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 IL4R 3566 broad.mit.edu 37 16 27367137 27367166 + In_Frame_Del DEL GAGCCCTTCGAGCAGCACCTCCTGCTGGGC GAGCCCTTCGAGCAGCACCTCCTGCTGGGC - TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr16:27367137_27367166delGAGCCCTTCGAGCAGCACCTCCTGCTGGGC ENST00000395762.2 + 8 938_967 c.679_708delGAGCCCTTCGAGCAGCACCTCCTGCTGGGC c.(679-708)gagcccttcgagcagcacctcctgctgggcdel p.EPFEQHLLLG227del IL4R_ENST00000565915.1_3'UTR|IL4R_ENST00000543915.2_In_Frame_Del_p.EPFEQHLLLG227del|IL4R_ENST00000380922.3_In_Frame_Del_p.EPFEQHLLLG212del|IL4R_ENST00000170630.2_In_Frame_Del_p.EPFEQHLLLG227del NM_000418.3 NP_000409.1 P24394 IL4RA_HUMAN interleukin 4 receptor 33 AGCCTACAGGGAGCCCTTCGAGCAGCACCTCCTGCTGGGCGTCAGCGTTT 0.622000 0 SO:0001651 inframe_deletion ENST00000395762.2 0 1 hg19 CCDS10629.1 TCGA-FB-AAQ2-01A-31D-A40W-08 IL4R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214104.4 1 0 0 18 327 0 49 0 7.365866e-01 0 49 0 49 2 0 0 0 0 0 0 1 0.999995 38 350 0 49 2 -19.581470 1 1 0 0 1 1 2 3 2.079698 0 0.460000 1.950000 0.468556 0.230000 1.400000e-01 1.000000 0.230000 0.283417 0.230000 0 1.800000e-01 3.100000e-01 PSTK 118672 broad.mit.edu 37 10 124746879 124746879 + Missense_Mutation SNP T T C TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr10:124746879T>C ENST00000368887.3 + 6 1347 c.907T>C c.(907-909)Ttt>Ctt p.F303L PSTK_ENST00000497219.1_3'UTR|PSTK_ENST00000405485.1_3'UTR NM_153336.2 NP_699167.2 Q8IV42 PSTK_HUMAN phosphoseryl-tRNA kinase 13 all_neural(114;0.169)|Glioma(114;0.222) agagatgacatttaagcaaag 0.423000 0 SO:0001583 missense ENST00000368887.3 0 1 hg19 CCDS7633.1 . . . . . . . . . . T 5.062 0.197044 0.09599 . . ENSG00000179988 ENST00000368887 T 0.49432 0.78 2.11 2.11 0.27256 . 0.974060 0.08343 N 0.960511 T 0.11879 0.0289 N 0.00179 -1.91 0.20638 N 0.999873 B 0.06786 0.001 B 0.10450 0.005 T 0.32375 -0.9909 10 0.07030 T 0.85 . 6.2226 0.20689 0.0:0.0:0.0:1.0 . 303 Q8IV42 PSTK_HUMAN L 303 ENSP00000357882:F303L ENSP00000357882:F303L F + 1 0 PSTK 124736869 0.000000 0.05858 0.087000 0.20705 0.903000 0.53119 0.284000 0.18864 1.227000 0.43598 0.533000 0.62120 TTT TCGA-FB-AAQ2-01A-31D-A40W-08 PSTK-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050811.1 0 0 0 4 136 0 27 0 3.367398e-02 0 8 0 27 2 0 0 0 0 0 2 1 0.886361 4 133 0 27 2 -7.313595 1 1 0 0 1 0 1 1 1.846396 1 0.460000 1.950000 0.399199 0.120000 3.000000e-02 0.260000 0.110000 0.136130 0.120000 0 7.000000e-02 1.900000e-01 GATA3 2625 broad.mit.edu 37 10 8100325 8100325 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr10:8100325G>A ENST00000346208.3 + 3 754 c.299G>A c.(298-300)gGc>gAc p.G100D GATA3_ENST00000379328.3_Missense_Mutation_p.G100D P23771 GATA3_HUMAN GATA binding protein 3 87 CTGGACGGCGGCAAAGCCCTG 0.677000 F, N, S breast HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE) Rec yes 10 10p15 2625 GATA binding protein 3 yes E 0 SO:0001583 missense ENST00000346208.3 0 1 hg19 CCDS7083.1 . . . . . . . . . . G 13.42 2.231371 0.39399 . . ENSG00000107485 ENST00000379328;ENST00000544011;ENST00000346208 D;D 0.96365 -3.99;-3.98 5.31 5.31 0.75309 . 0.194098 0.53938 D 0.000041 D 0.95242 0.8457 L 0.50333 1.59 0.45205 D 0.998212 B;B 0.29136 0.191;0.234 B;B 0.33750 0.062;0.169 D 0.93958 0.7238 10 0.59425 D 0.04 -24.0814 18.9617 0.92679 0.0:0.0:1.0:0.0 . 100;100 P23771;P23771-2 GATA3_HUMAN;. D 100 ENSP00000368632:G100D;ENSP00000341619:G100D ENSP00000341619:G100D G + 2 0 GATA3 8140331 1.000000 0.71417 0.935000 0.37517 0.204000 0.24138 7.816000 0.86201 2.469000 0.83416 0.561000 0.74099 GGC TCGA-FB-AAQ2-01A-31D-A40W-08 GATA3-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000046719.1 0 0 0 5 457 0 79 0 2.749956e-02 0 19 0 79 2 0 0 0 0 0 2 1 0.925253 5 425 0 75 2 -2.451450 0 1 0 0 1 0 1 1 1.846396 1 0.460000 1.950000 0.399199 0.040000 1.000000e-02 0.090000 0.040000 0.050350 0.040000 0 2.000000e-02 7.000000e-02 ZC3H12C 85463 broad.mit.edu 37 11 110007605 110007605 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr11:110007605C>T ENST00000278590.3 + 2 290 c.239C>T c.(238-240)gCg>gTg p.A80V ZC3H12C_ENST00000453089.2_Missense_Mutation_p.A49V|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.A81V NM_033390.1 NP_203748.1 Q9C0D7 ZC12C_HUMAN zinc finger CCCH-type containing 12C p.A80V(1) 37 all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-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) GAAAAAGAGGCGTCTGAAGAG 0.448000 1 Substitution - Missense(1) SO:0001583 missense ENST00000278590.3 1 1 hg19 CCDS44727.1 . . . . . . . . . . t 8.666 0.901758 0.17760 . . ENSG00000149289 ENST00000278590;ENST00000528673;ENST00000453089 T;T;T 0.30981 1.51;1.51;1.51 5.62 5.62 0.85841 . . . . . T 0.07234 0.0183 N 0.00289 -1.7 0.09310 N 0.999998 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.01281 0.0;0.0;0.0 T 0.31530 -0.9940 9 0.11182 T 0.66 -1.0609 6.3914 0.21589 0.0:0.2884:0.0:0.7116 . 81;80;80 B4DR47;B4DI65;Q9C0D7 .;.;ZC12C_HUMAN V 80;81;49 ENSP00000278590:A80V;ENSP00000431821:A81V;ENSP00000413094:A49V ENSP00000278590:A80V A + 2 0 ZC3H12C 109512815 0.021000 0.18746 1.000000 0.80357 0.098000 0.18820 0.260000 0.18424 0.966000 0.38159 -0.269000 0.10298 GCG TCGA-FB-AAQ2-01A-31D-A40W-08 ZC3H12C-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000390491.1 1 0 1 27 111 0 29 1 2.641232e-01 4 1 0 29 2 0 0 0 0 0 2 1 1.000000 27 109 0 28 2 -20.000000 1 1 120826 3 32 1 1 2 3 2.040000 0 0.460000 1.950000 0.462473 0.850000 5.900000e-01 1.000000 1.000000 0.852095 0.850000 1 7.100000e-01 1 OR8B2 26595 broad.mit.edu 37 11 124253123 124253123 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr11:124253123C>T ENST00000375013.2 - 1 135 c.117G>A c.(115-117)atG>atA p.M39I NM_001005468.1 NP_001005468.1 Q96RD0 OR8B2_HUMAN olfactory receptor, family 8, subfamily B, member 2 23 Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224) GGTTGCCTACCATGGTGACAA 0.418000 0 SO:0001583 missense ENST00000375013.2 1 1 hg19 CCDS31708.1 . . . . . . . . . . c 11.01 1.512128 0.27036 0.0 3.49E-4 ENSG00000204293 ENST00000375013 T 0.00524 6.82 4.2 1.17 0.20885 . 0.871881 0.10283 N 0.693231 T 0.00210 0.0006 N 0.01405 -0.89 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.42965 -0.9420 10 0.54805 T 0.06 . 1.6651 0.02800 0.1587:0.3523:0.3088:0.1803 . 39 Q96RD0 OR8B2_HUMAN I 39 ENSP00000364152:M39I ENSP00000364152:M39I M - 3 0 OR8B2 123758333 0.000000 0.05858 0.002000 0.10522 0.262000 0.26303 -0.293000 0.08320 0.151000 0.19162 0.400000 0.26472 ATG TCGA-FB-AAQ2-01A-31D-A40W-08 OR8B2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387290.1 0 0 0 37 787 1 190 0 0 0 1 190 2 0 0 0 0 0 2 1 0.999230 35 762 1 201 15 -2.456333 0 1 121412 10 49 1 1 2 3 2.040000 0 0.460000 1.950000 0.462473 0.190000 1.300000e-01 0.280000 0.200000 0.208490 0.190000 0 1.600000e-01 2.300000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-FB-AAQ2-01A-31D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 63 145 0 60 1 9.791257e-01 11 6 0 60 2 1 1 140 467 0 513 2 1 1.000000 62 142 0 59 2 -20.000000 1 1 121404 2 44 1 2 4 6 2.453125 1 0.460000 1.950000 0.557667 0.990000 9.900000e-01 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 LEPREL2 10536 broad.mit.edu 37 12 6939687 6939687 + RNA SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr12:6939687G>A ENST00000538102.1 + 0 40 LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000251761.8_RNA Q8IVL6 P3H3_HUMAN leprecan-like 2 10 L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126) ATGGGGCTGCGAGCCAGGGGG 0.642000 0 ENST00000538102.1 0 1 hg19 TCGA-FB-AAQ2-01A-31D-A40W-08 LEPREL2-006 KNOWN basic processed_transcript polymorphic_pseudogene OTTHUMT00000399998.1 0 0 0 6 54 0 13 0 5.580892e-01 0 17 0 13 2 0 0 0 0 0 2 1 0.965862 5 54 0 13 2 -12.220260 1 1 120502 10 32 1 1 3 4 2.984419 1 0.460000 1.950000 0.624217 0.680000 2.800000e-01 1.000000 1.000000 0.691933 0.680000 0 4.500000e-01 9.900000e-01 C1RL 51279 broad.mit.edu 37 12 7249506 7249506 + Silent SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr12:7249506C>T ENST00000266542.4 - 6 1037 c.945G>A c.(943-945)ggG>ggA p.G315G C1RL_ENST00000545280.1_Intron|C1RL_ENST00000544702.1_3'UTR|C1RL_ENST00000504702.2_Intron NM_016546.2 NP_057630.2 Q9NZP8 C1RL_HUMAN complement component 1, r subcomponent-like 16 CAGGGTGGTTCCCCAGTTTCA 0.552000 0 SO:0001819 synonymous_variant ENST00000266542.4 0 1 hg19 CCDS8573.1 . . . . . . . . . . C 3.389 -0.124736 0.06795 . . ENSG00000139178 ENST00000534950 . . . 4.98 -9.95 0.00446 . . . . . T 0.42063 0.1186 . . . 0.46185 D 0.998912 . . . . . . T 0.49835 -0.8897 4 . . . . 5.2161 0.15344 0.0767:0.1221:0.3579:0.4432 . . . . K 148 . . E - 1 0 C1RL 7140648 0.000000 0.05858 0.000000 0.03702 0.641000 0.38312 -2.582000 0.00905 -2.698000 0.00400 -0.350000 0.07774 GAA TCGA-FB-AAQ2-01A-31D-A40W-08 C1RL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398367.1 0 0 0 9 465 0 72 1 5.661677e-01 7 87 0 72 2 0 0 0 0 0 2 1 0.993475 9 451 0 70 2 -2.673493 1 1 0 0 1 1 3 4 2.984419 1 0.460000 1.950000 0.624217 0.120000 5.000000e-02 1.000000 0.120000 0.164091 0.120000 0 8.000000e-02 1.800000e-01 ACSS3 79611 broad.mit.edu 37 12 81647110 81647110 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr12:81647110G>A ENST00000548058.1 + 14 2654 c.1744G>A c.(1744-1746)Gca>Aca p.A582T ACSS3_ENST00000548324.1_Missense_Mutation_p.A264T|ACSS3_ENST00000261206.3_Missense_Mutation_p.A581T Q9H6R3 ACSS3_HUMAN acyl-CoA synthetase short-chain family member 3 51 TGGTACCGTGGCAGACTGTGC 0.373000 0 SO:0001583 missense ENST00000548058.1 1 1 hg19 CCDS9022.1 . . . . . . . . . . G 17.46 3.395361 0.62066 . . ENSG00000111058 ENST00000548058;ENST00000261206;ENST00000548324 T;T;T 0.62105 0.05;0.05;0.05 6.0 4.17 0.49024 AMP-dependent synthetase/ligase (1); 0.383935 0.28809 N 0.014067 T 0.63522 0.2518 M 0.81179 2.53 0.37366 D 0.911421 B;B 0.32526 0.374;0.0 B;B 0.29267 0.1;0.003 T 0.69614 -0.5098 10 0.72032 D 0.01 -0.5583 13.4013 0.60885 0.1288:0.0:0.8712:0.0 . 264;582 Q9H6R3-2;Q9H6R3 .;ACSS3_HUMAN T 582;581;264 ENSP00000449535:A582T;ENSP00000261206:A581T;ENSP00000448965:A264T ENSP00000261206:A581T A + 1 0 ACSS3 80171241 1.000000 0.71417 0.279000 0.24732 0.981000 0.71138 5.191000 0.65110 0.869000 0.35703 -0.261000 0.10672 GCA TCGA-FB-AAQ2-01A-31D-A40W-08 ACSS3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000407794.1 1 0 1 138 528 0 159 0 4.354520e-02 0 2 0 159 2 0 0 0 0 0 2 1 1.000000 138 520 0 158 2 -20.000000 1 1 0 0 1 0 1 1 1.701434 1 0.460000 1.950000 0.315068 0.700000 6.000000e-01 0.810000 0.710000 0.710950 0.700000 0 6.500000e-01 7.600000e-01 SPERT 220082 broad.mit.edu 37 13 46287859 46287859 + Silent SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr13:46287859C>T ENST00000310521.1 + 3 779 c.699C>T c.