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 CTNND1 1500 broad.mit.edu 37 11 57582920 57582920 + Frame_Shift_Del DEL G G - TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 G - G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr11:57582920delG ENST00000399050.4 + 19 3292 c.2756delG c.(2755-2757)cgafs p.R919fs CTNND1_ENST00000534579.1_Frame_Shift_Del_p.R859fs|CTNND1_ENST00000361332.4_Frame_Shift_Del_p.R913fs|CTNND1_ENST00000529873.1_Frame_Shift_Del_p.R838fs|CTNND1_ENST00000426142.2_Frame_Shift_Del_p.R812fs|CTNND1_ENST00000526938.1_Frame_Shift_Del_p.R898fs|CTNND1_ENST00000530748.1_Frame_Shift_Del_p.R865fs|CTNND1_ENST00000532245.1_Frame_Shift_Del_p.R812fs|CTNND1_ENST00000533667.1_Frame_Shift_Del_p.R569fs|CTNND1_ENST00000532463.1_Frame_Shift_Del_p.R812fs|CTNND1_ENST00000525902.1_Frame_Shift_Del_p.R596fs|CTNND1_ENST00000532787.1_Frame_Shift_Del_p.R791fs|CTNND1_ENST00000415361.2_Frame_Shift_Del_p.R818fs|CTNND1_ENST00000528621.1_Frame_Shift_Del_p.R859fs|CTNND1_ENST00000361796.4_Frame_Shift_Del_p.R913fs|CTNND1_ENST00000428599.2_Frame_Shift_Del_p.R913fs|CTNND1_ENST00000527467.1_Frame_Shift_Del_p.R596fs|CTNND1_ENST00000532844.1_Frame_Shift_Del_p.R865fs|CTNND1_ENST00000358694.6_Frame_Shift_Del_p.R913fs|CTNND1_ENST00000530094.1_Frame_Shift_Del_p.R812fs|CTNND1_ENST00000529986.1_Frame_Shift_Del_p.R812fs|CTNND1_ENST00000361391.6_Frame_Shift_Del_p.R892fs|CTNND1_ENST00000524630.1_Frame_Shift_Del_p.R913fs|CTNND1_ENST00000360682.6_Frame_Shift_Del_p.R898fs|CTNND1_ENST00000399039.4_Frame_Shift_Del_p.R919fs|CTNND1_ENST00000529919.1_Frame_Shift_Del_p.R919fs|CTNND1_ENST00000528232.1_Frame_Shift_Del_p.R818fs|CTNND1_ENST00000526772.1_Frame_Shift_Del_p.R590fs|CTNND1_ENST00000531014.1_Frame_Shift_Del_p.R590fs|CTNND1_ENST00000526357.1_Frame_Shift_Del_p.R859fs|CTNND1_ENST00000529526.1_Frame_Shift_Del_p.R859fs|CTNND1_ENST00000532649.1_Frame_Shift_Del_p.R859fs NM_001085458.1 NP_001078927.1 O60716 CTND1_HUMAN catenin (cadherin-associated protein), delta 1 45 all_epithelial(135;0.155) ACACTGGATCGATCGGGGGAT 0.393000 0 SO:0001589 frameshift_variant ENST00000399050.4 0 1 hg19 CCDS44604.1 TCGA-2J-AABK-01A-31D-A40W-08 CTNND1-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000393944.1 1 0 0 9 101 0 11 1 9.999980e-01 44 341 0 11 2 0 0 0 0 0 0 1 0.995277 9 103 0 12 2 -13.977320 1 1 0 0 1 0 0 0 1.944851 0 0.200000 1.880000 0.164927 0.780000 0.390000 1.000000 1.000000 0.779986 0.780000 0 0.560000 1.000000 SORCS1 114815 broad.mit.edu 37 10 108434807 108434807 + Splice_Site SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr10:108434807G>A ENST00000263054.6 - 14 1947 c.1940C>T c.(1939-1941)aCa>aTa p.T647I SORCS1_ENST00000344440.6_Splice_Site_p.T647I|SORCS1_ENST00000369698.1_Splice_Site_p.T182I NM_001206570.1|NM_052918.4 NP_001193499.1|NP_443150.3 Q8WY21 SORC1_HUMAN sortilin-related VPS10 domain containing receptor 1 127 Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168) TTCAACTTACGTCATGATGAG 0.403000 0 SO:0001630 splice_region_variant ENST00000263054.6 1 0 hg19 CCDS7559.1 . . . . . . . . . . G 27.0 4.787704 0.90367 . . ENSG00000108018 ENST00000369698;ENST00000263054;ENST00000344440 T;T;T 0.38560 1.13;1.13;1.13 5.92 5.92 0.95590 VPS10 (1); 0.000000 0.85682 D 0.000000 T 0.69043 0.3067 M 0.79805 2.47 0.58432 D 0.999999 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 0.999;1.0;1.0;0.999;1.0 T 0.68006 -0.5523 9 . . . -13.2981 20.3206 0.98668 0.0:0.0:1.0:0.0 . 647;647;647;647;647 A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2 .;.;.;SORC1_HUMAN;. I 182;647;647 ENSP00000358712:T182I;ENSP00000263054:T647I;ENSP00000345964:T647I . T - 2 0 SORCS1 108424797 1.000000 0.71417 1.000000 0.80357 0.953000 0.61014 7.628000 0.83189 2.809000 0.96659 0.655000 0.94253 ACA TCGA-2J-AABK-01A-31D-A40W-08 SORCS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050232.4 1 0 1 38 344 0 81 0 0 0 1 0 81 2 1 1 68 633 0 633 2 1 1.000000 38 344 0 81 2 -13.466610 1 1 121412 1 31 1 1 2 3 2.048293 0 0.200000 1.880000 0.207136 0.990000 0.730000 1.000000 1.000000 0.949924 0.990000 1 0.860000 1.000000 AHNAK 79026 broad.mit.edu 37 11 62293318 62293318 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr11:62293318G>A ENST00000378024.4 - 5 8845 c.8571C>T c.