.3_Missense_Mutation_p.S20R NM_001256054.1|NM_018325.3 NP_001242983.1|NP_060795.1 Q96LT7 CI072_HUMAN chromosome 9 open reading frame 72 23 all_neural(11;7.57e-10) GTGATTTGCCACTTAAAGCAA 0.458000 0 SO:0001583 missense ENST00000380003.3 0 1 hg19 CCDS6522.1 . . . . . . . . . . A 13.46 2.242614 0.39598 . . ENSG00000147894 ENST00000380003;ENST00000379997;ENST00000379995 T;T;T 0.44083 0.93;0.93;0.93 5.99 5.99 0.97316 . 0.225686 0.53938 D 0.000046 T 0.22859 0.0552 N 0.08118 0 0.33621 D 0.604779 B;B 0.16603 0.018;0.011 B;B 0.18871 0.023;0.003 T 0.32587 -0.9901 9 . . . . 11.5134 0.50507 0.931:0.0:0.069:0.0 . 20;20 Q96LT7-2;Q96LT7 .;CI072_HUMAN R 20 ENSP00000369339:S20R;ENSP00000369333:S20R;ENSP00000369331:S20R . S - 3 2 C9orf72 27557059 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 1.511000 0.35801 2.291000 0.77112 0.533000 0.62120 AGT TCGA-YY-A8LH-01A-11D-A36O-08 C9orf72-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051969.1 0 0 0 5 300 0 97 0 1.409316e-02 0 9 0 97 2 0 0 0 0 0 2 0 0.933018 0 297 0 97 2 0 0 0 0 97 2 -5.987158 1 0 0 0 1 1 2 3 1.623441 1 0.550000 3.730000 0.626943 0.080000 2.000000e-02 1.000000 0.080000 0.249547 0.080000 0 4.000000e-02 1.000000 ACSL4 2182 broad.mit.edu 37 X 108906514 108906514 + Missense_Mutation SNP T T C rs148996116 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:108906514T>C ENST00000469796.2 - 13 2027 c.1631A>G c.(1630-1632)gAt>gGt p.D544G ACSL4_ENST00000348502.6_Missense_Mutation_p.D503G|ACSL4_ENST00000340800.2_Missense_Mutation_p.D544G O60488 ACSL4_HUMAN acyl-CoA synthetase long-chain family member 4 22 Icosapent(DB00159)|Rosiglitazone(DB00412) TCCATTTTCATCCACAGAATA 0.378000 Pancreas(188;358 2127 38547 41466 45492) 0 SO:0001583 missense ENST00000469796.2 0 1 hg19 CCDS14548.1 . . . . . . . . . . T 25.1 4.608081 0.87258 2.61E-4 0.0 ENSG00000068366 ENST00000348502;ENST00000469796;ENST00000340800 T;T;T 0.13420 2.59;2.59;2.59 5.52 5.52 0.82312 AMP-dependent synthetase/ligase (1); 0.000000 0.85682 D 0.000000 T 0.49253 0.1546 H 0.94345 3.525 0.80722 D 1 D 0.76494 0.999 D 0.76575 0.988 T 0.64525 -0.6387 10 0.87932 D 0 -21.9098 14.6742 0.68967 0.0:0.0:0.0:1.0 . 544 O60488 ACSL4_HUMAN G 503;544;544 ENSP00000262835:D503G;ENSP00000419171:D544G;ENSP00000339787:D544G ENSP00000339787:D544G D - 2 0 ACSL4 108793170 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.035000 0.88872 1.846000 0.53633 0.486000 0.48141 GAT TCGA-YY-A8LH-01A-11D-A36O-08 ACSL4-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000358155.2 0 0 0 18 1304 0 351 0 1.005664e-01 0 37 0 351 2 0 0 0 0 0 2 1 0.999980 18 1295 0 349 2 0 0 0 0 351 2 -3.142737 1 1 121410 7 46 1 0 1 1 0.550000 3.730000 0.550000 0.040000 2.000000e-02 0.080000 0.050000 0.051789 0.040000 0 3.000000e-02 0.070000 ARHGAP36 158763 broad.mit.edu 37 X 130215846 130215846 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:130215846C>A ENST00000276211.5 + 2 552 c.207C>A c.