(697-699)caC>caT p.H233H SPERT_ENST00000378966.3_Silent_p.H197H NM_152719.1 NP_689932.1 Q8NA61 SPERT_HUMAN spermatid associated 15 Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556) KIRC - Kidney renal clear cell carcinoma(16;0.234) AGAAGGACCACGTCGCCCTGC 0.682000 0 SO:0001819 synonymous_variant ENST00000310521.1 1 1 hg19 CCDS9399.1 TCGA-FB-AAQ2-01A-31D-A40W-08 SPERT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044786.2 1 0 1 29 145 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 1.000000 29 141 0 23 2 -20.000000 1 1 121378 1 27 1 1 2 3 2.521774 1 0.460000 1.950000 0.560976 0.890000 6.200000e-01 1.000000 1.000000 0.881291 0.890000 1 7.500000e-01 1 IPO5 3843 broad.mit.edu 37 13 98658520 98658520 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr13:98658520C>T ENST00000490680.1 + 14 1699 c.1634C>T c.(1633-1635)gCg>gTg p.A545V IPO5_ENST00000539640.1_Missense_Mutation_p.A420V|IPO5_ENST00000261574.5_Missense_Mutation_p.A563V|IPO5_ENST00000493492.2_3'UTR O00410 IPO5_HUMAN importin 5 27 GTTGAGAATGCGGTTCAAAAA 0.378000 0 SO:0001583 missense ENST00000490680.1 0 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 35|35 5.423620|5.423620 0.96111|0.96111 .|. .|. ENSG00000065150|ENSG00000065150 ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640|ENST00000469360 T;T;T;T|. 0.24350|. 1.86;1.86;1.86;1.86|. 5.1|5.1 5.1|5.1 0.69264|0.69264 Armadillo-type fold (1);|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.76644|0.76644 0.4016|0.4016 M|M 0.73962|0.73962 2.25|2.25 0.80722|0.80722 D|D 1|1 P;D;D|. 0.69078|. 0.947;0.995;0.997|. P;P;P|. 0.54664|. 0.59;0.578;0.758|. T|T 0.76512|0.76512 -0.2932|-0.2932 10|5 0.72032|. D|. 0.01|. -10.5253|-10.5253 18.8688|18.8688 0.92305|0.92305 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 420;545;563|. B4E0R6;O00410;O00410-3|. .;IPO5_HUMAN;.|. V|W 563;545;545;420|547 ENSP00000261574:A563V;ENSP00000350219:A545V;ENSP00000418393:A545V;ENSP00000445126:A420V|. ENSP00000261574:A563V|. A|R +|+ 2|1 0|2 IPO5|IPO5 97456521|97456521 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.981000|0.981000 0.71138|0.71138 5.928000|5.928000 0.70088|0.70088 2.525000|2.525000 0.85131|0.85131 0.460000|0.460000 0.39030|0.39030 GCG|CGG TCGA-FB-AAQ2-01A-31D-A40W-08 IPO5-006 NOVEL alternative_5_UTR|basic|appris_principal protein_coding protein_coding OTTHUMT00000354655.1 0 0 0 5 538 0 89 0 7.946496e-01 0 315 0 89 2 0 0 0 0 0 2 1 0.936276 5 533 0 86 2 -1.999313 0 1 121412 1 26 1 1 2 3 2.521774 1 0.460000 1.950000 0.560976 0.050000 0 0.110000 0.060000 0.058057 0.050000 0 2.000000e-02 8.000000e-02 ZFYVE26 23503 broad.mit.edu 37 14 68233050 68233050 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr14:68233050C>T ENST00000347230.4 - 32 6043 c.5905G>A c.(5905-5907)Gag>Aag p.E1969K ZFYVE26_ENST00000555452.1_Missense_Mutation_p.E1969K NM_015346.3 NP_056161.2 Q68DK2 ZFY26_HUMAN zinc finger, FYVE domain containing 26 94 GCATCCACCTCTGGGTTGGTG 0.577000 0 SO:0001583 missense ENST00000347230.4 1 1 hg19 CCDS9788.1 . . . . . . . . . . C 35 5.573986 0.96553 . . ENSG00000072121 ENST00000347230;ENST00000411699;ENST00000555452 T;T 0.34667 1.5;1.35 5.71 5.71 0.89125 . 0.000000 0.85682 D 0.000000 T 0.64583 0.2611 M 0.77486 2.375 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.85130 0.997;0.994 T 0.66654 -0.5869 10 0.72032 D 0.01 -18.437 19.8574 0.96764 0.0:1.0:0.0:0.0 . 1969;1969 G3V2D8;Q68DK2 .;ZFY26_HUMAN K 1969;1948;1969 ENSP00000251119:E1969K;ENSP00000450603:E1969K ENSP00000251119:E1969K E - 1 0 ZFYVE26 67302803 1.000000 0.71417 1.000000 0.80357 0.824000 0.46624 7.771000 0.85420 2.704000 0.92352 0.555000 0.69702 GAG TCGA-FB-AAQ2-01A-31D-A40W-08 ZFYVE26-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412736.2 1 0 1 114 383 0 65 1 9.602587e-01 5 15 0 65 2 0 0 0 0 0 2 1 1.000000 112 375 0 63 2 -4.227237 1 1 0 0 1 1 2 3 2.067251 0 0.460000 1.950000 0.466139 0.990000 8.400000e-01 1.000000 1.000000 0.973325 0.990000 1 9.200000e-01 1 PLA2G4D 283748 broad.mit.edu 37 15 42362977 42362977 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr15:42362977G>A ENST00000290472.3 - 18 2075 c.1981C>T c.(1981-1983)Cgg>Tgg p.R661W NM_178034.3 NP_828848.3 Q86XP0 PA24D_HUMAN phospholipase A2, group IVD (cytosolic) 27 all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245) CGGCCTGGCCGGAACATGGAG 0.657000 0 SO:0001583 missense ENST00000290472.3 0 1 hg19 CCDS32203.1 . . . . . . . . . . G 15.03 2.711719 0.48517 . . ENSG00000159337 ENST00000290472 T 0.16073 2.37 4.46 3.54 0.40534 Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2); 0.216636 0.29884 N 0.010944 T 0.25680 0.0625 M 0.89715 3.055 0.42428 D 0.992664 B 0.17268 0.021 B 0.06405 0.002 T 0.14008 -1.0488 10 0.66056 D 0.02 -11.7079 7.7234 0.28746 0.0883:0.0:0.7119:0.1998 . 661 Q86XP0 PA24D_HUMAN W 661 ENSP00000290472:R661W ENSP00000290472:R661W R - 1 2 PLA2G4D 40150269 0.961000 0.32948 0.990000 0.47175 0.986000 0.74619 0.984000 0.29565 1.224000 0.43551 0.573000 0.79308 CGG TCGA-FB-AAQ2-01A-31D-A40W-08 PLA2G4D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000419317.1 1 0 0 15 30 0 9 0 0 0 0 9 2 0 0 0 0 0 2 1 0.999941 15 28 0 9 2 -20.000000 1 1 121196 2 17 1 0 1 1 1.895790 1 0.460000 1.950000 0.417098 0.990000 8.200000e-01 1.000000 1.000000 0.987303 0.990000 1 9.900000e-01 1 UBL7 84993 broad.mit.edu 37 15 74743165 74743165 + Missense_Mutation SNP C C A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr15:74743165C>A ENST00000567435.1 - 6 971 c.508G>T c.(508-510)Gct>Tct p.A170S UBL7_ENST00000564488.1_Missense_Mutation_p.A170S|UBL7_ENST00000565335.1_Missense_Mutation_p.A170S|UBL7_ENST00000361351.4_Missense_Mutation_p.A170S|UBL7_ENST00000395081.2_Missense_Mutation_p.A170S Q96S82 UBL7_HUMAN ubiquitin-like 7 9 TTGGGATCAGCGAAGACAGAG 0.502000 0 SO:0001583 missense ENST00000567435.1 1 1 hg19 CCDS10263.1 . . . . . . . . . . C 15.54 2.864125 0.51482 . . ENSG00000138629 ENST00000361351;ENST00000395081 T;T 0.43294 0.95;0.95 5.48 5.48 0.80851 . 0.169066 0.53938 D 0.000049 T 0.25754 0.0627 L 0.29908 0.895 0.42144 D 0.991528 P;P 0.44429 0.835;0.495 B;B 0.34824 0.19;0.145 T 0.07328 -1.0778 10 0.12103 T 0.63 -23.3972 12.6718 0.56872 0.0:0.9246:0.0:0.0754 . 210;170 D3DW56;Q96S82 .;UBL7_HUMAN S 170 ENSP00000354883:A170S;ENSP00000378518:A170S ENSP00000354883:A170S A - 1 0 UBL7 72530218 0.998000 0.40836 0.958000 0.39756 0.987000 0.75469 3.364000 0.52328 2.568000 0.86640 0.655000 0.94253 GCT TCGA-FB-AAQ2-01A-31D-A40W-08 UBL7-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000419627.1 0 0 0 14 348 1 103 0 3.730031e-01 4 161 1 103 8 0 0 0 0 0 2 1 0.638465 14 344 1 101 13 -3.837178 1 1 0 0 1 0 1 1 1.895790 1 0.460000 1.950000 0.417098 0.150000 8.000000e-02 0.250000 0.150000 0.165343 0.150000 0 1.100000e-01 2.100000e-01 RASGRF1 5923 broad.mit.edu 37 15 79350772 79350772 + Missense_Mutation SNP G G T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr15:79350772G>T ENST00000419573.3 - 3 709 c.435C>A c.(433-435)caC>caA p.H145Q RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Missense_Mutation_p.H145Q NM_002891.4 NP_002882.3 Q13972 RGRF1_HUMAN Ras protein-specific guanine nucleotide-releasing factor 1 71 TCTGCAGCAGGTGCAGGTATT 0.562000 0 SO:0001583 missense ENST00000419573.3 1 1 hg19 CCDS10309.1 . . . . . . . . . . G 18.23 3.578942 0.65878 . . ENSG00000058335 ENST00000419573;ENST00000394741 T 0.40756 1.02 4.59 3.65 0.41850 . 0.060814 0.64402 D 0.000003 T 0.56514 0.1990 M 0.65975 2.015 0.80722 D 1 D;D;D;D 0.76494 0.999;0.999;0.999;0.999 D;D;D;D 0.73708 0.958;0.958;0.958;0.981 T 0.58907 -0.7553 10 0.87932 D 0 . 7.329 0.26571 0.1963:0.0:0.8037:0.0 . 145;145;145;145 A8K270;Q8IUU5;Q13972;F8VPA5 .;.;RGRF1_HUMAN;. Q 145 ENSP00000405963:H145Q ENSP00000378224:H145Q H - 3 2 RASGRF1 77137827 1.000000 0.71417 1.000000 0.80357 0.953000 0.61014 3.502000 0.53332 2.366000 0.80165 0.542000 0.68232 CAC TCGA-FB-AAQ2-01A-31D-A40W-08 RASGRF1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000291371.3 1 0 0 38 258 0 41 0 8.690766e-02 0 4 0 41 2 0 0 0 0 0 2 1 1.000000 38 249 0 41 2 -17.033330 1 1 0 0 1 0 1 1 1.895790 1 0.460000 1.950000 0.417098 0.510000 3.700000e-01 0.670000 0.520000 0.524651 0.510000 0 4.400000e-01 6.000000e-01 FAM169B 283777 broad.mit.edu 37 15 98995216 98995216 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr15:98995216C>T ENST00000558256.1 - 5 457 c.208G>A c.(208-210)Ggt>Agt p.G70S FAM169B_ENST00000332908.4_Missense_Mutation_p.G70S NM_182562.2 NP_872368.2 Q8N8A8 F169B_HUMAN family with sequence similarity 169, member B 7 TAGCATGCACCGGTGCCATCA 0.592000 0 SO:0001583 missense ENST00000558256.1 1 1 hg19 CCDS45360.1 . . . . . . . . . . C 2.568 -0.300196 0.05532 . . ENSG00000185087 ENST00000332908 T 0.12039 2.72 4.53 1.29 0.21616 . 0.284924 0.33980 N 0.004373 T 0.05456 0.0144 L 0.27053 0.805 0.09310 N 1 P 0.40638 0.725 B 0.31290 0.127 T 0.33497 -0.9866 10 0.12766 T 0.61 -2.8104 4.1212 0.10106 0.1846:0.5603:0.0:0.2552 . 70 Q8N8A8 F169B_HUMAN S 70 ENSP00000332615:G70S ENSP00000332615:G70S G - 1 0 FAM169B 96812739 0.000000 0.05858 0.001000 0.08648 0.032000 0.12392 0.072000 0.14617 0.515000 0.28320 0.650000 0.86243 GGT TCGA-FB-AAQ2-01A-31D-A40W-08 FAM169B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415488.1 1 0 0 38 119 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 1.000000 38 116 0 21 2 -4.201373 1 1 121048 56 44 1 0 1 1 1.895790 1 0.460000 1.950000 0.417098 0.960000 7.200000e-01 1.000000 1.000000 0.934561 0.960000 1 8.300000e-01 1 IRX6 79190 broad.mit.edu 37 16 55362807 55362807 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr16:55362807G>A ENST00000290552.7 + 5 2249 c.917G>A c.(916-918)cGc>cAc p.R306H RP11-26L20.3_ENST00000558730.2_RNA NM_024335.2 NP_077311.2 P78412 IRX6_HUMAN iroquois homeobox 6 33 CGATTGGAGCGCAGGGAGTGC 0.662000 0 SO:0001583 missense ENST00000290552.7 1 1 hg19 CCDS32449.1 . . . . . . . . . . G 18.82 3.704584 0.68615 . . ENSG00000159387 ENST00000290552 D 0.89939 -2.59 5.27 4.11 0.48088 . 0.618078 0.16748 N 0.201144 T 0.80407 0.4617 N 0.24115 0.695 0.09310 N 0.999997 D 0.56287 0.975 B 0.42062 0.374 T 0.72600 -0.4244 10 0.40728 T 0.16 -15.6593 9.6842 0.40089 0.111:0.0:0.889:0.0 . 