(8569-8571)ggC>ggT p.G2857G AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron NM_001620.1 NP_001611.1 Q09666 AHNK_HUMAN AHNAK nucleoprotein 268 Melanoma(852;0.155) CTACCTTAGGGCCTGTAACAT 0.453000 0 SO:0001819 synonymous_variant ENST00000378024.4 1 1 hg19 CCDS31584.1 TCGA-2J-AABK-01A-31D-A40W-08 AHNAK-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395572.1 1 0 0 32 730 0 231 1 3.412846e-01 6 22 0 231 2 0 0 0 0 0 2 1 1.000000 32 722 0 226 2 -4.473745 1 1 0 0 1 0 0 0 1.944851 0 0.200000 1.880000 0.164927 0.400000 0.270000 0.550000 0.400000 0.411049 0.400000 0 0.330000 0.480000 AHNAK 79026 broad.mit.edu 37 11 62296207 62296207 + Silent SNP A A T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr11:62296207A>T ENST00000378024.4 - 5 5956 c.5682T>A c.(5680-5682)ccT>ccA p.P1894P AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron NM_001620.1 NP_001611.1 Q09666 AHNK_HUMAN AHNAK nucleoprotein 268 Melanoma(852;0.155) GCTCAACATCAGGCACCTCCA 0.517000 0 SO:0001819 synonymous_variant ENST00000378024.4 1 1 hg19 CCDS31584.1 TCGA-2J-AABK-01A-31D-A40W-08 AHNAK-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395572.1 0 0 0 33 824 1 201 0 3.183208e-01 1 28 1 201 2 0 0 0 0 0 2 1 0.994892 32 810 1 195 16 -3.507129 1 1 0 0 1 0 0 0 1.944851 0 0.200000 1.880000 0.164927 0.360000 0.250000 0.500000 0.370000 0.376947 0.360000 0 0.300000 0.440000 DCHS1 8642 broad.mit.edu 37 11 6653418 6653418 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr11:6653418G>A ENST00000299441.3 - 6 3736 c.3325C>T c.(3325-3327)Ccc>Tcc p.P1109S RP11-732A19.6_ENST00000526633.1_RNA NM_003737.2 NP_003728.1 Q96JQ0 PCD16_HUMAN dachsous cadherin-related 1 103 Medulloblastoma(188;0.00263)|all_neural(188;0.026) AGGAAGGTGGGATCCTCAGAC 0.607000 0 SO:0001583 missense ENST00000299441.3 0 1 hg19 CCDS7771.1 . . . . . . . . . . G 12.06 1.825234 0.32237 . . ENSG00000166341 ENST00000299441 T 0.05258 3.47 4.66 4.66 0.58398 Cadherin (3);Cadherin-like (1); 0.000000 0.46145 D 0.000310 T 0.07458 0.0188 N 0.03608 -0.345 0.32893 D 0.512082 D 0.69078 0.997 D 0.75484 0.986 T 0.38972 -0.9636 10 0.13108 T 0.6 . 12.2061 0.54353 0.0:0.0:0.8297:0.1703 . 1109 Q96JQ0 PCD16_HUMAN S 1109 ENSP00000299441:P1109S ENSP00000299441:P1109S P - 1 0 DCHS1 6609994 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.514000 0.60482 2.584000 0.87258 0.561000 0.74099 CCC TCGA-2J-AABK-01A-31D-A40W-08 DCHS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257258.1 1 0 0 5 104 0 16 0 9.656781e-03 0 3 0 16 2 0 0 0 0 0 2 1 0.937528 5 103 0 16 2 -8.424241 1 1 0 0 1 0 0 0 1.944851 0 0.200000 1.880000 0.164927 0.460000 0.180000 0.890000 0.430000 0.492451 0.460000 0 0.290000 0.680000 WSCD2 9671 broad.mit.edu 37 12 108604027 108604027 + Silent SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:108604027C>T ENST00000332082.4 + 5 1445 c.627C>T c.(625-627)ggC>ggT p.G209G WSCD2_ENST00000549903.1_Silent_p.G209G|WSCD2_ENST00000261400.3_Silent_p.G209G|WSCD2_ENST00000547525.1_Silent_p.G209G Q2TBF2 WSCD2_HUMAN WSC domain containing 2 57 TGTGCGGCGGCGCCAACCGCC 0.682000 0 SO:0001819 synonymous_variant ENST00000332082.4 0 1 hg19 CCDS41828.1 TCGA-2J-AABK-01A-31D-A40W-08 WSCD2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405554.1 0 0 0 5 62 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 0.923500 4 57 0 13 2 -10.123470 1 1 115198 4 32 1 0 0 0 2.002578 0 0.200000 1.880000 0.188641 0.750000 0.300000 1.000000 1.000000 0.748254 0.750000 0 0.490000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2J-AABK-01A-31D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 15 169 0 60 1 3.380320e-01 2 12 0 60 2 1 9.999999e-01 26 378 0 415 2 1 0.999884 15 167 0 60 2 -7.101348 1 1 0 0 1 0 0 0 2.002578 0 0.200000 1.880000 0.188641 0.800000 0.470000 1.000000 1.000000 0.804655 0.800000 0 0.620000 1.000000 KIF21A 55605 broad.mit.edu 37 12 39752115 39752115 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:39752115G>A ENST00000361418.5 - 8 1095 c.1080C>T c.(1078-1080)aaC>aaT p.N360N KIF21A_ENST00000361961.3_Silent_p.N360N|KIF21A_ENST00000541463.2_Silent_p.N360N|KIF21A_ENST00000544797.2_Silent_p.N360N|KIF21A_ENST00000395670.3_Silent_p.N360N Q7Z4S6 KI21A_HUMAN kinesin family member 21A 86 Lung NSC(34;0.179)|all_lung(34;0.213) ATTTCAGGGTGTTTAACGTTT 0.388000 0 SO:0001819 synonymous_variant ENST00000361418.5 0 1 hg19 CCDS53776.1 TCGA-2J-AABK-01A-31D-A40W-08 KIF21A-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403581.1 0 0 0 10 726 0 153 0 2.420322e-04 0 2 0 153 2 0 0 0 0 0 2 1 0.996793 10 721 0 151 2 -7.263989 1 1 0 0 1 0 0 0 2.002578 0 0.200000 1.880000 0.188641 0.130000 0.060000 0.240000 0.130000 0.146108 0.130000 0 0.090000 0.190000 TUBA1C 84790 broad.mit.edu 37 12 49666572 49666572 + Silent SNP A A G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:49666572A>G ENST00000301072.6 + 4 1187 c.912A>G c.