(205-207)caC>caA p.H69Q ARHGAP36_ENST00000370921.1_5'Flank|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.H57Q NM_144967.3 NP_659404.2 Q6ZRI8 RHG36_HUMAN Rho GTPase activating protein 36 71 CTGCTTACCACGAACTCGTGG 0.577000 0 SO:0001583 missense ENST00000276211.5 1 1 hg19 CCDS14628.1 . . . . . . . . . . C 10.74 1.436770 0.25900 . . ENSG00000147256 ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432 T;T;T 0.09255 3.0;3.0;3.01 4.36 -2.17 0.07059 . 0.475884 0.18258 N 0.146730 T 0.04363 0.0120 N 0.19112 0.55 0.80722 D 1 B;B;B 0.06786 0.001;0.001;0.001 B;B;B 0.08055 0.003;0.003;0.001 T 0.44050 -0.9353 10 0.22706 T 0.39 . 1.0036 0.01482 0.4372:0.2288:0.1417:0.1922 . 38;57;69 Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8 .;.;RHG36_HUMAN Q 69;57;21;38 ENSP00000276211:H69Q;ENSP00000359960:H57Q;ENSP00000408515:H38Q ENSP00000276211:H69Q H + 3 2 ARHGAP36 130043527 0.778000 0.28640 0.937000 0.37676 0.976000 0.68499 -0.888000 0.04148 -0.670000 0.05282 -0.268000 0.10319 CAC TCGA-YY-A8LH-01A-11D-A36O-08 ARHGAP36-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355073.1 1 0 0 40 736 0 205 0 0 0 1 0 205 2 0 0 0 0 0 2 1 1.000000 40 723 0 203 2 0 0 0 0 205 2 -6.349091 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.180000 1.300000e-01 0.250000 0.180000 0.191416 0.180000 0 1.500000e-01 0.220000 GPC4 2239 broad.mit.edu 37 X 132445300 132445300 + Missense_Mutation SNP C C A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:132445300C>A ENST00000370828.3 - 4 1387 c.863G>T c.(862-864)tGg>tTg p.W288L GPC4_ENST00000535467.1_Missense_Mutation_p.W218L NM_001448.2 NP_001439.2 O75487 GPC4_HUMAN glypican 4 28 Acute lymphoblastic leukemia(192;0.000127) GAAATTGTTCCATTCAAAATC 0.443000 0 SO:0001583 missense ENST00000370828.3 1 1 hg19 CCDS14637.1 . . . . . . . . . . C 26.7 4.763050 0.89932 . . ENSG00000076716 ENST00000370828;ENST00000536418;ENST00000535467 T;T 0.80566 -1.39;-1.39 5.61 5.61 0.85477 . 0.000000 0.85682 D 0.000000 D 0.91432 0.7296 M 0.90082 3.085 0.80722 D 1 D 0.63880 0.993 D 0.69142 0.962 D 0.93066 0.6478 10 0.87932 D 0 -19.8545 17.5641 0.87914 0.0:1.0:0.0:0.0 . 288 O75487 GPC4_HUMAN L 288;282;218 ENSP00000359864:W288L;ENSP00000444959:W218L ENSP00000359864:W288L W - 2 0 GPC4 132272966 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 7.754000 0.85163 2.363000 0.80096 0.600000 0.82982 TGG TCGA-YY-A8LH-01A-11D-A36O-08 GPC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058338.1 1 0 0 51 733 0 181 0 9.464658e-01 0 71 0 181 2 0 0 0 0 0 2 1 1.000000 51 724 0 177 2 0 0 0 0 181 2 -2.966611 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.230000 1.700000e-01 0.300000 0.240000 0.240308 0.230000 0 2.000000e-01 0.270000 FGF13 2258 broad.mit.edu 37 X 137793125 137793125 + Missense_Mutation SNP C C G TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:137793125C>G ENST00000315930.6 - 1 702 c.41G>C c.