306 P78412 IRX6_HUMAN H 306 ENSP00000290552:R306H ENSP00000290552:R306H R + 2 0 IRX6 53920308 0.000000 0.05858 1.000000 0.80357 0.893000 0.52053 0.202000 0.17295 2.463000 0.83235 0.462000 0.41574 CGC TCGA-FB-AAQ2-01A-31D-A40W-08 IRX6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417445.4 1 0 1 77 275 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 1.000000 73 267 0 75 2 -20.000000 1 1 121374 1 38 1 1 2 3 2.080562 0 0.460000 1.950000 0.468556 0.970000 7.800000e-01 1.000000 1.000000 0.947423 0.970000 1 8.700000e-01 1 WDR90 197335 broad.mit.edu 37 16 701015 701015 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr16:701015G>A ENST00000293879.4 + 6 580 c.580G>A c.(580-582)Gca>Aca p.A194T AL022341.3_ENST00000455294.1_RNA|WDR90_ENST00000549091.1_Missense_Mutation_p.A194T Q96KV7 WDR90_HUMAN WD repeat domain 90 37 Hepatocellular(780;0.0218) GGCCCAGTGGGCAAAGCTGCC 0.607000 0 SO:0001583 missense ENST00000293879.4 0 1 hg19 CCDS42092.1 . . . . . . . . . . G 11.67 1.708198 0.30322 . . ENSG00000161996 ENST00000549091;ENST00000293879 T;T 0.29917 1.59;1.55 4.95 0.105 0.14535 . 0.781301 0.10905 U 0.621191 T 0.20820 0.0501 L 0.41415 1.275 0.09310 N 1 B;B;B 0.23377 0.018;0.001;0.084 B;B;B 0.18561 0.008;0.007;0.022 T 0.24225 -1.0166 10 0.51188 T 0.08 . 3.5213 0.07743 0.163:0.1287:0.5759:0.1324 . 194;194;194 Q96KV7;C9JMK1;Q96KV7-3 WDR90_HUMAN;.;. T 194 ENSP00000448122:A194T;ENSP00000293879:A194T ENSP00000293879:A194T A + 1 0 WDR90 641016 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 0.073000 0.14640 -0.197000 0.10350 -1.020000 0.02445 GCA TCGA-FB-AAQ2-01A-31D-A40W-08 WDR90-002 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000404335.1 0 0 0 6 490 0 95 0 3.153814e-02 0 19 0 95 2 0 0 0 0 0 2 1 0.964060 6 485 0 91 2 -2.689949 1 1 0 0 1 1 2 3 2.079698 0 0.460000 1.950000 0.468556 0.050000 1.000000e-02 1.000000 0.060000 0.114274 0.050000 0 3.000000e-02 9.000000e-02 TP53 7157 broad.mit.edu 37 17 7577106 7577106 + Missense_Mutation SNP G G A rs17849781 TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr17:7577106G>A ENST00000269305.4 - 8 1021 c.832C>T c.(832-834)Cct>Tct p.P278S TP53_ENST00000445888.2_Missense_Mutation_p.P278S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.P278S|TP53_ENST00000420246.2_Missense_Mutation_p.P278S|TP53_ENST00000359597.4_Missense_Mutation_p.P278S|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.P278S(55)|p.P278A(24)|p.P278T(23)|p.0?(8)|p.P278F(3)|p.P278fs*67(3)|p.?(2)|p.P278fs*28(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.F270_D281del12(1)|p.C275fs*67(1)|p.V274_P278del(1)|p.S269fs*21(1)|p.C277_P278insXXXXXXX(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TCTCTCCCAGGACAGGCACAA 0.552000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 131 Substitution - Missense(105)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Insertion - Frameshift(2)|Unknown(2)|Insertion - In frame(1) GRCh37 CM011015|CM052927 TP53 M rs17849781 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 31 5.064500 0.93898 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99881 -7.47;-7.47;-7.47;-7.47;-7.47;-7.47 5.13 5.13 0.70059 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.050655 0.85682 D 0.000000 D 0.99906 0.9955 M 0.92459 3.31 0.80722 D 1 D;D;D;D 0.89917 0.999;1.0;0.999;1.0 D;D;D;D 0.97110 0.988;1.0;0.987;0.975 D 0.96190 0.9137 10 0.87932 D 0 -13.7877 16.1198 0.81342 0.0:0.0:1.0:0.0 . 278;278;278;278 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. S 278;278;278;278;278;267;146 ENSP00000352610:P278S;ENSP00000269305:P278S;ENSP00000398846:P278S;ENSP00000391127:P278S;ENSP00000391478:P278S;ENSP00000425104:P146S ENSP00000269305:P278S P - 1 0 TP53 7517831 1.000000 0.71417 1.000000 0.80357 0.980000 0.70556 9.573000 0.98181 2.667000 0.90743 0.462000 0.41574 CCT TCGA-FB-AAQ2-01A-31D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 43 75 0 30 1 1 95 15 0 30 2 1 1 348 944 0 1203 2 1 1.000000 39 72 0 29 2 -20.000000 1 1 0 0 1 0 1 1 1.628294 1 0.460000 1.950000 0.300790 0.960000 8.100000e-01 1.000000 1.000000 0.951672 0.960000 1 8.900000e-01 1 CCDC40 55036 broad.mit.edu 37 17 78039368 78039368 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr17:78039368C>T ENST00000397545.4 + 10 1552 c.1525C>T c.(1525-1527)Cgc>Tgc p.R509C CCDC40_ENST00000374877.3_Missense_Mutation_p.R509C|CCDC40_ENST00000269318.5_Missense_Mutation_p.R509C|CCDC40_ENST00000374876.4_Intron NM_017950.3 NP_060420.2 Q4G0X9 CCD40_HUMAN coiled-coil domain containing 40 p.R509G(2) 38 all_neural(118;0.167) OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149) CATGAAGCACCGCGACGAGGC 0.692000 2 Substitution - Missense(2) SO:0001583 missense ENST00000397545.4 1 1 hg19 CCDS42395.1 . . . . . . . . . . C 14.52 2.560125 0.45590 . . ENSG00000141519 ENST00000374877;ENST00000269318;ENST00000397545 T;D;T 0.85171 0.02;-1.95;0.17 5.14 5.14 0.70334 . . . . . D 0.92639 0.7661 M 0.84846 2.72 0.58432 D 0.999992 D;D 0.89917 1.0;1.0 D;D 0.97110 0.999;1.0 D 0.93632 0.6957 9 0.87932 D 0 -17.7899 14.2557 0.66051 0.1497:0.8503:0.0:0.0 . 509;292 Q4G0X9;Q4G0X9-3 CCD40_HUMAN;. C 509 ENSP00000364011:R509C;ENSP00000269318:R509C;ENSP00000380679:R509C ENSP00000269318:R509C R + 1 0 CCDC40 75653963 0.993000 0.37304 0.038000 0.18304 0.025000 0.11179 3.700000 0.54786 2.390000 0.81377 0.655000 0.94253 CGC TCGA-FB-AAQ2-01A-31D-A40W-08 CCDC40-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256005.2 1 0 0 24 348 0 81 0 2.509171e-02 0 4 0 81 2 0 0 0 0 0 2 1 1.000000 24 343 0 79 2 -2.578481 1 1 121050 4 38 1 1 2 3 2.041021 0 0.460000 1.950000 0.462473 0.280000 1.800000e-01 0.430000 0.280000 0.298000 0.280000 0 2.300000e-01 3.500000e-01 RNF152 220441 broad.mit.edu 37 18 59483165 59483165 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr18:59483165C>T ENST00000312828.3 - 2 1631 c.532G>A c.(532-534)Gtc>Atc p.V178I NM_173557.2 NP_775828.1 Q8N8N0 RN152_HUMAN ring finger protein 152 17 Colorectal(73;0.186) AAGACCAAGACGCAAGCCACC 0.592000 0 SO:0001583 missense ENST00000312828.3 1 1 hg19 CCDS11978.1 . . . . . . . . . . C 13.78 2.338338 0.41398 . . ENSG00000176641 ENST00000312828 D 0.84146 -1.81 4.69 4.69 0.59074 . 0.069218 0.56097 D 0.000024 T 0.75817 0.3901 N 0.17082 0.46 0.47862 D 0.999534 B 0.20550 0.046 B 0.14023 0.01 T 0.70733 -0.4791 10 0.32370 T 0.25 -0.1111 17.8094 0.88611 0.0:1.0:0.0:0.0 . 178 Q8N8N0 RN152_HUMAN I 178 ENSP00000316628:V178I ENSP00000316628:V178I V - 1 0 RNF152 57634145 1.000000 0.71417 1.000000 0.80357 0.957000 0.61999 5.036000 0.64164 2.461000 0.83175 0.563000 0.77884 GTC TCGA-FB-AAQ2-01A-31D-A40W-08 RNF152-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256180.1 1 0 1 87 244 0 73 1 2.865318e-01 3 1 0 73 2 0 0 0 0 0 2 1 1.000000 86 240 0 73 2 -20.000000 1 1 121412 3 36 1 0 1 1 1.634360 1 0.460000 1.950000 0.306982 0.870000 7.200000e-01 1.000000 1.000000 0.881595 0.870000 1 8.000000e-01 9.600000e-01 ZNF536 9745 broad.mit.edu 37 19 30935540 30935540 + Silent SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:30935540G>A ENST00000355537.3 + 2 1218 c.1071G>A c.(1069-1071)gcG>gcA p.A357A NM_014717.1 NP_055532.1 O15090 ZN536_HUMAN zinc finger protein 536 182 Esophageal squamous(110;0.0834) TCAGCCAGGCGTGGTTCCTCA 0.652000 0 SO:0001819 synonymous_variant ENST00000355537.3 1 1 hg19 CCDS32984.1 TCGA-FB-AAQ2-01A-31D-A40W-08 ZNF536-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459667.2 1 0 1 166 610 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 1.000000 165 607 0 128 2 -20.000000 1 1 121410 14 44 1 1 2 3 2.057369 0 0.460000 1.950000 0.464923 0.930000 8.100000e-01 1.000000 1.000000 0.935802 0.930000 1 8.700000e-01 1 RYR1 6261 broad.mit.edu 37 19 39016037 39016037 + Silent SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:39016037G>A ENST00000359596.3 + 71 10521 c.10521G>A c.(10519-10521)acG>acA p.T3507T RYR1_ENST00000360985.3_Silent_p.T3507T|AC067969.1_ENST00000597015.1_RNA|RYR1_ENST00000355481.4_Silent_p.T3502T 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) CTGTGCAGACGTCACTGATCG 0.627000 0 SO:0001819 synonymous_variant ENST00000359596.3 1 1 hg19 CCDS33011.1 TCGA-FB-AAQ2-01A-31D-A40W-08 RYR1-010 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000462137.1 1 0 1 88 270 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1.000000 86 263 0 45 2 -20.000000 1 1 121412 5 41 1 1 2 3 2.057369 0 0.460000 1.950000 0.464923 0.990000 8.800000e-01 1.000000 1.000000 0.989177 0.990000 1 9.700000e-01 1 CEACAM4 1089 broad.mit.edu 37 19 42132119 42132119 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:42132119C>T ENST00000221954.2 - 2 390 c.280G>A c.(280-282)Gca>Aca p.A94T CEACAM4_ENST00000600925.1_Missense_Mutation_p.A94T NM_001817.2 NP_001808.2 O75871 CEAM4_HUMAN carcinoembryonic antigen-related cell adhesion molecule 4 p.A94T(1) 16 CCACTGTATGCGGCCCCTGGG 0.488000 1 Substitution - Missense(1) SO:0001583 missense ENST00000221954.2 0 1 hg19 CCDS33033.1 . . . . . . . . . . C 14.79 2.639939 0.47153 . . ENSG00000105352 ENST00000221954 T 0.66280 -0.2 1.76 1.76 0.24704 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.76278 0.3965 M 0.84219 2.685 0.09310 N 1 D;D 0.89917 0.997;1.0 D;D 0.73380 0.921;0.98 T 0.61207 -0.7109 9 0.66056 D 0.02 . 6.9535 0.24558 0.0:1.0:0.0:0.0 . 94;94 E7EMX3;O75871 .;CEAM4_HUMAN T 94 ENSP00000221954:A94T ENSP00000221954:A94T A - 1 0 CEACAM4 46823959 0.000000 0.05858 0.009000 0.14445 0.015000 0.08874 0.618000 0.24373 1.281000 0.44480 0.205000 0.17691 GCA TCGA-FB-AAQ2-01A-31D-A40W-08 CEACAM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321148.1 0 0 0 6 723 1 186 0 0 0 1 1 186 2 0 0 0 0 0 2 1 0.963695 6 714 0 183 2 -1.550370 0 1 121412 4 41 1 1 2 3 2.105113 0 0.460000 1.950000 0.470951 0.030000 0 1.000000 0.040000 0.111762 0.030000 0 1.000000e-02 7.000000e-02 TEX101 83639 broad.mit.edu 37 19 43922079 43922079 + Silent SNP G G T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:43922079G>T ENST00000598265.1 + 5 607 c.441G>T c.(439-441)ggG>ggT p.G147G TEX101_ENST00000601707.1_3'UTR|TEX101_ENST00000602198.1_Silent_p.G165G|TEX101_ENST00000253435.7_Silent_p.G165G NM_001130011.1 NP_001123483.1 Q9BY14 TX101_HUMAN testis expressed 101 p.G165G(1) 15 Prostate(69;0.0199) TGGCTTTGGGGACCTGTTTCA 0.493000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000598265.1 0 1 hg19 CCDS59393.1 TCGA-FB-AAQ2-01A-31D-A40W-08 TEX101-004 KNOWN non_canonical_other|basic|CCDS protein_coding protein_coding OTTHUMT00000463176.1 0 0 0 8 665 0 145 0 0 0 0 145 2 0 0 0 0 0 2 1 0.988474 7 652 0 143 2 -2.319452 0 1 0 0 1 1 2 3 2.105113 0 0.460000 1.950000 0.470951 0.050000 1.000000e-02 1.000000 0.060000 0.127564 0.050000 0 3.000000e-02 9.000000e-02 PRKD2 25865 broad.mit.edu 37 19 47193872 47193872 + Silent SNP T T C TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:47193872T>C ENST00000291281.4 - 13 2019 c.1794A>G c.