(910-912)aaA>aaG p.K304K TUBA1C_ENST00000541364.1_Silent_p.K374K|RP11-161H23.5_ENST00000550468.2_RNA NM_032704.3 NP_116093.1 Q9BQE3 TBA1C_HUMAN tubulin, alpha 1c 13 AGATGGTGAAATGTGACCCTC 0.498000 0 SO:0001819 synonymous_variant ENST00000301072.6 1 1 hg19 CCDS8782.1 TCGA-2J-AABK-01A-31D-A40W-08 TUBA1C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404424.1 1 0 0 44 393 0 96 1 1 133 371 0 96 2 0 0 0 0 0 2 1 1.000000 43 359 0 114 2 -20.000000 1 1 0 0 1 0 0 0 2.002578 0 0.200000 1.880000 0.188641 0.980000 0.730000 1.000000 1.000000 0.944191 0.980000 1 0.850000 1.000000 KDM5A 5927 broad.mit.edu 37 12 498206 498206 + Missense_Mutation SNP C C G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:498206C>G ENST00000399788.2 - 1 414 c.52G>C c.(52-54)Gag>Cag p.E18Q KDM5A_ENST00000382815.4_Missense_Mutation_p.E18Q|CCDC77_ENST00000540180.1_5'Flank|CCDC77_ENST00000422000.1_5'Flank NM_001042603.1 NP_001036068.1 P29375 KDM5A_HUMAN lysine (K)-specific demethylase 5A 77 ACGGGGCACTCTGGCGGTGGC 0.677000 T NUP98 AML Dom yes 12 12p11 5927 lysine (K)-specific demethylase 5A, JARID1A L 0 SO:0001583 missense ENST00000399788.2 1 1 hg19 CCDS41736.1 . . . . . . . . . . C 20.6 4.014012 0.75161 . . ENSG00000073614 ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760;ENST00000535014;ENST00000543507 D;D;D;T;D 0.87334 -2.24;-2.05;-1.67;-1.33;-1.86 5.42 4.53 0.55603 Transcription factor jumonji, JmjN (1); 0.000000 0.85682 D 0.000000 D 0.89588 0.6758 M 0.80847 2.515 0.53688 D 0.999971 B;B;B;B 0.33612 0.084;0.221;0.295;0.419 B;B;B;B 0.41036 0.034;0.244;0.188;0.346 D 0.89846 0.4006 10 0.87932 D 0 -16.9434 14.0654 0.64826 0.0:0.9272:0.0:0.0728 . 18;18;18;18 B4DVX3;F5H1F7;P29375;P29375-2 .;.;KDM5A_HUMAN;. Q 18 ENSP00000382688:E18Q;ENSP00000372265:E18Q;ENSP00000440622:E18Q;ENSP00000443854:E18Q;ENSP00000444251:E18Q ENSP00000261253:E18Q E - 1 0 KDM5A 368467 1.000000 0.71417 0.862000 0.33874 0.120000 0.20174 7.364000 0.79526 1.288000 0.44600 0.491000 0.48974 GAG TCGA-2J-AABK-01A-31D-A40W-08 KDM5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397812.1 1 0 0 16 189 0 44 0 3.765799e-02 0 4 0 44 2 0 0 0 0 0 2 1 0.999917 16 179 0 42 2 -19.969460 1 1 0 0 1 0 0 0 1.999859 0 0.200000 1.880000 0.186992 0.770000 0.460000 1.000000 1.000000 0.776760 0.770000 0 0.600000 0.960000 SDR9C7 121214 broad.mit.edu 37 12 57323240 57323240 + Nonsense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:57323240G>A ENST00000293502.1 - 3 801 c.658C>T c.(658-660)Cga>Tga p.R220* NM_148897.2 NP_683695.1 Q8NEX9 DR9C7_HUMAN short chain dehydrogenase/reductase family 9C, member 7 7 CAAAGCTTTCGCATGCGTGAC 0.562000 0 SO:0001587 stop_gained ENST00000293502.1 0 1 hg19 CCDS8926.1 . . . . . . . . . . G 33 5.232819 0.95207 . . ENSG00000170426 ENST00000293502 . . . 5.45 3.51 0.40186 . 0.624103 0.14118 N 0.340258 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.17369 T 0.5 . 8.5096 0.33208 0.0:0.2657:0.4449:0.2895 . . . . X 220 . ENSP00000293502:R220X R - 1 2 SDR9C7 55609507 0.000000 0.05858 0.165000 0.22776 0.353000 0.29299 -0.435000 0.06931 0.706000 0.31912 0.650000 0.86243 CGA TCGA-2J-AABK-01A-31D-A40W-08 SDR9C7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411211.1 1 0 1 49 451 0 73 0 0 0 1 0 73 2 0 0 0 0 0 2 1 1.000000 47 438 0 72 2 -15.441740 1 1 121412 3 35 1 0 0 0 2.002578 0 0.200000 1.880000 0.188641 0.960000 0.720000 1.000000 1.000000 0.933355 0.960000 1 0.830000 1.000000 C12orf66 144577 broad.mit.edu 37 12 64588215 64588215 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:64588215C>T ENST00000398055.3 - 3 798 c.745G>A c.(745-747)Gtg>Atg p.V249M C12orf66_ENST00000311915.8_Missense_Mutation_p.V249M|C12orf66_ENST00000544871.1_Missense_Mutation_p.V196M NM_152440.4 NP_689653 Q96MD2 CL066_HUMAN chromosome 12 open reading frame 66 5 GGAGGCTGCACGGCCTTCTGA 0.493000 0 SO:0001583 missense ENST00000398055.3 1 1 hg19 CCDS41803.1 . . . . . . . . . . C 13.47 2.247672 0.39697 . . ENSG00000174206 ENST00000311915;ENST00000544871;ENST00000398055 T;T;T 0.40756 1.02;1.02;1.02 5.94 5.05 0.67936 . 0.117224 0.64402 D 0.000011 T 0.48484 0.1502 L 0.41236 1.265 0.53688 D 0.999976 D;D 0.65815 0.99;0.995 P;P 0.55260 0.747;0.772 T 0.40887 -0.9539 9 . . . -14.3474 15.4147 0.74956 0.0:0.9333:0.0:0.0667 . 