(40-42)aGg>aCg p.R14T FGF13-AS1_ENST00000438238.1_RNA|FGF13_ENST00000305414.4_Intron|FGF13_ENST00000541469.1_Intron|FGF13-AS1_ENST00000446383.1_RNA|FGF13_ENST00000441825.2_Intron|FGF13_ENST00000370603.3_Intron NM_004114.3 NP_004105.1 Q92913 FGF13_HUMAN fibroblast growth factor 13 24 Acute lymphoblastic leukemia(192;0.000127) GCGGGCTTGCCTCTTCTGACG 0.597000 0 SO:0001583 missense ENST00000315930.6 1 1 hg19 CCDS14665.1 . . . . . . . . . . C 23.9 4.473036 0.84640 . . ENSG00000129682 ENST00000315930 D 0.84944 -1.92 4.29 4.29 0.51040 . . . . . D 0.86464 0.5939 L 0.60455 1.87 0.80722 D 1 P 0.46277 0.875 P 0.48524 0.58 D 0.88447 0.3046 9 0.72032 D 0.01 . 15.3424 0.74309 0.0:1.0:0.0:0.0 . 14 Q92913 FGF13_HUMAN T 14 ENSP00000322390:R14T ENSP00000322390:R14T R - 2 0 FGF13 137620791 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.318000 0.79029 1.889000 0.54706 0.529000 0.55759 AGG TCGA-YY-A8LH-01A-11D-A36O-08 FGF13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058534.2 0 0 0 13 450 0 127 0 0 0 0 127 2 0 0 0 0 0 2 1 0.999468 12 440 0 126 2 0 0 0 0 127 2 -11.792490 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.100000 5.000000e-02 0.170000 0.100000 0.109271 0.100000 0 7.000000e-02 0.140000 PASD1 139135 broad.mit.edu 37 X 150817142 150817142 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:150817142G>A ENST00000370357.4 + 9 930 c.685G>A c.(685-687)Gct>Act p.A229T NM_173493.2 NP_775764.2 Q8IV76 PASD1_HUMAN PAS domain containing 1 48 Acute lymphoblastic leukemia(192;6.56e-05) CGTTGAACCCgctgctgctgc 0.438000 0 SO:0001583 missense ENST00000370357.4 1 0 hg19 CCDS35431.1 . . . . . . . . . . G 11.20 1.567649 0.28003 . . ENSG00000166049 ENST00000370357 T 0.70869 -0.52 4.14 -1.2 0.09554 . . . . . T 0.34135 0.0887 N 0.14661 0.345 0.09310 N 1 P 0.37997 0.614 B 0.24006 0.05 T 0.39542 -0.9609 9 0.02654 T 1 . 0.9417 0.01357 0.3078:0.1545:0.3775:0.1602 . 229 Q8IV76 PASD1_HUMAN T 229 ENSP00000359382:A229T ENSP00000359382:A229T A + 1 0 PASD1 150567798 0.000000 0.05858 0.000000 0.03702 0.110000 0.19582 -0.428000 0.06991 -0.573000 0.05998 0.422000 0.28245 GCT TCGA-YY-A8LH-01A-11D-A36O-08 PASD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060879.2 1 0 1 308 327 0 183 0 0 0 0 183 2 0 0 0 0 0 2 1 1.000000 157 170 0 90 2 0 0 0 0 183 2 -20.000000 1 1 120992 1 41 1 0 1 1 0.550000 3.730000 0.550000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 MECP2 4204 broad.mit.edu 37 X 153296299 153296299 + Missense_Mutation SNP G G A rs61751369 TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:153296299G>A ENST00000303391.6 - 4 1229 c.980C>T c.