(1792-1794)gaA>gaG p.E598E PRKD2_ENST00000595515.1_Silent_p.E598E|RN7SL364P_ENST00000473668.2_RNA|PRKD2_ENST00000433867.1_Silent_p.E598E|PRKD2_ENST00000601806.1_Silent_p.E441E|PRKD2_ENST00000600194.1_Silent_p.E441E Q9BZL6 KPCD2_HUMAN protein kinase D2 41 Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212) GAATGGCCACTTCATTCCGGA 0.577000 0 SO:0001819 synonymous_variant ENST00000291281.4 1 1 hg19 CCDS12689.1 TCGA-FB-AAQ2-01A-31D-A40W-08 PRKD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466591.1 1 0 1 63 308 0 107 1 9.999987e-01 34 65 0 107 2 0 0 0 0 0 2 1 1.000000 63 306 0 106 2 -20.000000 1 1 0 0 1 1 2 3 2.105113 0 0.460000 1.950000 0.470951 0.760000 5.900000e-01 1.000000 0.750000 0.776535 0.760000 0 6.700000e-01 8.700000e-01 SULT2B1 6820 broad.mit.edu 37 19 49079301 49079301 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:49079301C>T ENST00000201586.2 + 2 353 c.175C>T c.(175-177)Cgg>Tgg p.R59W SULT2B1_ENST00000323090.4_Missense_Mutation_p.R44W NM_177973.1 NP_814444.1 O00204 ST2B1_HUMAN sulfotransferase family, cytosolic, 2B, member 1 11 all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) CCAAGATGTGCGGGACGACGA 0.632000 0 SO:0001583 missense ENST00000201586.2 1 1 hg19 CCDS12723.1 . . . . . . . . . . C 10.66 1.413766 0.25465 0.0 1.16E-4 ENSG00000088002 ENST00000201586;ENST00000323090 T;T 0.02421 4.3;4.3 4.61 1.17 0.20885 . 0.895653 0.09103 N 0.848233 T 0.01387 0.0045 N 0.14661 0.345 0.25224 N 0.989883 B;P 0.41008 0.412;0.735 B;B 0.20955 0.026;0.032 T 0.46541 -0.9184 10 0.87932 D 0 . 3.1284 0.06415 0.2122:0.5639:0.0:0.2239 . 44;59 O00204-2;O00204 .;ST2B1_HUMAN W 59;44 ENSP00000201586:R59W;ENSP00000312880:R44W ENSP00000201586:R59W R + 1 2 SULT2B1 53771113 0.078000 0.21339 0.973000 0.42090 0.141000 0.21300 -0.040000 0.12104 1.061000 0.40601 0.561000 0.74099 CGG TCGA-FB-AAQ2-01A-31D-A40W-08 SULT2B1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000466140.1 1 0 1 117 381 0 80 1 1 37 46 0 80 2 0 0 0 0 0 2 1 1.000000 112 369 0 77 2 -4.668788 1 0 0 0 1 1 2 3 2.105113 0 0.460000 1.950000 0.470951 0.990000 8.800000e-01 1.000000 1.000000 0.985575 0.990000 1 9.600000e-01 1 NUP62 23636 broad.mit.edu 37 19 50412073 50412073 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr19:50412073G>A ENST00000596217.1 - 2 2879 c.992C>T c.(991-993)gCg>gTg p.A331V NUP62_ENST00000597723.1_Intron|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000413454.1_Missense_Mutation_p.A331V|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_Missense_Mutation_p.A331V|NUP62_ENST00000597029.1_Missense_Mutation_p.A331V|NUP62_ENST00000422090.2_Missense_Mutation_p.A331V P37198 NUP62_HUMAN nucleoporin 62kDa 19 all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481) CTCCAGCTGCGCGTAGGTCAT 0.682000 0 SO:0001583 missense ENST00000596217.1 1 1 hg19 CCDS12788.1 . . . . . . . . . . G 13.89 2.373391 0.42105 0.0 1.16E-4 ENSG00000213024 ENST00000352066;ENST00000422090;ENST00000413454 T;T;T 0.76709 -1.04;-1.04;-1.04 5.2 4.14 0.48551 Nucleoporin, NSP1-like, C-terminal (2); 0.075566 0.51477 U 0.000094 T 0.74596 0.3737 L 0.55481 1.735 0.49213 D 0.99976 P 0.42584 0.784 B 0.42495 0.389 T 0.74368 -0.3688 9 . . . -9.4439 13.7291 0.62776 0.0:0.1556:0.8444:0.0 . 331 P37198 NUP62_HUMAN V 331 ENSP00000305503:A331V;ENSP00000407331:A331V;ENSP00000387991:A331V . A - 2 0 NUP62 55103885 1.000000 0.71417 0.491000 0.27477 0.408000 0.30992 5.070000 0.64376 1.530000 0.49136 0.655000 0.94253 GCG TCGA-FB-AAQ2-01A-31D-A40W-08 NUP62-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464991.1 1 0 1 94 405 0 97 1 9.999438e-01 24 39 0 97 2 0 0 0 0 0 2 1 1.000000 90 398 0 94 2 -20.000000 1 1 121378 1 31 1 1 2 3 2.105113 0 0.460000 1.950000 0.470951 0.840000 6.800000e-01 1.000000 0.840000 0.850589 0.840000 0 7.600000e-01 9.400000e-01 GSTM5 2949 broad.mit.edu 37 1 110256173 110256173 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:110256173G>A ENST00000256593.3 + 4 303 c.245G>A c.(244-246)cGc>cAc p.R82H GSTM5_ENST00000369812.5_Missense_Mutation_p.R101H|GSTM5_ENST00000369813.1_Missense_Mutation_p.R41H|GSTM5_ENST00000492718.1_3'UTR NM_000851.3 NP_000842.2 P46439 GSTM5_HUMAN glutathione S-transferase mu 5 21 all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244) Glutathione(DB00143) TACATTGCCCGCAAGCACAAC 0.557000 0 SO:0001583 missense ENST00000256593.3 0 1 hg19 CCDS811.1 . . . . . . . . . . G 21.4 4.140693 0.77775 . . ENSG00000134201 ENST00000256593;ENST00000369813;ENST00000369812 T;T;T 0.08634 3.07;3.07;3.07 4.42 3.51 0.40186 Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (1); 0.000000 0.64402 U 0.000001 T 0.20170 0.0485 M 0.90252 3.1 0.45261 D 0.998267 D;D 0.69078 0.997;0.995 D;P 0.65010 0.931;0.866 T 0.02925 -1.1093 10 0.66056 D 0.02 . 9.8076 0.40803 0.0983:0.0:0.9017:0.0 . 41;82 Q5T8Q9;P46439 .;GSTM5_HUMAN H 82;41;101 ENSP00000256593:R82H;ENSP00000358828:R41H;ENSP00000358827:R101H ENSP00000256593:R82H R + 2 0 GSTM5 110057696 1.000000 0.71417 0.996000 0.52242 0.980000 0.70556 4.262000 0.58847 1.211000 0.43351 0.597000 0.82753 CGC TCGA-FB-AAQ2-01A-31D-A40W-08 GSTM5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000032200.1 0 0 0 7 841 0 167 0 1.446995e-03 0 6 0 167 2 0 0 0 0 0 2 0 0.019291 7 831 1 166 18 -1.827667 0 1 121412 1 44 1 1 2 3 2.109455 0 0.460000 1.950000 0.472141 0.030000 0 1.000000 0.040000 0.119151 0.030000 0 2.000000e-02 7.000000e-02 OR6K3 391114 broad.mit.edu 37 1 158686997 158686997 + Silent SNP C C G TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:158686997C>G ENST00000368146.1 - 1 956 c.957G>C c.(955-957)ctG>ctC p.L319L OR6K3_ENST00000368145.1_Silent_p.L303L Q8NGY3 OR6K3_HUMAN olfactory receptor, family 6, subfamily K, member 3 41 all_hematologic(112;0.0378) GAAGACAGAACAGTTTTTTAA 0.388000 0 SO:0001819 synonymous_variant ENST00000368146.1 0 1 hg19 TCGA-FB-AAQ2-01A-31D-A40W-08 OR6K3-201 KNOWN basic protein_coding protein_coding 0 0 0 6 629 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 0.963703 6 621 0 106 2 -2.800664 1 1 0 0 1 1 2 3 2.109430 0 0.460000 1.950000 0.472141 0.040000 0 1.000000 0.040000 0.125653 0.040000 0 2.000000e-02 8.000000e-02 ATP1A2 477 broad.mit.edu 37 1 160098496 160098496 + Missense_Mutation SNP A A G TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:160098496A>G ENST00000361216.3 + 9 1161 c.1072A>G c.(1072-1074)Aac>Gac p.N358D ATP1A2_ENST00000392233.3_Missense_Mutation_p.N358D NM_000702.3 NP_000693.1 P50993 AT1A2_HUMAN ATPase, Na+/K+ transporting, alpha 2 polypeptide 69 all_cancers(52;1.11e-16)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246) CCTGGTGAAGAACCTGGAGGC 0.587000 0 SO:0001583 missense ENST00000361216.3 0 1 hg19 CCDS1196.1 . . . . . . . . . . A 29.3 4.994443 0.93167 . . ENSG00000018625 ENST00000538123;ENST00000361216;ENST00000392233;ENST00000435866 D;D 0.88896 -2.44;-2.44 4.77 4.77 0.60923 ATPase, P-type, ATPase-associated domain (1); 0.000000 0.85682 D 0.000000 D 0.92299 0.7557 M 0.70903 2.155 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;0.999;1.0 D 0.93459 0.6809 10 0.87932 D 0 . 13.5914 0.61961 1.0:0.0:0.0:0.0 . 203;358;258;358 B4DHD7;B1AKY9;F5GXJ7;P50993 .;.;.;AT1A2_HUMAN D 203;358;358;61 ENSP00000354490:N358D;ENSP00000376066:N358D ENSP00000354490:N358D N + 1 0 ATP1A2 158365120 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.264000 0.95635 1.912000 0.55364 0.459000 0.35465 AAC TCGA-FB-AAQ2-01A-31D-A40W-08 ATP1A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060642.2 0 0 0 13 393 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 0.999535 13 391 0 82 2 -3.611855 1 1 0 0 1 1 2 3 2.109430 0 0.460000 1.950000 0.472141 0.140000 7.000000e-02 1.000000 0.140000 0.220792 0.140000 0 1.000000e-01 2.100000e-01 ATP1A4 480 broad.mit.edu 37 1 160151577 160151577 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:160151577G>A ENST00000368081.4 + 19 3311 c.2840G>A c.(2839-2841)cGc>cAc p.R947H ATP1A4_ENST00000418334.1_3'UTR|ATP1A4_ENST00000470705.1_Missense_Mutation_p.R83H NM_144699.3 NP_653300.2 Q13733 AT1A4_HUMAN ATPase, Na+/K+ transporting, alpha 4 polypeptide 75 all_cancers(52;2.56e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) AAGACTCGCCGCAACTCACTT 0.527000 0 SO:0001583 missense ENST00000368081.4 0 1 hg19 CCDS1197.1 . . . . . . . . . . G 16.99 3.273977 0.59649 . . ENSG00000132681 ENST00000368081;ENST00000470705 D;D 0.89050 -2.46;-2.46 4.16 4.16 0.48862 ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type, transmembrane domain (1); 0.000000 0.85682 D 0.000000 D 0.94978 0.8375 M 0.93898 3.47 0.53688 D 0.999979 D 0.89917 1.0 D 0.69824 0.966 D 0.95874 0.8893 10 0.87932 D 0 . 14.3343 0.66578 0.0:0.0:1.0:0.0 . 947 Q13733 AT1A4_HUMAN H 947;83 ENSP00000357060:R947H;ENSP00000433094:R83H ENSP00000357060:R947H R + 2 0 ATP1A4 158418201 0.992000 0.36948 0.712000 0.30502 0.048000 0.14542 5.550000 0.67268 2.315000 0.78130 0.455000 0.32223 CGC TCGA-FB-AAQ2-01A-31D-A40W-08 ATP1A4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077415.1 0 0 0 8 454 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 0.988514 9 442 0 72 2 -2.023284 0 1 121412 2 32 1 1 2 3 2.109430 0 0.460000 1.950000 0.472141 0.080000 3.000000e-02 1.000000 0.080000 0.160002 0.080000 0 5.000000e-02 1.300000e-01 ASTN1 460 broad.mit.edu 37 1 176845741 176845741 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:176845741C>T ENST00000367654.3 - 21 3630 c.3419G>A c.(3418-3420)cGg>cAg p.R1140Q ASTN1_ENST00000367657.3_Missense_Mutation_p.R1132Q|ASTN1_ENST00000361833.2_Missense_Mutation_p.R1132Q|ASTN1_ENST00000424564.2_Missense_Mutation_p.R1132Q NM_004319.1 NP_004310.1 O14525 ASTN1_HUMAN astrotactin 1 p.R1132L(1) 153 CCTGGAGCGCCGTCCTGTGTT 0.572000 1 Substitution - Missense(1) SO:0001583 missense ENST00000367654.3 1 1 hg19 . . . . . . . . . . C 36 5.786407 0.96937 . . ENSG00000152092 ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808 T;T;T;T 0.16196 2.36;2.78;2.78;2.36 5.19 5.19 0.71726 . 0.000000 0.85682 D 0.000000 T 0.39489 0.1080 L 0.53249 1.67 0.80722 D 1 D;D 0.71674 0.998;0.998 D;D 0.75484 0.986;0.986 T 0.16041 -1.0416 10 0.72032 D 0.01 -17.3769 18.3051 0.90177 0.0:1.0:0.0:0.0 . 