196;249 F5H2Q3;Q96MD2 .;CL066_HUMAN M 249;196;249 ENSP00000311486:V249M;ENSP00000445481:V196M;ENSP00000381132:V249M . V - 1 0 C12orf66 62874482 0.998000 0.40836 0.716000 0.30569 0.987000 0.75469 5.846000 0.69444 1.523000 0.49018 0.561000 0.74099 GTG TCGA-2J-AABK-01A-31D-A40W-08 C12orf66-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400921.1 1 0 0 28 276 0 57 0 2.445876e-01 1 9 0 57 2 0 0 0 0 0 2 1 1.000000 28 269 0 56 2 -10.392120 1 1 120884 7 38 1 0 0 0 2.002578 0 0.200000 1.880000 0.188641 0.900000 0.620000 1.000000 1.000000 0.887133 0.900000 1 0.750000 1.000000 CD163L1 283316 broad.mit.edu 37 12 7548911 7548911 + Silent SNP G G A rs140225151 byFrequency TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr12:7548911G>A ENST00000313599.3 - 8 1887 c.1830C>T c.(1828-1830)gaC>gaT p.D610D CD163L1_ENST00000396630.1_Silent_p.D610D|CD163L1_ENST00000416109.2_Silent_p.D620D Q9NR16 C163B_HUMAN CD163 molecule-like 1 96 TGTTCCAGCCGTCATCACACA 0.567000 0 SO:0001819 synonymous_variant ENST00000313599.3 1 1 hg19 CCDS8577.1 TCGA-2J-AABK-01A-31D-A40W-08 CD163L1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000399329.1 1 0 0 13 143 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999534 13 139 0 31 2 -6.597734 1 1 121410 3 38 1 0 0 0 1.999859 0 0.200000 1.880000 0.186992 0.820000 0.460000 1.000000 1.000000 0.814431 0.820000 0 0.620000 1.000000 SOHLH2 54937 broad.mit.edu 37 13 36767849 36767849 + Silent SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr13:36767849C>T ENST00000379881.3 - 4 427 c.339G>A c.(337-339)ggG>ggA p.G113G SOHLH2_ENST00000317764.6_Silent_p.G113G|SOHLH2_ENST00000554962.1_Silent_p.G190G|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.G190G NM_017826.2 NP_060296.2 Q9NX45 SOLH2_HUMAN spermatogenesis and oogenesis specific basic helix-loop-helix 2 26 Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) CCATTCCATGCCCTGAAATAC 0.308000 0 SO:0001819 synonymous_variant ENST00000379881.3 1 1 hg19 CCDS9355.1 TCGA-2J-AABK-01A-31D-A40W-08 SOHLH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044477.2 0 0 0 17 562 0 129 0 0 0 0 129 2 0 0 0 0 0 2 1 0.999965 17 560 0 128 2 -3.244149 1 1 0 0 1 1 2 3 2.041809 0 0.200000 1.880000 0.205561 0.300000 0.180000 1.000000 0.290000 0.348375 0.300000 0 0.230000 0.400000 EIF2B2 8892 broad.mit.edu 37 14 75469848 75469848 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr14:75469848G>A ENST00000266126.5 + 1 235 c.155G>A c.(154-156)aGc>aAc p.S52N RP11-950C14.3_ENST00000554430.1_RNA NM_014239.3 NP_055054.1 P49770 EI2BB_HUMAN eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa 11 CACCGCTGGAGCAACGCGGGT 0.672000 0 SO:0001583 missense ENST00000266126.5 1 1 hg19 CCDS9836.1 . . . . . . . . . . G 12.50 1.957275 0.34565 . . ENSG00000119718 ENST00000266126 D 0.92545 -3.06 5.73 4.83 0.62350 . 0.163209 0.64402 N 0.000002 T 0.79747 0.4499 N 0.04686 -0.185 0.38742 D 0.953916 B 0.02656 0.0 B 0.10450 0.005 T 0.73538 -0.3951 10 0.06099 T 0.92 -15.1504 11.3171 0.49399 0.1477:0.0:0.8523:0.0 . 52 P49770 EI2BB_HUMAN N 52 ENSP00000266126:S52N ENSP00000266126:S52N S + 2 0 EIF2B2 74539601 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 2.131000 0.42074 1.535000 0.49220 0.555000 0.69702 AGC TCGA-2J-AABK-01A-31D-A40W-08 EIF2B2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414993.1 1 0 0 11 168 0 27 1 7.907695e-01 8 39 0 27 2 0 0 0 0 0 2 1 0.998347 10 166 0 27 2 -14.921970 1 1 121374 2 30 1 1 2 3 2.037781 0 0.200000 1.880000 0.204771 0.640000 0.340000 1.000000 1.000000 0.665158 0.640000 0 0.470000 0.870000 VPS13C 54832 broad.mit.edu 37 15 62172889 62172889 + Silent SNP T T A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr15:62172889T>A ENST00000261517.5 - 73 9994 c.9921A>T c.(9919-9921)ctA>ctT p.L3307L VPS13C_ENST00000395896.4_Silent_p.L3307L|VPS13C_ENST00000395898.3_Silent_p.L3264L|VPS13C_ENST00000249837.3_Silent_p.L3264L|VPS13C_ENST00000558919.1_5'UTR NM_020821.2 NP_065872.1 vacuolar protein sorting 13 homolog C (S. cerevisiae) 117 ATTCTGCATTTAGAGCATCAA 0.269000 0 SO:0001819 synonymous_variant ENST00000261517.5 1 1 hg19 CCDS32257.1 TCGA-2J-AABK-01A-31D-A40W-08 VPS13C-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000415997.1 1 0 0 13 127 0 24 1 6.088365e-01 5 16 0 24 2 0 0 0 0 0 2 1 0.999618 13 127 0 24 2 -19.610310 1 1 0 0 1 0 0 0 2.008378 0 0.200000 1.880000 0.191919 0.920000 0.520000 1.000000 1.000000 0.874913 0.920000 1 0.700000 1.000000 CSPG4 1464 broad.mit.edu 37 15 75974724 75974724 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr15:75974724G>A ENST00000308508.5 - 8 4952 c.4860C>T c.