(979-981)aCc>aTc p.T327I MECP2_ENST00000453960.2_Missense_Mutation_p.T339I|MECP2_ENST00000460227.1_5'Flank NM_004992.3 NP_004983.1 P51608 MECP2_HUMAN methyl CpG binding protein 2 p.T327N(1) 23 all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CTCACCGAGGGTGGACACCAG 0.617000 1 Substitution - Missense(1) SO:0001583 missense ENST00000303391.6 1 1 hg19 CCDS14741.1 . . . . . . . . . . G 14.65 2.599919 0.46318 . . ENSG00000169057 ENST00000303391;ENST00000545451;ENST00000453960 D;D 0.91295 -2.82;-2.81 5.06 5.06 0.68205 . 0.554194 0.19741 N 0.107108 T 0.81531 0.4842 N 0.14661 0.345 0.80722 D 1 B;B 0.26400 0.144;0.148 B;B 0.27170 0.077;0.035 T 0.76683 -0.2869 10 0.19147 T 0.46 -5.948 11.8253 0.52263 0.0:0.0:0.8245:0.1755 . 339;327 P51608-2;P51608 .;MECP2_HUMAN I 327;327;339 ENSP00000301948:T327I;ENSP00000395535:T339I ENSP00000301948:T327I T - 2 0 MECP2 152949493 0.912000 0.30974 0.128000 0.21923 0.887000 0.51463 5.301000 0.65727 2.344000 0.79699 0.600000 0.82982 ACC TCGA-YY-A8LH-01A-11D-A36O-08 MECP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000061144.1 0 0 0 13 446 0 118 1 8.692156e-01 5 122 0 118 2 0 0 0 0 0 2 1 0.999505 12 442 0 116 2 0 0 0 0 118 2 -11.963040 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.100000 5.000000e-02 0.170000 0.100000 0.110218 0.100000 0 7.000000e-02 0.140000 VBP1 7411 broad.mit.edu 37 X 154464621 154464621 + Nonsense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:154464621C>T ENST00000286428.5 + 5 613 c.496C>T c.(496-498)Cga>Tga p.R166* VBP1_ENST00000459836.1_3'UTR|VBP1_ENST00000535916.1_Nonsense_Mutation_p.R161* NM_003372.5 NP_003363.1 P61758 PFD3_HUMAN von Hippel-Lindau binding protein 1 p.R166G(1) 12 all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) TGACTTTCTTCGAGATCAATT 0.353000 1 Substitution - Missense(1) SO:0001587 stop_gained ENST00000286428.5 0 1 hg19 CCDS14765.1 . . . . . . . . . . C 37 6.295580 0.97449 . . ENSG00000155959 ENST00000535916;ENST00000286428 . . . 4.86 4.86 0.63082 . 0.109676 0.64402 D 0.000016 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -1.9083 10.1751 0.42933 0.1991:0.8008:0.0:0.0 . . . . X 161;166 . ENSP00000286428:R166X R + 1 2 VBP1 154117815 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.440000 0.52886 2.324000 0.78689 0.594000 0.82650 CGA TCGA-YY-A8LH-01A-11D-A36O-08 VBP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058806.1 0 0 0 9 739 0 168 0 4.759532e-01 0 123 0 168 2 0 0 0 0 0 2 1 0.993692 9 726 0 166 2 0 0 0 0 168 2 -2.598769 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.040000 1.000000e-02 0.080000 0.040000 0.048611 0.040000 0 2.000000e-02 0.060000 MAGEB6 158809 broad.mit.edu 37 X 26213024 26213024 + Missense_Mutation SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:26213024G>A ENST00000379034.1 + 2 1210 c.1061G>A c.(1060-1062)tGc>tAc p.C354Y NM_173523.2 NP_775794.2 Q8N7X4 MAGB6_HUMAN melanoma antigen family B, 6 33 GATCCTCCATGCTATGAGTTC 0.498000 0 SO:0001583 missense ENST00000379034.1 0 1 hg19 CCDS14217.1 . . . . . . . . . . G 5.430 0.264533 0.10294 . . ENSG00000176746 ENST00000379034 T 0.04706 3.57 3.29 -2.14 0.07123 . 