1132;1132 O14525-2;B1AJS1 .;. Q 1132;1132;1140;1132;1132 ENSP00000356629:R1132Q;ENSP00000354536:R1132Q;ENSP00000356626:R1140Q;ENSP00000395041:R1132Q ENSP00000354536:R1132Q R - 2 0 ASTN1 175112364 1.000000 0.71417 0.994000 0.49952 0.962000 0.63368 7.390000 0.79816 2.400000 0.81607 0.655000 0.94253 CGG TCGA-FB-AAQ2-01A-31D-A40W-08 ASTN1-201 KNOWN basic protein_coding protein_coding 1 0 1 43 145 0 39 0 5.456048e-02 0 2 0 39 2 0 0 0 0 0 2 1 1.000000 42 142 0 39 2 -3.665143 1 1 121412 1 32 1 1 2 3 2.109430 0 0.460000 1.950000 0.472141 0.990000 7.700000e-01 1.000000 1.000000 0.960936 0.990000 1 8.900000e-01 1 RCC2 55920 broad.mit.edu 37 1 17740096 17740096 + Missense_Mutation SNP G G C TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:17740096G>C ENST00000375436.4 - 9 1331 c.1144C>G c.(1144-1146)Cct>Gct p.P382A AC004824.1_ENST00000583469.1_RNA|RCC2_ENST00000375433.3_Missense_Mutation_p.P382A NM_018715.3 NP_061185.1 Q9P258 RCC2_HUMAN regulator of chromosome condensation 2 17 Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439) CCACGCCCAGGGAAGTCAAAC 0.582000 0 SO:0001583 missense ENST00000375436.4 0 1 hg19 CCDS181.1 . . . . . . . . . . G 28.0 4.877573 0.91664 . . ENSG00000179051 ENST00000375436;ENST00000375433 T;T 0.79749 -1.3;-1.3 5.4 5.4 0.78164 Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2); 0.000000 0.85682 D 0.000000 D 0.83124 0.5186 L 0.35341 1.055 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.76342 -0.2994 10 0.07482 T 0.82 -25.2313 18.1015 0.89507 0.0:0.0:1.0:0.0 . 382 Q9P258 RCC2_HUMAN A 382 ENSP00000364585:P382A;ENSP00000364582:P382A ENSP00000364582:P382A P - 1 0 RCC2 17612683 1.000000 0.71417 0.997000 0.53966 0.956000 0.61745 9.831000 0.99420 2.687000 0.91594 0.655000 0.94253 CCT TCGA-FB-AAQ2-01A-31D-A40W-08 RCC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007144.1 0 0 0 6 505 1 79 0 3.271760e-03 0 224 1 79 11 0 0 0 0 0 2 0 0.002262 6 497 1 79 21 -2.877995 1 1 0 0 1 2 2 4 2.152078 1 0.460000 1.950000 0.492672 0.050000 1.000000e-02 1.000000 0.050000 0.167612 0.050000 0 3.000000e-02 1.100000e-01 SSBP3 23648 broad.mit.edu 37 1 54708959 54708959 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:54708959C>T ENST00000371320.3 - 10 1075 c.665G>A c.(664-666)gGc>gAc p.G222D SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000357475.4_Missense_Mutation_p.G202D|SSBP3_ENST00000371319.3_Missense_Mutation_p.G195D|SSBP3_ENST00000417664.2_Missense_Mutation_p.G112D NM_145716.2 NP_663768.1 Q9BWW4 SSBP3_HUMAN single stranded DNA binding protein 3 11 TGGTCTCATGCCGCTGCCGTA 0.562000 0 SO:0001583 missense ENST00000371320.3 0 1 hg19 CCDS591.1 . . . . . . . . . . c 25.8 4.676502 0.88445 . . ENSG00000157216 ENST00000417664;ENST00000371320;ENST00000371319;ENST00000357475;ENST00000444533;ENST00000525990 . . . 3.94 3.94 0.45596 . 0.000000 0.85682 U 0.000000 T 0.78717 0.4327 M 0.75085 2.285 0.80722 D 1 D;P;P 0.89917 1.0;0.951;0.866 D;P;P 0.97110 1.0;0.743;0.686 T 0.81534 -0.0889 9 0.59425 D 0.04 -1.6526 17.3039 0.87189 0.0:1.0:0.0:0.0 . 195;202;222 Q9BWW4-2;Q9BWW4-3;Q9BWW4 .;.;SSBP3_HUMAN D 112;222;195;202;53;85 . ENSP00000350067:G202D G - 2 0 SSBP3 54481547 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 6.969000 0.76092 2.493000 0.84123 0.479000 0.44913 GGC TCGA-FB-AAQ2-01A-31D-A40W-08 SSBP3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000022721.1 0 0 0 7 1099 0 154 0 2.299315e-01 0 125 0 154 2 0 0 0 0 0 2 1 0.978091 5 1064 0 150 2 -1.724745 0 1 0 0 1 0.460000 1.950000 0 0 LRRIQ3 127255 broad.mit.edu 37 1 74507071 74507071 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:74507071C>T ENST00000395089.1 - 6 1543 c.1544G>A c.(1543-1545)cGt>cAt p.R515H LRRIQ3_ENST00000354431.4_Missense_Mutation_p.R515H A6PVS8 LRIQ3_HUMAN leucine-rich repeats and IQ motif containing 3 p.R515H(1) 73 AACTAATAAACGCTCTGAAGC 0.363000 1 Substitution - Missense(1) SO:0001583 missense ENST00000395089.1 1 1 hg19 CCDS41350.1 . . . . . . . . . . C 6.084 0.383714 0.11524 . . ENSG00000162620 ENST00000395089;ENST00000354431 T;T 0.10382 2.88;2.88 5.86 2.52 0.30459 . . . . . T 0.02047 0.0064 L 0.29908 0.895 0.09310 N 1 B 0.34255 0.445 B 0.20184 0.028 T 0.44452 -0.9327 9 0.35671 T 0.21 . 8.4238 0.32716 0.0:0.7631:0.0:0.2369 . 515 A6PVS8 LRIQ3_HUMAN H 515 ENSP00000378524:R515H;ENSP00000346414:R515H ENSP00000346414:R515H R - 2 0 LRRIQ3 74279659 0.273000 0.24181 0.016000 0.15963 0.029000 0.11900 0.609000 0.24238 0.295000 0.22570 0.650000 0.86243 CGT TCGA-FB-AAQ2-01A-31D-A40W-08 LRRIQ3-008 NOVEL not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316539.1 1 0 1 109 492 0 119 0 0 0 0 119 2 0 0 0 0 0 2 1 1.000000 108 486 0 118 2 -20.000000 1 1 120766 32 47 1 1 2 3 2.109455 0 0.460000 1.950000 0.472141 0.810000 6.700000e-01 1.000000 0.800000 0.825143 0.810000 0 7.300000e-01 9.100000e-01 SLC25A33 84275 broad.mit.edu 37 1 9642431 9642431 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr1:9642431C>T ENST00000302692.6 + 7 1048 c.838C>T c.(838-840)Cgg>Tgg p.R280W NM_032315.2 NP_115691.1 Q9BSK2 S2533_HUMAN solute carrier family 25 (pyrimidine nucleotide carrier), member 33 9 all_lung(157;0.246) all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) CCTGGTGTTCCGGGAAGAAGG 0.488000 0 SO:0001583 missense ENST00000302692.6 0 1 hg19 CCDS103.1 . . . . . . . . . . C 17.12 3.307851 0.60305 . . ENSG00000171612 ENST00000302692 T 0.80738 -1.41 5.98 5.98 0.97165 Mitochondrial carrier domain (2); 0.329961 0.32852 N 0.005573 D 0.86896 0.6043 H 0.95950 3.745 0.47949 D 0.999552 B 0.33413 0.411 B 0.33254 0.16 D 0.88291 0.2943 10 0.87932 D 0 -12.7821 14.3012 0.66355 0.1483:0.8517:0.0:0.0 . 280 Q9BSK2 S2533_HUMAN W 280 ENSP00000306328:R280W ENSP00000306328:R280W R + 1 2 SLC25A33 9565018 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.812000 0.55628 2.835000 0.97688 0.650000 0.86243 CGG TCGA-FB-AAQ2-01A-31D-A40W-08 SLC25A33-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000003851.2 0 0 0 4 235 0 41 0 3.577612e-01 0 62 0 41 2 0 0 0 0 0 2 1 0.886092 4 230 0 41 2 -2.986550 1 1 121412 5 36 1 2 2 4 2.140883 0 0.460000 1.950000 0.490470 0.090000 2.000000e-02 1.000000 0.070000 0.189462 0.090000 0 5.000000e-02 1.700000e-01 ZNF831 128611 broad.mit.edu 37 20 57769239 57769239 + Silent SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr20:57769239G>A ENST00000371030.2 + 1 3165 c.3165G>A c.(3163-3165)ccG>ccA p.P1055P NM_178457.1 NP_848552.1 Q5JPB2 ZN831_HUMAN zinc finger protein 831 125 all_lung(29;0.0085) CCTCCTCCCCGCCCACTCCAA 0.647000 0 SO:0001819 synonymous_variant ENST00000371030.2 0 1 hg19 CCDS42894.1 TCGA-FB-AAQ2-01A-31D-A40W-08 ZNF831-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000079916.2 1 0 0 8 93 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 0.987580 8 87 0 17 2 -3.144579 1 1 120994 1 26 1 1 2 3 2.073867 0 0.460000 1.950000 0.467351 0.370000 1.700000e-01 1.000000 0.350000 0.409922 0.370000 0 2.500000e-01 5.300000e-01 NPHP1 4867 broad.mit.edu 37 2 110922260 110922260 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr2:110922260C>T ENST00000393272.3 - 8 873 c.776G>A c.(775-777)gGc>gAc p.G259D NPHP1_ENST00000445609.2_Intron|NPHP1_ENST00000355301.4_Intron|NPHP1_ENST00000417665.1_Intron|NPHP1_ENST00000316534.4_Missense_Mutation_p.G259D NM_000272.3|NM_207181.2 NP_000263.2|NP_997064.2 O15259 NPHP1_HUMAN nephronophthisis 1 (juvenile) 24 ACAGAAGATGCCCGCCTCTGA 0.458000 0 SO:0001583 missense ENST00000393272.3 0 1 hg19 CCDS46385.1 . . . . . . . . . . C 9.500 1.102886 0.20632 . . ENSG00000144061 ENST00000316534;ENST00000393272 T;T 0.64438 -0.1;-0.06 4.59 3.72 0.42706 . 0.678739 0.14107 N 0.341008 T 0.49321 0.1550 N 0.22421 0.69 0.19300 N 0.99997 P;P 0.44946 0.761;0.846 B;B 0.43194 0.234;0.411 T 0.39333 -0.9619 10 0.66056 D 0.02 -3.7449 8.7413 0.34558 0.0:0.8968:0.0:0.1032 . 259;259 O15259;O15259-4 NPHP1_HUMAN;. D 259 ENSP00000313169:G259D;ENSP00000376953:G259D ENSP00000313169:G259D G - 2 0 NPHP1 110279549 0.009000 0.17119 0.004000 0.12327 0.017000 0.09413 1.848000 0.39309 1.180000 0.42898 -0.219000 0.12488 GGC TCGA-FB-AAQ2-01A-31D-A40W-08 NPHP1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000253919.3 0 0 0 6 747 0 139 0 0 0 1 0 139 2 0 0 0 0 0 2 1 0.951448 6 669 0 124 2 -1.801325 0 1 0 0 1 1 2 3 2.077827 0 0.460000 1.950000 0.467351 0.030000 0 1.000000 0.040000 0.085496 0.030000 0 1.000000e-02 6.000000e-02 TPO 7173 broad.mit.edu 37 2 1426896 1426896 + Missense_Mutation SNP G G T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr2:1426896G>T ENST00000345913.4 + 3 265 c.174G>T c.(172-174)atG>atT p.M58I TPO_ENST00000382201.3_Missense_Mutation_p.M58I|TPO_ENST00000382269.3_Missense_Mutation_p.M58I|TPO_ENST00000539820.1_Missense_Mutation_p.M58I|TPO_ENST00000382198.1_Missense_Mutation_p.M58I|TPO_ENST00000337415.3_Missense_Mutation_p.M58I|TPO_ENST00000329066.4_Missense_Mutation_p.M58I|TPO_ENST00000349624.3_Missense_Mutation_p.M58I|TPO_ENST00000497517.2_Intron|TPO_ENST00000346956.3_Missense_Mutation_p.M58I NM_000547.5 NP_000538.3 P07202 PERT_HUMAN thyroid peroxidase 95 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550) ACGCCACGATGCAGAGGTGAG 0.597000 0 SO:0001583 missense ENST00000345913.4 1 1 hg19 CCDS1643.1 . . . . . . . . . . G 10.54 1.377425 0.24944 . . ENSG00000115705 ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198 T;T;T;T;T;T;T;T;T;T 0.56776 0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44 3.72 3.72 0.42706 . 0.282519 0.34652 N 0.003786 T 0.40909 0.1136 L 0.50919 1.6 0.09310 N 1 B;B;B;B;B 0.33807 0.008;0.426;0.264;0.008;0.006 B;B;B;B;B 0.25405 0.007;0.06;0.033;0.007;0.004 T 0.30563 -0.9974 10 0.29301 T 0.29 -29.3298 11.2868 0.49226 0.0:0.0:1.0:0.0 . 58;58;58;58;58 P07202-4;P07202-5;E9PFM6;P07202-2;P07202 .;.;.;.;PERT_HUMAN I 58 ENSP00000371704:M58I;ENSP00000337263:M58I;ENSP00000318820:M58I;ENSP00000263886:M58I;ENSP00000332044:M58I;ENSP00000444840:M58I;ENSP00000329869:M58I;ENSP00000371636:M58I;ENSP00000390994:M58I;ENSP00000371633:M58I ENSP00000329869:M58I M + 3 0 TPO 1405903 0.251000 0.23961 0.039000 0.18376 0.038000 0.13279 1.497000 0.35649 2.347000 0.79759 0.467000 0.42956 ATG TCGA-FB-AAQ2-01A-31D-A40W-08 TPO-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000206594.2 1 0 1 31 119 0 24 0 0 0 1 0 24 2 0 0 0 0 0 2 1 1.000000 31 118 0 24 2 -20.000000 1 1 0 0 1 1 2 3 2.077827 0 0.460000 1.950000 0.467351 0.910000 6.500000e-01 1.000000 1.000000 0.898491 0.910000 1 7.700000e-01 1 ZNF385B 151126 broad.mit.edu 37 2 180308122 180308122 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr2:180308122G>A ENST00000410066.1 - 10 1874 c.1271C>T c.