(4858-4860)taC>taT p.Y1620Y NM_001897.4 NP_001888.2 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 48 GCACCACACGGTAGAGCAGGA 0.667000 0 SO:0001819 synonymous_variant ENST00000308508.5 0 1 hg19 CCDS10284.1 TCGA-2J-AABK-01A-31D-A40W-08 CSPG4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286472.1 0 0 0 5 259 0 46 0 3.383816e-03 0 4 0 46 2 0 0 0 0 0 2 1 0.931603 4 250 0 43 2 -6.249720 1 0 0 0 1 0 0 0 2.008378 0 0.200000 1.880000 0.191919 0.200000 0.070000 0.400000 0.190000 0.219759 0.200000 0 0.120000 0.300000 IQGAP1 8826 broad.mit.edu 37 15 91017344 91017344 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr15:91017344C>T ENST00000268182.5 + 22 2678 c.2554C>T c.(2554-2556)Cgg>Tgg p.R852W IQGAP1_ENST00000560738.1_Missense_Mutation_p.R280W NM_003870.3 NP_003861.1 P46940 IQGA1_HUMAN IQ motif containing GTPase activating protein 1 59 Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488) BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194) AAACAAAGCTCGGGATGACTA 0.423000 0 SO:0001583 missense ENST00000268182.5 1 1 hg19 CCDS10362.1 . . . . . . . . . . C 21.8 4.195221 0.78902 . . ENSG00000140575 ENST00000268182 T 0.03496 3.91 5.49 4.57 0.56435 . 0.063360 0.64402 D 0.000007 T 0.22551 0.0544 M 0.89785 3.06 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.04229 -1.0967 10 0.72032 D 0.01 -10.2579 13.4279 0.61037 0.0:0.9247:0.0:0.0752 . 852 P46940 IQGA1_HUMAN W 852 ENSP00000268182:R852W ENSP00000268182:R852W R + 1 2 IQGAP1 88818348 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 3.856000 0.55964 1.453000 0.47775 0.655000 0.94253 CGG TCGA-2J-AABK-01A-31D-A40W-08 IQGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313493.1 1 0 1 20 176 0 37 1 9.864188e-01 14 50 0 37 2 0 0 0 0 0 2 1 0.999996 20 174 0 35 2 -3.017830 1 1 0 0 1 0 0 0 2.008378 0 0.200000 1.880000 0.191919 0.990000 0.640000 1.000000 1.000000 0.929861 0.990000 1 0.810000 1.000000 TPSD1 23430 broad.mit.edu 37 16 1306801 1306801 + Silent SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr16:1306801C>T ENST00000211076.3 + 3 406 c.258C>T c.(256-258)gaC>gaT p.D86D RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.D79D NM_012217.2 NP_036349.1 Q9BZJ3 TRYD_HUMAN tryptase delta 1 20 Hepatocellular(780;0.00369) TGCCCAGGGACATCAAGGATC 0.682000 0 SO:0001819 synonymous_variant ENST00000211076.3 0 1 hg19 CCDS10432.1 TCGA-2J-AABK-01A-31D-A40W-08 TPSD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250320.2 0 0 0 7 153 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 0.977586 6 146 0 20 2 -4.022665 1 1 121404 1 19 1 1 2 3 2.066066 0 0.200000 1.880000 0.210267 0.490000 0.210000 1.000000 0.430000 0.541415 0.490000 0 0.320000 0.770000 PRSS36 146547 broad.mit.edu 37 16 31161352 31161352 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr16:31161352G>A ENST00000268281.4 - 1 63 c.5C>T c.(4-6)gCc>gTc p.A2V PRSS36_ENST00000418068.2_Missense_Mutation_p.A2V|PRSS36_ENST00000569305.1_Missense_Mutation_p.A2V NM_001258290.1|NM_173502.4 NP_001245219.1|NP_775773.2 Q5K4E3 POLS2_HUMAN protease, serine, 36 17 CAGGTGCCGGGCCATGGCGCT 0.652000 0 SO:0001583 missense ENST00000268281.4 0 1 hg19 CCDS32436.1 . . . . . . . . . . G 10.32 1.318445 0.23994 . . ENSG00000178226 ENST00000268281;ENST00000418068 D;D 0.89485 -2.52;-2.5 4.97 3.95 0.45737 . . . . . T 0.77322 0.4113 N 0.08118 0 0.21355 N 0.999715 B;B;B 0.19817 0.039;0.039;0.039 B;B;B 0.17433 0.011;0.011;0.018 T 0.67181 -0.5735 9 0.51188 T 0.08 . 8.5374 0.33371 0.1204:0.0:0.8796:0.0 . 2;2;2 E7EX56;B7ZMK8;Q5K4E3 .;.;POLS2_HUMAN V 2 ENSP00000268281:A2V;ENSP00000407160:A2V ENSP00000268281:A2V A - 2 0 PRSS36 31068853 1.000000 0.71417 1.000000 0.80357 0.008000 0.06430 1.152000 0.31663 1.093000 0.41377 0.557000 0.71058 GCC TCGA-2J-AABK-01A-31D-A40W-08 PRSS36-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000433542.1 0 0 0 6 533 1 90 0 0 0 1 90 2 0 0 0 0 0 2 0 0.003709 6 524 1 88 20 -2.577514 1 1 121412 1 31 1 1 2 3 2.030792 0 0.200000 1.880000 0.203980 0.120000 0.040000 1.000000 0.110000 0.162168 0.120000 0 0.070000 0.190000 CDH13 1012 broad.mit.edu 37 16 83704515 83704515 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr16:83704515G>A ENST00000566620.1 + 9 1512 c.1222G>A c.(1222-1224)Ggg>Agg p.G408R CDH13_ENST00000268613.10_Missense_Mutation_p.G455R|CDH13_ENST00000428848.3_Missense_Mutation_p.G369R NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4 NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1 P55290 CAD13_HUMAN cadherin 13 1 all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09) CGGAAACCCCGGGCAGAGCTT 0.498000 0 SO:0001583 missense ENST00000566620.1 1 1 hg19 CCDS58486.1 . . . . . . . . . . G 18.80 3.701232 0.68501 . . ENSG00000140945 ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000540531 T 0.53423 0.62 5.75 5.75 0.90469 Cadherin (4);Cadherin-like (1); . . . . T 0.54046 0.1834 L 0.29908 0.895 0.80722 D 1 D;P;D 0.76494 0.991;0.676;0.999 P;B;P 0.58970 0.739;0.283;0.849 T 0.44952 -0.9294 9 0.30854 T 0.27 . 