0.617794 0.14414 U 0.321058 T 0.04770 0.0129 M 0.66439 2.03 0.09310 N 1 B 0.10296 0.003 B 0.17979 0.02 T 0.49881 -0.8892 10 0.08381 T 0.77 . 5.8566 0.18722 0.2283:0.511:0.2607:0.0 . 354 Q8N7X4 MAGB6_HUMAN Y 354 ENSP00000368320:C354Y ENSP00000368320:C354Y C + 2 0 MAGEB6 26122945 0.000000 0.05858 0.000000 0.03702 0.022000 0.10575 -1.416000 0.02467 -0.702000 0.05056 -0.957000 0.02645 TGC TCGA-YY-A8LH-01A-11D-A36O-08 MAGEB6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056123.1 0 0 0 26 367 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 1.000000 20 319 0 202 2 0 0 0 0 138 2 -7.329741 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.230000 1.500000e-01 0.340000 0.240000 0.248030 0.230000 0 1.900000e-01 0.290000 BCOR 54880 broad.mit.edu 37 X 39922163 39922163 + Missense_Mutation SNP C C T TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:39922163C>T ENST00000378444.4 - 9 4237 c.4009G>A c.(4009-4011)Gaa>Aaa p.E1337K BCOR_ENST00000378463.1_Missense_Mutation_p.E180K|BCOR_ENST00000342274.4_Missense_Mutation_p.E1303K|BCOR_ENST00000397354.3_Missense_Mutation_p.E1303K|BCOR_ENST00000378455.4_Missense_Mutation_p.E1285K NM_001123385.1 NP_001116857.1 Q6W2J9 BCOR_HUMAN BCL6 corepressor 126 TCCTCTTCTTCGTCTGCACAC 0.532000 F, N, S, T RARA retinoblastoma, AML, APL(translocation) oculo-facio-cardio-dental genetic Rec yes X Xp11.4 54880 BCL6 corepressor yes 0 SO:0001583 missense ENST00000378444.4 1 1 hg19 CCDS48093.1 . . . . . . . . . . C 24.3 4.518746 0.85495 0.0 1.49E-4 ENSG00000183337 ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018 T;T;T;T;T;T;T 0.70516 -0.42;0.97;1.0;0.98;0.93;0.98;-0.49 5.67 5.67 0.87782 . . . . . T 0.75845 0.3905 N 0.19112 0.55 0.53005 D 0.999965 D;D;D 0.89917 1.0;1.0;0.997 D;D;P 0.78314 0.951;0.991;0.896 T 0.78889 -0.2026 9 0.56958 D 0.05 -10.0684 18.7655 0.91871 0.0:1.0:0.0:0.0 . 1285;1337;1303 Q6W2J9-4;Q6W2J9;Q6W2J9-2 .;BCOR_HUMAN;. K 207;180;1285;1303;1337;1303;10 ENSP00000408006:E207K;ENSP00000367724:E180K;ENSP00000367716:E1285K;ENSP00000380512:E1303K;ENSP00000367705:E1337K;ENSP00000345923:E1303K;ENSP00000387552:E10K ENSP00000345923:E1303K E - 1 0 BCOR 39807107 1.000000 0.71417 0.350000 0.25708 0.966000 0.64601 3.518000 0.53451 2.376000 0.81061 0.600000 0.82982 GAA TCGA-YY-A8LH-01A-11D-A36O-08 BCOR-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000060666.2 1 0 1 9 138 0 43 1 9.788593e-01 29 77 0 43 2 0 0 0 0 0 2 1 0.994332 8 137 0 42 2 0 0 0 0 43 2 -4.988409 1 1 121388 6 28 1 0 1 1 0.550000 3.730000 0.550000 0.220000 1.100000e-01 0.390000 0.220000 0.242687 0.220000 0 1.600000e-01 0.310000 ZXDB 158586 broad.mit.edu 37 X 57620752 57620752 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:57620752G>A ENST00000374888.1 + 1 2484 c.2271G>A c.