(1270-1272)gCg>gTg p.A424V ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409692.1_Missense_Mutation_p.A322V|ZNF385B_ENST00000409343.1_Missense_Mutation_p.A348V|ZNF385B_ENST00000336917.5_Missense_Mutation_p.A322V NM_152520.4 NP_689733.3 Q569K4 Z385B_HUMAN zinc finger protein 385B 26 Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201) CACGGCTGCCGCCGCTGCGAG 0.607000 Colon(155;204 2491 32774 51842) 0 SO:0001583 missense ENST00000410066.1 1 1 hg19 CCDS33339.1 . . . . . . . . . . G 16.00 2.998461 0.54147 . . ENSG00000144331 ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692 T;T;T;T 0.35973 1.28;1.3;1.28;1.3 5.49 5.49 0.81192 . 0.257134 0.40728 N 0.001021 T 0.47248 0.1435 L 0.39147 1.195 0.58432 D 0.999999 D;D 0.65815 0.995;0.976 P;P 0.54815 0.761;0.488 T 0.43442 -0.9391 10 0.62326 D 0.03 -20.3691 19.3766 0.94512 0.0:0.0:1.0:0.0 . 424;348 Q569K4;Q569K4-2 Z385B_HUMAN;. V 424;322;348;322 ENSP00000386845:A424V;ENSP00000338225:A322V;ENSP00000386379:A348V;ENSP00000386507:A322V ENSP00000338225:A322V A - 2 0 ZNF385B 180016367 1.000000 0.71417 0.160000 0.22671 0.013000 0.08279 7.203000 0.77864 2.565000 0.86533 0.561000 0.74099 GCG TCGA-FB-AAQ2-01A-31D-A40W-08 ZNF385B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335972.1 1 0 1 18 69 0 21 0 0 0 1 0 21 2 0 0 0 0 0 2 1 0.999990 18 67 0 20 2 -20.000000 1 1 0 0 1 1 2 3 2.077827 0 0.460000 1.950000 0.467351 0.920000 5.800000e-01 1.000000 1.000000 0.888388 0.920000 1 7.400000e-01 1 LTBP1 4052 broad.mit.edu 37 2 33572565 33572565 + Missense_Mutation SNP C C T rs144093447 TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr2:33572565C>T ENST00000404816.2 + 26 4341 c.3988C>T c.(3988-3990)Cgg>Tgg p.R1330W LTBP1_ENST00000272273.5_Missense_Mutation_p.R228W|LTBP1_ENST00000407925.1_Missense_Mutation_p.R1004W|LTBP1_ENST00000390003.4_Missense_Mutation_p.R1005W|LTBP1_ENST00000404525.1_Missense_Mutation_p.R951W|LTBP1_ENST00000402934.1_Missense_Mutation_p.R951W|LTBP1_ENST00000354476.3_Missense_Mutation_p.R1331W|LTBP1_ENST00000418533.2_Missense_Mutation_p.R962W Q14766 LTBP1_HUMAN latent transforming growth factor beta binding protein 1 p.R1331R(1) 108 all_hematologic(175;0.115) Medulloblastoma(90;0.215) GTGCCGCTCCCGGACCTCCAC 0.557000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000404816.2 0 1 hg19 CCDS33177.2 . . . . . . . . . . C 27.0 4.788854 0.90367 2.27E-4 0.0 ENSG00000049323 ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669 D;D;T;T;T;T;T;D;D 0.85339 -1.53;-1.52;-1.46;-1.41;-1.45;-1.42;-1.42;-1.97;-1.61 5.19 5.19 0.71726 . . . . . D 0.90896 0.7139 L 0.55213 1.73 0.53005 D 0.999965 D;D;D;D;D;D;D 0.89917 0.998;0.998;1.0;0.972;0.971;0.987;0.999 P;P;D;P;P;P;P 0.75484 0.895;0.794;0.986;0.742;0.685;0.768;0.899 D 0.91362 0.5112 9 0.66056 D 0.02 . 19.0846 0.93198 0.0:1.0:0.0:0.0 . 228;1330;962;951;1004;1005;1331 E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4 .;LTBP1_HUMAN;.;.;.;.;. W 1330;1331;1005;962;951;951;1004;228;166 ENSP00000386043:R1330W;ENSP00000346467:R1331W;ENSP00000374653:R1005W;ENSP00000393057:R962W;ENSP00000384373:R951W;ENSP00000385359:R951W;ENSP00000384091:R1004W;ENSP00000272273:R228W;ENSP00000395211:R166W ENSP00000272273:R228W R + 1 2 LTBP1 33426069 0.493000 0.26035 0.536000 0.28039 0.799000 0.45148 2.319000 0.43788 2.594000 0.87642 0.561000 0.74099 CGG TCGA-FB-AAQ2-01A-31D-A40W-08 LTBP1-014 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000326227.2 0 0 0 7 333 1 44 0 4.187404e-03 1 70 1 44 7 0 0 0 0 0 2 0 0.001795 7 328 1 42 23 -2.360295 0 1 121412 8 43 1 1 2 3 2.077827 0 0.460000 1.950000 0.467351 0.090000 3.000000e-02 1.000000 0.090000 0.144900 0.090000 0 6.000000e-02 1.500000e-01 KALRN 8997 broad.mit.edu 37 3 123813705 123813705 + Missense_Mutation SNP C C G TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr3:123813705C>G ENST00000240874.3 + 1 178 c.21C>G c.(19-21)gaC>gaG p.D7E KALRN_ENST00000460856.1_Missense_Mutation_p.D7E|KALRN_ENST00000477496.1_3'UTR|KALRN_ENST00000360013.3_Missense_Mutation_p.D7E NM_003947.4 NP_003938.1 O60229 KALRN_HUMAN kalirin, RhoGEF kinase 83 GCTTCTGGGACCAGTGGTATC 0.557000 0 SO:0001583 missense ENST00000240874.3 1 1 hg19 CCDS3027.1 . . . . . . . . . . c 14.72 2.619680 0.46736 . . ENSG00000160145 ENST00000460856;ENST00000240874;ENST00000360013 T;T;T 0.59772 0.78;0.71;0.24 3.7 2.81 0.32909 . 0.724489 0.11133 U 0.596093 T 0.40767 0.1130 N 0.08118 0 0.80722 D 1 P;P;P 0.41597 0.643;0.643;0.756 B;B;P 0.49752 0.417;0.417;0.621 T 0.31558 -0.9939 10 0.02654 T 1 . 8.5829 0.33640 0.2295:0.7705:0.0:0.0 . 7;7;7 C9IZQ6;O60229;O60229-2 .;KALRN_HUMAN;. E 7 ENSP00000418611:D7E;ENSP00000240874:D7E;ENSP00000353109:D7E ENSP00000240874:D7E D + 3 2 KALRN 125296395 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 0.530000 0.23036 1.118000 0.41863 0.486000 0.48141 GAC TCGA-FB-AAQ2-01A-31D-A40W-08 KALRN-005 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000258843.4 0 0 1 46 165 1 36 0 0 0 1 36 2 1 1 89 339 0 332 2 1 0.999958 45 164 1 36 18 -20.000000 1 1 0 0 1 1 2 3 2.068481 0 0.460000 1.950000 0.466139 0.960000 7.200000e-01 1.000000 1.000000 0.933336 0.960000 1 8.300000e-01 1 RASA2 5922 broad.mit.edu 37 3 141292025 141292025 + Missense_Mutation SNP A A G TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr3:141292025A>G ENST00000452898.1 + 13 1356 c.1321A>G c.(1321-1323)Att>Gtt p.I441V RASA2_ENST00000286364.3_Missense_Mutation_p.I441V NM_006506.2 NP_006497.2 Q15283 RASA2_HUMAN RAS p21 protein activator 2 34 AATCGATCCTATTAAATTGAA 0.264000 0 SO:0001583 missense ENST00000452898.1 1 1 hg19 . . . . . . . . . . A 1.433 -0.569702 0.03910 . . ENSG00000155903 ENST00000286364;ENST00000452898;ENST00000423660 T;T 0.79141 -1.24;-1.24 5.48 2.98 0.34508 Rho GTPase activation protein (1);Ras GTPase-activating protein (4); 0.209202 0.42682 N 0.000671 T 0.51398 0.1672 N 0.03194 -0.395 0.29030 N 0.885756 B;B;B;B 0.06786 0.001;0.0;0.0;0.0 B;B;B;B 0.15484 0.013;0.006;0.003;0.006 T 0.42716 -0.9435 10 0.25106 T 0.35 . 7.8427 0.29408 0.692:0.2346:0.0734:0.0 . 33;441;441;441 E7EU60;A8K7K1;G3V0F9;Q15283 .;.;.;RASA2_HUMAN V 441;441;33 ENSP00000286364:I441V;ENSP00000391677:I441V ENSP00000286364:I441V I + 1 0 RASA2 142774715 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.229000 0.42990 1.041000 0.40125 0.533000 0.62120 ATT TCGA-FB-AAQ2-01A-31D-A40W-08 RASA2-201 KNOWN basic protein_coding protein_coding 1 0 1 54 212 0 79 1 9.420178e-01 9 12 0 79 2 0 0 0 0 0 2 1 1.000000 54 210 0 79 2 -20.000000 1 1 0 0 1 1 2 3 2.068481 0 0.460000 1.950000 0.466139 0.890000 6.900000e-01 1.000000 1.000000 0.892065 0.890000 1 7.800000e-01 1 SETD5 55209 broad.mit.edu 37 3 9506122 9506122 + Silent SNP A A G TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr3:9506122A>G ENST00000406341.1 + 17 2680 c.2490A>G c.(2488-2490)ccA>ccG p.P830P SETD5_ENST00000402466.1_Silent_p.P732P|SETD5_ENST00000402198.1_Silent_p.P830P|SETD5_ENST00000302463.6_Silent_p.P732P|SETD5_ENST00000488236.1_3'UTR|SETD5_ENST00000407969.1_Silent_p.P849P Q9C0A6 SETD5_HUMAN SET domain containing 5 47 Medulloblastoma(99;0.227) TGTTGAGCCCATTAAAGAAAT 0.428000 0 SO:0001819 synonymous_variant ENST00000406341.1 1 1 hg19 CCDS46741.1 . . . . . . . . . . A 10.07 1.249061 0.22880 . . ENSG00000168137 ENST00000399686;ENST00000421188 . . . 5.78 3.28 0.37604 . . . . . T 0.54464 0.1860 . . . 0.80722 D 1 . . . . . . T 0.45381 -0.9265 4 . . . -10.4749 5.9389 0.19181 0.4756:0.1792:0.0:0.3452 . . . . V 498;142 . . I + 1 0 SETD5 9481122 0.998000 0.40836 1.000000 0.80357 0.998000 0.95712 0.507000 0.22675 0.386000 0.24997 0.533000 0.62120 ATT TCGA-FB-AAQ2-01A-31D-A40W-08 SETD5-001 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318425.1 1 0 1 198 638 0 146 1 9.999202e-01 20 26 0 146 2 0 0 0 0 0 2 1 1.000000 196 629 0 144 2 -20.000000 1 1 0 0 1 1 2 3 2.063797 0 0.460000 1.950000 0.466139 0.990000 9.100000e-01 1.000000 1.000000 0.990642 0.990000 1 9.700000e-01 1 TET2 54790 broad.mit.edu 37 4 106155430 106155430 + Nonsense_Mutation SNP A A T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr4:106155430A>T ENST00000540549.1 + 3 1191 c.331A>T c.(331-333)Aaa>Taa p.K111* TET2_ENST00000380013.4_Nonsense_Mutation_p.K111*|TET2_ENST00000413648.2_Nonsense_Mutation_p.K111*|TET2_ENST00000305737.2_Nonsense_Mutation_p.K111*|TET2_ENST00000513237.1_Nonsense_Mutation_p.K132*|TET2_ENST00000394764.1_Nonsense_Mutation_p.K111*|TET2_ENST00000545826.1_Nonsense_Mutation_p.K111* Q6N021 TET2_HUMAN tet methylcytosine dioxygenase 2 p.L107fs*8(1) 1314 Myeloproliferative disorder(5;0.0393) TCAGATCAAGAAATTGAAACA 0.413000 Mis N, F MDS Rec yes 4 4q24 54790 tet oncogene family member 2 L 1 Deletion - Frameshift(1) SO:0001587 stop_gained ENST00000540549.1 0 1 hg19 CCDS47120.1 . . . . . . . . . . A 35 5.499172 0.96355 . . ENSG00000168769 ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110 . . . 5.51 5.51 0.81932 . 0.464604 0.16713 N 0.202570 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 15.6604 0.77182 1.0:0.0:0.0:0.0 . . . . X 111;111;111;132;111;111;111;111 . ENSP00000265149:K111X K + 1 0 TET2 106374879 1.000000 0.71417 0.891000 0.34965 0.970000 0.65996 6.405000 0.73272 2.095000 0.63458 0.528000 0.53228 AAA TCGA-FB-AAQ2-01A-31D-A40W-08 TET2-202 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000253952.2 0 0 0 6 244 1 58 0 1.639057e-02 0 7 1 58 2 0 0 0 0 0 2 0 0.032484 6 240 1 58 15 -7.841932 1 1 0 0 1 0 1 1 1.895516 1 0.460000 1.950000 0.409772 0.090000 3.000000e-02 0.200000 0.100000 0.109863 0.090000 0 6.000000e-02 1.500000e-01 PROL1 58503 broad.mit.edu 37 4 71275677 71275677 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr4:71275677G>A ENST00000399575.2 + 3 806 c.632G>A c.(631-633)cGt>cAt p.R211H NM_021225.4 NP_067048.4 Q99935 PROL1_HUMAN proline rich, lacrimal 1 15 all_hematologic(202;0.196) CTCGCCAACCGTCCTCACACA 0.448000 0 SO:0001583 missense ENST00000399575.2 0 1 hg19 CCDS43235.1 . . . . . . . . . . C 13.85 2.361243 0.41801 0.0 2.39E-4 ENSG00000171199 ENST00000399575 T 0.42131 0.98 3.08 1.33 0.21861 . . . . . T 0.18718 0.0449 N 0.08118 0 0.09310 N 1 B 0.24368 0.102 B 0.08055 0.003 T 0.15206 -1.0445 9 0.44086 T 0.13 . 3.3539 0.07162 0.0:0.5226:0.2206:0.2569 . 