18.9266 0.92548 0.0:0.0:1.0:0.0 . 369;455;408 B7Z590;B7Z9B1;P55290 .;.;CAD13_HUMAN R 455;408;369;110;98 ENSP00000268613:G455R ENSP00000268613:G455R G + 1 0 CDH13 82262016 1.000000 0.71417 0.954000 0.39281 0.452000 0.32318 5.494000 0.66905 2.717000 0.92951 0.585000 0.79938 GGG TCGA-2J-AABK-01A-31D-A40W-08 CDH13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432917.1 1 0 1 57 516 0 97 0 2.884758e-02 0 3 0 97 2 0 0 0 0 0 2 1 1.000000 57 507 0 94 2 -2.329789 0 1 120882 26 48 1 1 2 3 2.030792 0 0.200000 1.880000 0.203980 0.990000 0.770000 1.000000 1.000000 0.955253 0.990000 1 0.880000 1.000000 MYH4 4622 broad.mit.edu 37 17 10366281 10366281 + Missense_Mutation SNP C C A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr17:10366281C>A ENST00000255381.2 - 11 1019 c.909G>T c.(907-909)atG>atT p.M303I RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA NM_017533.2 NP_060003.2 Q9Y623 MYH4_HUMAN myosin, heavy chain 4, skeletal muscle 149 TGATCAGAAGCATTTCTGAAC 0.433000 0 SO:0001583 missense ENST00000255381.2 1 1 hg19 CCDS11154.1 . . . . . . . . . . C 17.21 3.332814 0.60853 . . ENSG00000141048 ENST00000255381 D 0.87103 -2.21 5.38 5.38 0.77491 Myosin head, motor domain (2); 0.000000 0.45361 U 0.000374 D 0.89361 0.6693 M 0.84683 2.71 0.53688 D 0.999972 B 0.02656 0.0 B 0.09377 0.004 D 0.86226 0.1634 10 0.52906 T 0.07 . 19.4872 0.95033 0.0:1.0:0.0:0.0 . 303 Q9Y623 MYH4_HUMAN I 303 ENSP00000255381:M303I ENSP00000255381:M303I M - 3 0 MYH4 10307006 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 3.183000 0.50918 2.671000 0.90904 0.655000 0.94253 ATG TCGA-2J-AABK-01A-31D-A40W-08 MYH4-001 KNOWN NAGNAG_splice_site|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252731.1 0 0 0 15 242 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 0.999878 14 241 0 52 2 -5.491055 1 1 0 0 1 0 1 1 1.862315 1 0.200000 1.880000 0.120879 0.530000 0.310000 0.800000 0.520000 0.546105 0.530000 0 0.410000 0.670000 TP53 7157 broad.mit.edu 37 17 7577123 7577123 + Missense_Mutation SNP A A G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS targeted Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr17:7577123A>G ENST00000269305.4 - 8 1004 c.815T>C c.(814-816)gTg>gCg p.V272A TP53_ENST00000445888.2_Missense_Mutation_p.V272A|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.V272A|TP53_ENST00000420246.2_Missense_Mutation_p.V272A|TP53_ENST00000359597.4_Missense_Mutation_p.V272A|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.0?(8)|p.V272E(8)|p.V272A(7)|p.V272G(6)|p.?(2)|p.F270fs*72(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.E271fs*73(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ACAAACACGCACCTCAAAGCT 0.532000 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 39 Substitution - Missense(21)|Whole gene deletion(8)|Deletion - In frame(4)|Deletion - Frameshift(4)|Unknown(2) GRCh37 CM942122 TP53 M 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 0 1 hg19 CCDS11118.1 . . . . . . . . . . A 15.32 2.797806 0.50208 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99822 -6.94;-6.94;-6.94;-6.94;-6.94;-6.94 5.13 2.87 0.33458 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.057604 0.64402 D 0.000002 D 0.99622 0.9862 M 0.75447 2.3 0.80722 D 1 D;D;D;D 0.89917 0.999;1.0;1.0;0.992 D;D;D;D 0.83275 0.996;0.996;0.996;0.99 D 0.99204 1.0874 10 0.28530 T 0.3 -27.8222 6.511 0.22222 0.7602:0.1564:0.0833:0.0 . 272;272;272;272 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. A 272;272;272;272;272;261;140 ENSP00000352610:V272A;ENSP00000269305:V272A;ENSP00000398846:V272A;ENSP00000391127:V272A;ENSP00000391478:V272A;ENSP00000425104:V140A ENSP00000269305:V272A V - 2 0 TP53 7517848 0.032000 0.19561 0.353000 0.25747 0.798000 0.45092 0.523000 0.22925 0.396000 0.25283 0.379000 0.24179 GTG TCGA-2J-AABK-01A-31D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 15 103 0 14 1 9.976036e-01 21 51 0 14 2 1 1 84 820 0 1108 2 1 0.999896 15 101 0 14 2 -19.999920 1 1 0 0 1 0 1 1 1.862315 1 0.200000 1.880000 0.120879 0.940000 0.610000 1.000000 1.000000 0.904703 0.940000 1 0.780000 1.000000 RNF213 57674 broad.mit.edu 37 17 78337556 78337556 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr17:78337556G>A ENST00000582970.1 + 41 11859 c.11716G>A c.