(2269-2271)gcG>gcA p.A757A NM_007157.3 NP_009088.1 P98169 ZXDB_HUMAN zinc finger, X-linked, duplicated B p.A757A(1) 27 CAACCAAAGCGGAGTGGAACG 0.488000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000374888.1 1 1 hg19 CCDS35313.1 TCGA-YY-A8LH-01A-11D-A36O-08 ZXDB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056922.1 0 0 1 89 283 1 122 0 7.787196e-01 0 11 1 122 2 0 0 0 0 0 2 1 1.000000 87 279 1 119 12 0 0 0 1 122 2 -4.614652 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.860000 7.100000e-01 1.000000 1.000000 0.870873 0.860000 1 7.800000e-01 0.950000 MAGEE2 139599 broad.mit.edu 37 X 75004797 75004797 + Silent SNP G G A TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:75004797G>A ENST00000373359.2 - 1 282 c.90C>T c.(88-90)aaC>aaT p.N30N NM_138703.4 NP_619648.1 Q8TD90 MAGE2_HUMAN melanoma antigen family E, 2 p.N30N(2) 34 ACCCGGAGGCGTTAGTAGCTT 0.577000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000373359.2 1 1 hg19 CCDS14431.1 TCGA-YY-A8LH-01A-11D-A36O-08 MAGEE2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057288.1 1 0 1 89 145 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 1.000000 87 143 0 55 2 0 0 0 0 56 2 -20.000000 1 1 118024 4 40 1 0 1 1 0.550000 3.730000 0.550000 0.990000 9.900000e-01 1.000000 1.000000 0.999994 0.990000 1 9.900000e-01 1.000000 RPS6KA6 27330 broad.mit.edu 37 X 83362013 83362013 + Missense_Mutation SNP G G C TCGA-YY-A8LH-01A-11D-A36O-08 TCGA-YY-A8LH-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 527590f9-cf74-408c-a748-c698f1be8d37 81f01f7f-56f1-4882-914f-76940d0d117d g.chrX:83362013G>C ENST00000262752.2 - 14 1154 c.1147C>G c.(1147-1149)Cag>Gag p.Q383E RPS6KA6_ENST00000495332.1_5'Flank|RPS6KA6_ENST00000543399.1_Missense_Mutation_p.Q383E NM_014496.4 NP_055311.1 Q9UK32 KS6A6_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 6 46 TTGAAGAGCTGATGAGCATTT 0.343000 0 SO:0001583 missense ENST00000262752.2 1 1 hg19 CCDS14451.1 . . . . . . . . . . G 10.19 1.280893 0.23392 . . ENSG00000072133 ENST00000262752;ENST00000543399 T;T 0.50548 0.74;0.74 4.93 4.93 0.64822 Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2); 0.115806 0.64402 D 0.000014 T 0.26738 0.0654 N 0.04148 -0.265 0.80722 D 1 B;B 0.12013 0.001;0.005 B;B 0.18263 0.021;0.015 T 0.12243 -1.0555 10 0.09843 T 0.71 . 17.563 0.87912 0.0:0.0:1.0:0.0 . 383;383 B7ZL90;Q9UK32 .;KS6A6_HUMAN E 383 ENSP00000262752:Q383E;ENSP00000440830:Q383E ENSP00000262752:Q383E Q - 1 0 RPS6KA6 83248669 1.000000 0.71417 0.998000 0.56505 0.994000 0.84299 7.577000 0.82486 2.162000 0.67917 0.600000 0.82982 CAG TCGA-YY-A8LH-01A-11D-A36O-08 RPS6KA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057372.1 1 0 0 24 341 0 78 0 0 0 1 0 78 2 0 0 0 0 0 2 1 1.000000 24 339 0 76 2 0 0 0 0 78 2 -20.000000 1 1 0 0 1 0 1 1 0.550000 3.730000 0.550000 0.230000 1.500000e-01 0.340000 0.240000 0.247140 0.230000 0 1.900000e-01 0.290000