211 Q99935 PROL1_HUMAN H 211 ENSP00000382485:R211H ENSP00000382485:R211H R + 2 0 PROL1 71310266 0.000000 0.05858 0.001000 0.08648 0.036000 0.12997 -0.417000 0.07088 0.045000 0.15804 -0.187000 0.12897 CGT TCGA-FB-AAQ2-01A-31D-A40W-08 PROL1-001 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000362639.1 0 0 0 6 408 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 0.963628 6 402 0 62 2 -2.486083 0 1 121002 17 45 1 0 1 1 1.895516 1 0.460000 1.950000 0.409772 0.050000 1.000000e-02 0.120000 0.060000 0.066713 0.050000 0 3.000000e-02 9.000000e-02 DSPP 1834 broad.mit.edu 37 4 88534264 88534264 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr4:88534264G>A ENST00000282478.7 + 3 959 c.926G>A c.(925-927)gGc>gAc p.G309D DSPP_ENST00000399271.1_Missense_Mutation_p.G309D|RP11-742B18.1_ENST00000506480.1_RNA Q9NZW4 DSPP_HUMAN dentin sialophosphoprotein 47 Hepatocellular(203;0.114)|all_hematologic(202;0.236) GACCCTGAAGGCAAAGAAGAT 0.438000 0 SO:0001583 missense ENST00000282478.7 0 1 hg19 CCDS43248.1 . . . . . . . . . . G 5.743 0.321511 0.10845 . . ENSG00000152591 ENST00000399271;ENST00000282478 D;D 0.87809 -2.3;-2.3 4.54 -3.71 0.04424 . . . . . T 0.74898 0.3777 L 0.34521 1.04 0.09310 N 1 B 0.12630 0.006 B 0.14023 0.01 T 0.59721 -0.7401 9 0.05959 T 0.93 1.6285 10.5668 0.45177 0.2505:0.1385:0.6109:0.0 . 309 Q9NZW4 DSPP_HUMAN D 309 ENSP00000382213:G309D;ENSP00000282478:G309D ENSP00000282478:G309D G + 2 0 DSPP 88753288 0.000000 0.05858 0.000000 0.03702 0.071000 0.16799 -0.014000 0.12656 -0.930000 0.03752 -0.484000 0.04775 GGC TCGA-FB-AAQ2-01A-31D-A40W-08 DSPP-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000363616.3 0 0 0 4 132 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 0.891506 4 132 0 18 2 -3.535246 1 1 0 0 1 0 1 1 1.895516 1 0.460000 1.950000 0.409772 0.120000 4.000000e-02 0.270000 0.120000 0.142610 0.120000 0 7.000000e-02 2.000000e-01 DNAH5 1767 broad.mit.edu 37 5 13900472 13900472 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr5:13900472G>A ENST00000265104.4 - 15 2206 c.2102C>T c.(2101-2103)cCa>cTa p.P701L CTB-51A17.1_ENST00000503244.1_RNA NM_001369.2 NP_001360.1 Q8TE73 DYH5_HUMAN dynein, axonemal, heavy chain 5 378 Lung NSC(4;0.00476) CCCTGTGCCTGGAGCCTTCAC 0.413000 Kartagener syndrome 0 SO:0001583 missense Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000265104.4 1 1 hg19 CCDS3882.1 . . . . . . . . . . G 17.34 3.365928 0.61513 . . ENSG00000039139 ENST00000265104 T 0.55413 0.52 5.5 5.5 0.81552 Dynein heavy chain, domain-1 (1); 0.108809 0.64402 D 0.000006 T 0.67363 0.2885 M 0.85542 2.76 0.80722 D 1 B 0.31655 0.334 B 0.41174 0.349 T 0.67998 -0.5525 10 0.44086 T 0.13 . 19.3805 0.94530 0.0:0.0:1.0:0.0 . 701 Q8TE73 DYH5_HUMAN L 701 ENSP00000265104:P701L ENSP00000265104:P701L P - 2 0 DNAH5 13953472 1.000000 0.71417 0.900000 0.35374 0.939000 0.58152 7.508000 0.81686 2.583000 0.87209 0.650000 0.86243 CCA TCGA-FB-AAQ2-01A-31D-A40W-08 DNAH5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207057.2 1 0 1 69 239 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 69 236 0 56 2 -4.084364 1 1 0 0 1 1 2 3 2.084407 0 0.460000 1.950000 0.468556 0.990000 7.900000e-01 1.000000 1.000000 0.957588 0.990000 1 8.800000e-01 1 GABRA6 2559 broad.mit.edu 37 5 161128572 161128572 + Silent SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr5:161128572C>T ENST00000274545.5 + 9 1588 c.1155C>T c.(1153-1155)tcC>tcT p.S385S GABRA6_ENST00000523217.1_Silent_p.S375S Q16445 GBRA6_HUMAN gamma-aminobutyric acid (GABA) A receptor, alpha 6 p.S385S(1) 57 Renal(175;0.00259) 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)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897) TTTCATCTTCCGAGGCCAATA 0.453000 TCGA Ovarian(5;0.080) 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000274545.5 1 1 hg19 CCDS4356.1 TCGA-FB-AAQ2-01A-31D-A40W-08 GABRA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252707.2 1 0 1 94 317 0 91 0 0 0 0 91 2 0 0 0 0 0 2 1 1.000000 92 315 0 88 2 -3.714679 1 1 0 0 1 1 2 3 2.084407 0 0.460000 1.950000 0.468556 0.990000 8.300000e-01 1.000000 1.000000 0.971615 0.990000 1 9.200000e-01 1 ADAMTS16 170690 broad.mit.edu 37 5 5239387 5239387 + Splice_Site SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr5:5239387C>T ENST00000274181.7 + 15 2416 c.2278C>T c.(2278-2280)Cag>Tag p.Q760* NM_139056.2 NP_620687.2 Q8TE57 ATS16_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 16 107 CCACACCAACCGTGAGTACTT 0.512000 0 SO:0001630 splice_region_variant ENST00000274181.7 0 1 hg19 CCDS43299.1 . . . . . . . . . . C 40 8.165790 0.98686 . . ENSG00000145536 ENST00000274181;ENST00000536857 . . . 5.85 4.96 0.65561 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.66056 D 0.02 . 15.5469 0.76108 0.0:0.8611:0.1389:0.0 . . . . X 760 . ENSP00000274181:Q760X Q + 1 0 ADAMTS16 5292387 1.000000 0.71417 1.000000 0.80357 0.891000 0.51852 2.676000 0.46883 1.410000 0.46936 0.655000 0.94253 CAG TCGA-FB-AAQ2-01A-31D-A40W-08 ADAMTS16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365657.1 0 0 0 101 344 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 1.000000 100 332 0 86 2 -3.481176 1 1 120848 3 38 1 1 2 3 2.084407 0 0.460000 1.950000 0.468556 0.990000 8.300000e-01 1.000000 1.000000 0.969545 0.990000 1 9.100000e-01 1 TTC37 9652 broad.mit.edu 37 5 94803623 94803623 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr5:94803623G>A ENST00000358746.2 - 42 4865 c.4567C>T c.(4567-4569)Cgt>Tgt p.R1523C NM_014639.3 NP_055454.1 Q6PGP7 TTC37_HUMAN tetratricopeptide repeat domain 37 47 AGGTACCAACGTGCAGTTGAT 0.358000 0 SO:0001583 missense ENST00000358746.2 1 1 hg19 CCDS4072.1 . . . . . . . . . . G 26.4 4.737379 0.89482 . . ENSG00000198677 ENST00000358746 D 0.81659 -1.52 5.27 5.27 0.74061 . 0.073499 0.64402 D 0.000001 D 0.88540 0.6464 M 0.61703 1.905 0.80722 D 1 D 0.89917 1.0 D 0.73708 0.981 D 0.89541 0.3792 10 0.87932 D 0 . 18.4885 0.90838 0.0:0.0:1.0:0.0 . 1523 Q6PGP7 TTC37_HUMAN C 1523 ENSP00000351596:R1523C ENSP00000351596:R1523C R - 1 0 TTC37 94829379 1.000000 0.71417 0.993000 0.49108 0.981000 0.71138 4.660000 0.61511 2.471000 0.83476 0.561000 0.74099 CGT TCGA-FB-AAQ2-01A-31D-A40W-08 TTC37-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000241651.1 1 0 0 14 201 0 53 1 9.992495e-01 7 172 0 53 2 0 0 0 0 0 2 1 0.999785 14 201 0 52 2 -5.689277 1 1 121408 2 32 1 1 2 3 2.084407 0 0.460000 1.950000 0.468556 0.290000 1.600000e-01 1.000000 0.290000 0.342592 0.290000 0 2.200000e-01 4.000000e-01 WNT2 7472 broad.mit.edu 37 7 116960785 116960785 + Missense_Mutation SNP C C A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr7:116960785C>A ENST00000265441.3 - 2 445 c.146G>T c.(145-147)aGc>aTc p.S49I AC002465.2_ENST00000436097.1_RNA NM_003391.2 NP_003382.1 P09544 WNT2_HUMAN wingless-type MMTV integration site family member 2 31 all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109) STAD - Stomach adenocarcinoma(10;0.000512) CCGCTGGCTGCTCACCAGGCC 0.592000 0 SO:0001583 missense ENST00000265441.3 1 1 hg19 CCDS5771.1 . . . . . . . . . . C 19.46 3.831442 0.71258 . . ENSG00000105989 ENST00000265441;ENST00000491214 T;T 0.76578 -1.03;-1.03 5.42 5.42 0.78866 . 0.040486 0.85682 D 0.000000 T 0.77691 0.4168 M 0.72894 2.215 0.44123 D 0.996904 P 0.44776 0.843 B 0.41917 0.37 T 0.79743 -0.1675 10 0.49607 T 0.09 . 14.2281 0.65873 0.0:0.851:0.149:0.0 . 49 P09544 WNT2_HUMAN I 49 ENSP00000265441:S49I;ENSP00000419466:S49I ENSP00000265441:S49I S - 2 0 WNT2 116748021 0.998000 0.40836 1.000000 0.80357 0.989000 0.77384 0.573000 0.23699 2.691000 0.91804 0.655000 0.94253 AGC TCGA-FB-AAQ2-01A-31D-A40W-08 WNT2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059749.3 1 0 1 18 74 0 13 0 0 0 1 0 13 2 0 0 0 0 0 2 1 0.999987 17 71 0 13 2 -20.000000 1 1 0 0 1 1 2 3 2.066335 0 0.460000 1.950000 0.466139 0.870000 5.500000e-01 1.000000 1.000000 0.855480 0.870000 1 6.900000e-01 1 CUL1 8454 broad.mit.edu 37 7 148427298 148427298 + Silent SNP C C A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr7:148427298C>A ENST00000325222.4 + 2 363 c.84C>A c.(82-84)atC>atA p.I28I CUL1_ENST00000602748.1_Silent_p.I28I|CUL1_ENST00000409469.1_Silent_p.I28I|AC005229.1_ENST00000578165.1_RNA NM_003592.2 NP_003583.2 Q13616 CUL1_HUMAN cullin 1 40 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00291) GAGCCGGCATCCAGCAGGTGT 0.547000 0 SO:0001819 synonymous_variant ENST00000325222.4 1 1 hg19 CCDS34772.1 TCGA-FB-AAQ2-01A-31D-A40W-08 CUL1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000467785.1 1 0 0 22 376 0 55 1 9.101935e-01 5 68 0 55 2 0 0 0 0 0 2 1 0.999999 21 372 0 53 2 -19.999900 1 1 0 0 1 1 2 3 2.066335 0 0.460000 1.950000 0.466139 0.240000 1.500000e-01 1.000000 0.240000 0.280549 0.240000 0 1.900000e-01 3.100000e-01 ABCB4 5244 broad.mit.edu 37 7 87069091 87069091 + Silent SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr7:87069091G>A ENST00000265723.4 - 14 1734 c.1623C>T c.(1621-1623)atC>atT p.I541I ABCB4_ENST00000358400.3_Silent_p.I541I|ABCB4_ENST00000453593.1_Silent_p.I541I|ABCB4_ENST00000545634.1_Silent_p.I541I|ABCB4_ENST00000359206.3_Silent_p.I541I NM_000443.3|NM_018849.2 NP_000434.1|NP_061337.1 P21439 MDR3_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 4 77 Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203) Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207) GTGCAATGGCGATCCTCTGCT 0.532000 0 SO:0001819 synonymous_variant ENST00000265723.4 0 1 hg19 CCDS5606.1 TCGA-FB-AAQ2-01A-31D-A40W-08 ABCB4-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000336083.1 0 0 0 6 403 0 82 0 0 0 0 82 2 0 0 0 0 0 2 1 0.961597 6 390 0 81 2 -2.888738 1 1 121412 2 38 1 1 2 3 2.066335 0 0.460000 1.950000 0.466139 0.060000 2.000000e-02 1.000000 0.060000 0.109845 0.060000 0 4.000000e-02 1.100000e-01 KCNQ3 3786 broad.mit.edu 37 8 133150166 133150166 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr8:133150166C>T ENST00000388996.4 - 12 2086 c.1666G>A c.(1666-1668)Gac>Aac p.D556N KCNQ3_ENST00000521134.1_Missense_Mutation_p.D436N|KCNQ3_ENST00000519445.1_Missense_Mutation_p.D556N NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) GAAAGCATGTCGAGATGCCCG 0.453000 0 SO:0001583 missense ENST00000388996.4 1 1 hg19 CCDS34943.1 . . . . . . . . . . C 35 5.507800 0.96386 . . ENSG00000184156 ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790 D;D;D 0.99758 -6.65;-6.65;-6.65 5.46 5.46 0.80206 Potassium channel, voltage dependent, KCNQ, C-terminal (1); 0.000000 0.85682 D 0.000000 D 0.99527 0.9831 L 0.33093 0.98 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.98336 1.0536 10 0.87932 D 0 -28.2666 18.6955 0.91599 0.0:1.0:0.0:0.0 . 