(11716-11718)Ggg>Agg p.G3906R CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.G3955R|RNF213_ENST00000336301.6_Missense_Mutation_p.G1979R|CTD-2047H16.4_ENST00000572151.1_RNA NM_001256071.1 NP_001243000.1 Q63HN8 RN213_HUMAN ring finger protein 213 130 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) GCAAGGCAGCGGGAGCCTGGC 0.617000 0 SO:0001583 missense ENST00000582970.1 0 1 hg19 CCDS58606.1 . . . . . . . . . . G 16.25 3.070011 0.55539 . . ENSG00000173821 ENST00000508628;ENST00000411702;ENST00000336301 T 0.23348 1.91 5.03 -0.504 0.11997 . 0.293863 0.37483 N 0.002079 T 0.45054 0.1323 M 0.77820 2.39 0.09310 N 1 P;D 0.89917 0.76;1.0 B;D 0.72625 0.147;0.978 T 0.32798 -0.9893 10 0.87932 D 0 . 9.053 0.36387 0.4393:0.0:0.5607:0.0 . 3955;1979 C9JCP4;Q63HN8 .;RN213_HUMAN R 3906;3955;1979 ENSP00000338218:G1979R ENSP00000338218:G1979R G + 1 0 RNF213 75952151 0.932000 0.31603 0.000000 0.03702 0.001000 0.01503 1.647000 0.37260 -0.314000 0.08716 -0.150000 0.13652 GGG TCGA-2J-AABK-01A-31D-A40W-08 RNF213-020 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000443298.1 1 0 0 9 101 0 19 1 7.401726e-01 4 27 0 19 2 1 9.999423e-01 60 409 1 493 6 1 0.994859 9 101 0 18 2 -2.921914 1 1 0 0 1 0 1 1 1.867580 1 0.200000 1.880000 0.124726 0.720000 0.370000 1.000000 1.000000 0.727711 0.720000 0 0.520000 0.930000 FAM129C 199786 broad.mit.edu 37 19 17653012 17653012 + Missense_Mutation SNP G G A rs149574830 TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr19:17653012G>A ENST00000335393.4 + 11 1469 c.1331G>A c.(1330-1332)cGg>cAg p.R444Q FAM129C_ENST00000595684.1_Missense_Mutation_p.R444Q|FAM129C_ENST00000332386.5_Missense_Mutation_p.R444Q|FAM129C_ENST00000599164.1_Missense_Mutation_p.R413Q|FAM129C_ENST00000601861.1_Missense_Mutation_p.R413Q|FAM129C_ENST00000600871.1_Missense_Mutation_p.R390Q|FAM129C_ENST00000352727.3_Missense_Mutation_p.R444Q|FAM129C_ENST00000300971.2_Missense_Mutation_p.R444Q|FAM129C_ENST00000599124.1_Missense_Mutation_p.R413Q|FAM129C_ENST00000449408.2_Missense_Mutation_p.R170Q NM_173544.4 NP_775815 Q86XR2 NIBL2_HUMAN family with sequence similarity 129, member C 33 GAGGCCGAGCGGAGCCGGGGG 0.607000 0 SO:0001583 missense ENST00000335393.4 1 1 hg19 CCDS12362.1 . . . . . . . . . . g 5.022 0.189829 0.09547 2.27E-4 2.33E-4 ENSG00000167483 ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971;ENST00000449408;ENST00000435646 T;T;T;T;T 0.22945 2.27;2.29;1.98;1.99;1.93 4.77 1.28 0.21552 . 0.297213 0.23053 N 0.052468 T 0.10637 0.0260 L 0.28400 0.85 0.09310 N 1 P;P;P;P;B;P 0.39624 0.535;0.681;0.681;0.681;0.366;0.681 B;B;B;B;B;B 0.31016 0.049;0.123;0.071;0.071;0.05;0.071 T 0.16837 -1.0389 10 0.13108 T 0.6 -22.8782 3.1616 0.06522 0.2352:0.0:0.4981:0.2667 . 390;444;444;444;170;444 E7ENP6;Q86XR2;Q86XR2-3;Q86XR2-4;B4DNU3;Q86XR2-2 .;NIBL2_HUMAN;.;.;.;. Q 444;444;444;444;170;390 ENSP00000335040:R444Q;ENSP00000333447:R444Q;ENSP00000341067:R444Q;ENSP00000300971:R444Q;ENSP00000394929:R170Q ENSP00000300971:R444Q R + 2 0 FAM129C 17514012 0.000000 0.05858 0.000000 0.03702 0.007000 0.05969 0.160000 0.16462 0.455000 0.26910 0.586000 0.80456 CGG TCGA-2J-AABK-01A-31D-A40W-08 FAM129C-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000464206.1 1 0 0 38 794 0 189 0 0 0 0 189 2 0 0 0 0 0 2 1 1.000000 38 784 0 184 2 -3.191299 1 1 121412 4 47 1 1 2 3 2.034460 0 0.200000 1.880000 0.204771 0.460000 0.330000 1.000000 0.460000 0.493211 0.460000 0 0.390000 0.560000 PNMAL2 57469 broad.mit.edu 37 19 46998384 46998384 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr19:46998384G>A ENST00000377655.2 - 1 338 c.339C>T c.(337-339)gaC>gaT p.D113D PNMAL2_ENST00000594749.1_Intron|PNMAL2_ENST00000599531.1_Silent_p.D113D|AC011484.1_ENST00000377652.3_Silent_p.P165P Q9ULN7 PNML2_HUMAN paraneoplastic Ma antigen family-like 2 8 Ovarian(192;0.00965)|all_neural(266;0.0459) GCGTGGGCCCGTCATCCAGCA 0.692000 0 SO:0001819 synonymous_variant ENST00000377655.2 1 1 hg19 TCGA-2J-AABK-01A-31D-A40W-08 PNMAL2-201 KNOWN basic protein_coding protein_coding 1 0 0 59 550 0 114 0 9.787876e-03 0 2 0 114 2 0 0 0 0 0 2 1 1.000000 55 539 0 111 2 -17.054310 1 1 0 0 1 1 2 3 2.034460 0 0.200000 1.880000 0.204771 0.970000 0.750000 1.000000 1.000000 0.944724 0.970000 1 0.860000 1.000000 CCDC114 93233 broad.mit.edu 37 19 48800579 48800579 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr19:48800579G>A ENST00000315396.7 - 14 2349 c.1667C>T c.(1666-1668)tCt>tTt p.S556F NM_144577.3 NP_653178.3 Q96M63 CC114_HUMAN coiled-coil domain containing 114 24 all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113) GTGGCCAAGAGAGCCACGGTC 0.642000 0 SO:0001583 missense ENST00000315396.7 0 1 hg19 CCDS12714.2 . . . . . . . . . . G 14.35 2.509077 0.44660 . . ENSG00000105479 ENST00000315396 T 0.32272 1.46 3.66 2.61 0.31194 . . . . . T 0.24236 0.0587 L 0.32530 0.975 0.09310 N 1 P 0.41784 0.762 B 0.41135 0.348 T 0.09707 -1.0662 9 0.66056 D 0.02 -8.5304 7.6387 0.28282 0.127:0.0:0.873:0.0 . 