556;556 E7ET42;O43525 .;KCNQ3_HUMAN N 556;436;556;545;435 ENSP00000373648:D556N;ENSP00000429799:D436N;ENSP00000428790:D556N ENSP00000373648:D556N D - 1 0 KCNQ3 133219348 1.000000 0.71417 0.964000 0.40570 0.962000 0.63368 7.818000 0.86416 2.733000 0.93635 0.655000 0.94253 GAC TCGA-FB-AAQ2-01A-31D-A40W-08 KCNQ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268621.2 1 0 1 189 589 0 134 0 0 0 0 134 2 0 0 0 0 0 2 1 1.000000 183 584 0 132 2 -20.000000 1 1 121412 1 31 1 3 4 7 2.788746 1 0.460000 1.950000 0.608554 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ARHGEF10 9639 broad.mit.edu 37 8 1857468 1857468 + Missense_Mutation SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr8:1857468C>T ENST00000398564.1 + 18 2050 c.2050C>T c.(2050-2052)Cat>Tat p.H684Y ARHGEF10_ENST00000520359.1_Missense_Mutation_p.H621Y|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.H683Y|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.H659Y|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.H684Y O15013 ARHGA_HUMAN Rho guanine nucleotide exchange factor (GEF) 10 35 Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834) CAGCCCCTCTCATGACAGCCG 0.502000 0 SO:0001583 missense ENST00000398564.1 1 1 hg19 . . . . . . . . . . C 9.289 1.050147 0.19827 . . ENSG00000104728 ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435 T;T;T;T;T;T 0.17854 2.25;2.25;2.25;2.25;2.25;2.25 4.83 4.83 0.62350 . 1.318090 0.04904 N 0.451894 T 0.19127 0.0459 L 0.41961 1.31 0.58432 D 0.999998 B;B;B 0.09022 0.002;0.001;0.002 B;B;B 0.10450 0.002;0.002;0.005 T 0.08166 -1.0735 10 0.30854 T 0.27 -11.2687 10.5542 0.45107 0.0:0.9011:0.0:0.0989 . 684;621;659 O15013;O15013-7;O15013-5 ARHGA_HUMAN;.;. Y 659;621;683;684;684;332 ENSP00000340297:H659Y;ENSP00000427909:H621Y;ENSP00000431012:H683Y;ENSP00000381571:H684Y;ENSP00000262112:H684Y;ENSP00000427768:H332Y ENSP00000262112:H684Y H + 1 0 ARHGEF10 1844875 0.530000 0.26330 0.020000 0.16555 0.010000 0.07245 1.655000 0.37345 2.382000 0.81193 0.644000 0.83932 CAT TCGA-FB-AAQ2-01A-31D-A40W-08 ARHGEF10-203 KNOWN basic protein_coding protein_coding 1 0 1 189 483 0 175 1 8.905151e-01 9 3 0 175 2 0 0 0 0 0 2 1 1.000000 187 477 0 175 2 -10.026950 1 0 121412 1 33 1 0 1 1 1.598183 1 0.460000 1.950000 0.298701 0.920000 8.200000e-01 1.000000 0.940000 0.925250 0.920000 1 8.700000e-01 9.700000e-01 ALDOB 229 broad.mit.edu 37 9 104187759 104187759 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr9:104187759G>A ENST00000374855.4 - 7 899 c.775C>T c.(775-777)Cgt>Tgt p.R259C ALDOB_ENST00000468981.3_5'Flank NM_000035.3 NP_000026.2 P05062 ALDOB_HUMAN aldolase B, fructose-bisphosphate 24 Acute lymphoblastic leukemia(62;0.0559) GGAACAGTACGGTGGAGAGCT 0.507000 0 SO:0001583 missense ENST00000374855.4 1 1 hg19 CCDS6756.1 . . . . . . . . . . G 18.08 3.543298 0.65198 . . ENSG00000136872 ENST00000374855;ENST00000374853;ENST00000430164 D 0.89875 -2.58 6.06 4.2 0.49525 Aldolase-type TIM barrel (1); 0.000000 0.85682 D 0.000000 D 0.95510 0.8541 H 0.95260 3.645 0.80722 D 1 D 0.89917 1.0 D 0.72625 0.978 D 0.95203 0.8318 10 0.87932 D 0 -5.352 10.3726 0.44064 0.0695:0.0:0.792:0.1385 . 259 P05062 ALDOB_HUMAN C 259;186;259 ENSP00000363988:R259C ENSP00000363986:R186C R - 1 0 ALDOB 103227580 1.000000 0.71417 0.880000 0.34516 0.291000 0.27294 6.636000 0.74299 0.854000 0.35336 0.650000 0.86243 CGT TCGA-FB-AAQ2-01A-31D-A40W-08 ALDOB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053434.2 1 0 1 72 247 0 54 0 9.199893e-01 0 17 0 54 2 0 0 0 0 0 2 1 1.000000 72 244 0 54 2 -3.432400 1 1 121412 2 37 1 1 2 3 2.088270 0 0.460000 1.950000 0.469756 0.990000 8.000000e-01 1.000000 1.000000 0.963023 0.990000 1 8.900000e-01 1 ST6GALNAC6 30815 broad.mit.edu 37 9 130649855 130649855 + Silent SNP C C T TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr9:130649855C>T ENST00000373146.1 - 6 899 c.720G>A c.(718-720)tcG>tcA p.S240S ST6GALNAC6_ENST00000485320.1_5'UTR|RP11-203J24.9_ENST00000476274.2_RNA|ST6GALNAC6_ENST00000291839.5_Silent_p.S240S|ST6GALNAC6_ENST00000542456.1_Silent_p.S40S|ST6GALNAC6_ENST00000373141.1_Silent_p.S206S|ST6GALNAC6_ENST00000373144.3_Silent_p.S206S|ST6GALNAC6_ENST00000373142.1_Silent_p.S240S Q969X2 SIA7F_HUMAN ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 14 TGCTCAACCACGAATGAGACT 0.597000 0 SO:0001819 synonymous_variant ENST00000373146.1 1 1 hg19 CCDS6882.1 TCGA-FB-AAQ2-01A-31D-A40W-08 ST6GALNAC6-007 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000054278.1 1 0 1 31 101 0 31 1 1 29 87 0 31 2 0 0 0 0 0 2 1 1.000000 31 99 0 30 2 -20.000000 1 1 0 0 1 1 2 3 2.088270 0 0.460000 1.950000 0.469756 0.990000 7.400000e-01 1.000000 1.000000 0.960402 0.990000 1 8.800000e-01 1 ANXA1 301 broad.mit.edu 37 9 75775747 75775747 + Missense_Mutation SNP T T G TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr9:75775747T>G ENST00000376911.1 + 5 1295 c.413T>G c.(412-414)aTt>aGt p.I138S ANXA1_ENST00000257497.6_Missense_Mutation_p.I138S P04083 ANXA1_HUMAN annexin A1 8 all_epithelial(88;2.54e-11) Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741) GATACTCTAATTGAGATTTTG 0.358000 0 SO:0001583 missense ENST00000376911.1 1 1 hg19 CCDS6645.1 . . . . . . . . . . T 15.17 2.754013 0.49362 . . ENSG00000135046 ENST00000257497;ENST00000456643;ENST00000376911 T;T;T 0.06933 3.24;3.24;3.24 5.86 2.23 0.28157 Annexin repeat, conserved site (1); 0.189835 0.56097 D 0.000034 T 0.16342 0.0393 M 0.91459 3.21 0.58432 D 0.999997 B 0.22276 0.067 B 0.24006 0.05 T 0.01604 -1.1314 10 0.87932 D 0 . 8.3775 0.32451 0.1446:0.0724:0.0:0.7829 . 138 P04083 ANXA1_HUMAN S 138;149;138 ENSP00000257497:I138S;ENSP00000412489:I149S;ENSP00000366109:I138S ENSP00000257497:I138S I + 2 0 ANXA1 74965567 1.000000 0.71417 0.987000 0.45799 0.948000 0.59901 3.066000 0.50002 0.130000 0.18549 0.533000 0.62120 ATT TCGA-FB-AAQ2-01A-31D-A40W-08 ANXA1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052665.1 1 0 1 186 629 0 192 1 1 1715 2408 0 192 2 0 0 0 0 0 2 1 1.000000 184 625 0 192 2 -20.000000 1 1 0 0 1 1 2 3 2.088270 0 0.460000 1.950000 0.469756 0.990000 8.800000e-01 1.000000 1.000000 0.980873 0.990000 1 9.400000e-01 1 OMD 4958 broad.mit.edu 37 9 95179346 95179346 + Missense_Mutation SNP T T A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chr9:95179346T>A ENST00000375550.4 - 2 770 c.495A>T c.(493-495)gaA>gaT p.E165D CENPP_ENST00000375587.3_Intron NM_005014.2 NP_005005.1 Q99983 OMD_HUMAN osteomodulin 16 GAAGGAGTCTTTCCAGAGATT 0.353000 T USP6 aneurysmal bone cysts Dom yes 9 9q22.31 4958 osteomodulin M 0 SO:0001583 missense ENST00000375550.4 1 1 hg19 CCDS6696.1 . . . . . . . . . . t 16.29 3.081856 0.55861 . . ENSG00000127083 ENST00000375550 T 0.05258 3.47 5.41 4.27 0.50696 . 0.071747 0.53938 D 0.000044 T 0.06462 0.0166 L 0.60067 1.865 0.31296 N 0.688889 P 0.42692 0.787 B 0.33121 0.158 T 0.13255 -1.0516 10 0.56958 D 0.05 -20.6279 7.6328 0.28249 0.0:0.2438:0.0:0.7562 . 165 Q99983 OMD_HUMAN D 165 ENSP00000364700:E165D ENSP00000364700:E165D E - 3 2 OMD 94219167 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 0.745000 0.26259 1.001000 0.39076 0.477000 0.44152 GAA TCGA-FB-AAQ2-01A-31D-A40W-08 OMD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053090.1 1 0 1 86 296 0 72 0 0 0 1 0 72 2 0 0 0 0 0 2 1 1.000000 86 294 1 72 18 -20.000000 1 1 0 0 1 1 2 3 2.088270 0 0.460000 1.950000 0.469756 0.990000 8.100000e-01 1.000000 1.000000 0.964831 0.990000 1 9.000000e-01 1 AFF2 2334 broad.mit.edu 37 X 148055040 148055040 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chrX:148055040G>A ENST00000370460.2 + 16 3786 c.3307G>A c.(3307-3309)Gcc>Acc p.A1103T AFF2_ENST00000370457.5_Missense_Mutation_p.A1068T|AFF2_ENST00000342251.3_Missense_Mutation_p.A1070T|AFF2_ENST00000286437.5_Missense_Mutation_p.A744T NM_001169123.1|NM_002025.3 NP_001162594.1|NP_002016.2 P51816 AFF2_HUMAN AF4/FMR2 family, member 2 p.A1103T(1) 109 Acute lymphoblastic leukemia(192;6.56e-05) TGCTGATGCCGCCCTCTCCTT 0.468000 1 Substitution - Missense(1) SO:0001583 missense ENST00000370460.2 1 1 hg19 CCDS14684.1 . . . . . . . . . . G 33 5.215490 0.95104 . . ENSG00000155966 ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437 T;T;T;T 0.66815 -0.23;-0.23;-0.23;-0.23 5.72 5.72 0.89469 . 0.000000 0.85682 D 0.000000 D 0.83211 0.5205 M 0.80616 2.505 0.58432 D 0.999999 D;D;D;D;D;D 0.89917 0.996;0.998;1.0;1.0;1.0;1.0 D;P;D;D;D;D 0.75020 0.955;0.889;0.985;0.939;0.939;0.964 D 0.85022 0.0912 10 0.66056 D 0.02 . 18.8728 0.92322 0.0:0.0:1.0:0.0 . 744;1068;1068;1064;1093;1103 B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816 .;.;.;.;.;AFF2_HUMAN T 1103;1068;1070;744 ENSP00000359489:A1103T;ENSP00000359486:A1068T;ENSP00000345459:A1070T;ENSP00000286437:A744T ENSP00000286437:A744T A + 1 0 AFF2 147862729 1.000000 0.71417 0.964000 0.40570 0.734000 0.41952 9.827000 0.99397 2.404000 0.81709 0.600000 0.82982 GCC TCGA-FB-AAQ2-01A-31D-A40W-08 AFF2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058673.2 1 0 1 106 300 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 105 296 0 106 2 -5.860837 1 1 0 0 1 0 1 1 0.460000 1.950000 0.460000 0.990000 9.500000e-01 1.000000 1.000000 0.997233 0.990000 1 9.900000e-01 1 BMX 660 broad.mit.edu 37 X 15554529 15554529 + Missense_Mutation SNP G G A TCGA-FB-AAQ2-01A-31D-A40W-08 TCGA-FB-AAQ2-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5b4231a8-75a7-4fe6-bd09-a75f97bee933 880b3248-8493-4948-bc90-14cae9e8761b g.chrX:15554529G>A ENST00000357607.2 + 13 1389 c.1201G>A c.(1201-1203)Gac>Aac p.D401N BMX_ENST00000342014.6_Missense_Mutation_p.D401N|BMX_ENST00000348343.6_Missense_Mutation_p.D401N P51813 BMX_HUMAN BMX non-receptor tyrosine kinase 30 Hepatocellular(33;0.183) CAAGGTCCCCGACTCTGTGTC 0.408000 0 SO:0001583 missense ENST00000357607.2 1 1 hg19 CCDS14168.1 . . . . . . . . . . g 5.048 0.194624 0.09599 . . ENSG00000102010 ENST00000357607;ENST00000348343;ENST00000342014 D;D;D 0.88975 -2.45;-2.45;-2.45 4.94 -0.125 0.13519 Protein kinase-like domain (1); 1.355510 0.04879 N 0.447326 T 0.73497 0.3594 N 0.08118 0 0.09310 N 1 B 0.12013 0.005 B 0.01281 0.0 T 0.60250 -0.7300 10 0.21014 T 0.42 . 1.3363 0.02145 0.2017:0.1429:0.4229:0.2324 . 401 P51813 BMX_HUMAN N 401 ENSP00000350224:D401N;ENSP00000308774:D401N;ENSP00000340082:D401N ENSP00000340082:D401N D + 1 0 BMX 15464450 0.000000 0.05858 0.000000 0.03702 0.143000 0.21401 -0.656000 0.05342 0.242000 0.21303 0.519000 0.50382 GAC TCGA-FB-AAQ2-01A-31D-A40W-08 BMX-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055877.1 1 0 1 128 317 0 88 0 4.478229e-01 0 5 0 88 2 0 0 0 0 0 2 1 1.000000 124 309 0 81 2 -20.000000 1 1 0 0 1 0 1 1 0.460000 1.950000 0.460000 0.990000 9.900000e-01 1.000000 1.000000 0.999938 0.990000 1 9.900000e-01 1