556 Q96M63 CC114_HUMAN F 556 ENSP00000318429:S556F ENSP00000318429:S556F S - 2 0 CCDC114 53492391 0.320000 0.24616 0.023000 0.16930 0.007000 0.05969 3.696000 0.54757 0.820000 0.34516 0.555000 0.69702 TCT TCGA-2J-AABK-01A-31D-A40W-08 CCDC114-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000343207.1 0 0 0 18 219 1 47 0 6.624826e-03 0 2 1 47 2 0 0 0 0 0 2 1 0.627231 17 219 1 46 17 -19.999540 1 1 0 0 1 1 2 3 2.034460 0 0.200000 1.880000 0.204771 0.780000 0.480000 1.000000 1.000000 0.785802 0.780000 0 0.610000 0.990000 NLRP13 126204 broad.mit.edu 37 19 56424320 56424320 + Missense_Mutation SNP T T A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr19:56424320T>A ENST00000342929.3 - 5 862 c.863A>T c.(862-864)gAt>gTt p.D288V NLRP13_ENST00000588751.1_Missense_Mutation_p.D288V NM_176810.2 NP_789780.2 Q86W25 NAL13_HUMAN NLR family, pyrin domain containing 13 109 Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218) ATCGGGCCAATCCAAAGAAAT 0.393000 0 SO:0001583 missense ENST00000342929.3 1 1 hg19 CCDS33119.1 . . . . . . . . . . T 12.15 1.852815 0.32699 . . ENSG00000173572 ENST00000342929 D 0.83506 -1.73 2.7 1.66 0.24008 NACHT nucleoside triphosphatase (1); . . . . D 0.85995 0.5827 M 0.67397 2.05 0.09310 N 0.999993 D 0.65815 0.995 D 0.63381 0.914 T 0.73591 -0.3934 9 0.66056 D 0.02 . 3.7405 0.08528 0.0:0.1879:0.0:0.8121 . 288 Q86W25 NAL13_HUMAN V 288 ENSP00000343891:D288V ENSP00000343891:D288V D - 2 0 NLRP13 61116132 0.039000 0.19947 0.129000 0.21949 0.006000 0.05464 0.488000 0.22371 1.211000 0.43351 0.482000 0.46254 GAT TCGA-2J-AABK-01A-31D-A40W-08 NLRP13-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396560.1 1 0 0 31 322 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1.000000 31 318 0 65 2 -10.539440 1 1 0 0 1 1 2 3 2.065882 0 0.200000 1.880000 0.210267 0.910000 0.620000 1.000000 1.000000 0.890494 0.910000 1 0.750000 1.000000 ZSCAN5B 342933 broad.mit.edu 37 19 56702324 56702324 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr19:56702324G>A ENST00000586855.2 - 4 934 c.621C>T c.(619-621)gaC>gaT p.D207D ZSCAN5B_ENST00000358992.3_Silent_p.D207D A6NJL1 ZSA5B_HUMAN zinc finger and SCAN domain containing 5B 37 CACCTGTTACGTCAATACTCT 0.507000 0 SO:0001819 synonymous_variant ENST00000586855.2 1 1 hg19 CCDS46203.1 TCGA-2J-AABK-01A-31D-A40W-08 ZSCAN5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457834.2 0 0 0 36 453 1 131 0 0 0 1 1 131 2 0 0 0 0 0 2 1 0.999618 36 450 1 129 14 -9.229429 1 1 121412 6 42 1 1 2 3 2.065882 0 0.200000 1.880000 0.210267 0.760000 0.530000 1.000000 0.740000 0.781359 0.760000 0 0.640000 0.950000 GSTM5 2949 broad.mit.edu 37 1 110254908 110254908 + Translation_Start_Site SNP T T A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:110254908T>A ENST00000256593.3 + 0 32 GSTM5_ENST00000369812.5_De_novo_Start_OutOfFrame|GSTM5_ENST00000369813.1_De_novo_Start_OutOfFrame 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) CTGATGCCTGTCTGCAGAATC 0.682000 0 ENST00000256593.3 0 1 hg19 CCDS811.1 TCGA-2J-AABK-01A-31D-A40W-08 GSTM5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000032200.1 0 0 0 74 637 0 133 0 1.113412e-02 0 2 0 133 2 0 0 0 0 0 2 1 1.000000 71 626 0 130 2 -20.000000 1 1 0 0 1 0 1 1 1.860983 1 0.200000 1.880000 0.125683 0.930000 0.750000 1.000000 1.000000 0.928076 0.930000 1 0.840000 1.000000 MLLT11 10962 broad.mit.edu 37 1 151039879 151039879 + Missense_Mutation SNP A A G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:151039879A>G ENST00000368921.3 + 2 2981 c.179A>G c.(178-180)aAc>aGc p.N60S CDC42SE1_ENST00000439374.2_Intron NM_006818.3 NP_006809.1 Q13015 AF1Q_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11 1 Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211) CAGGAGAAAAACCCTGAAGGT 0.532000 0 SO:0001583 missense ENST00000368921.3 1 1 hg19 CCDS982.1 . . . . . . . . . . A 9.105 1.005000 0.19199 . . ENSG00000213190 ENST00000368921 . . . 6.06 -12.1 0.00011 . 1.158550 0.06646 N 0.761875 T 0.03263 0.0095 . . . 0.09310 N 1 B 0.06786 0.001 B 0.04013 0.001 T 0.15350 -1.0440 8 0.10111 T 0.7 -3.2682 6.6906 0.23169 0.1975:0.4743:0.25:0.0781 . 60 Q13015 AF1Q_HUMAN S 60 . ENSP00000357917:N60S N + 2 0 MLLT11 149306503 0.000000 0.05858 0.065000 0.19835 0.750000 0.42670 -0.453000 0.06778 -2.338000 0.00627 -0.250000 0.11733 AAC TCGA-2J-AABK-01A-31D-A40W-08 MLLT11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085103.1 0 0 0 21 526 0 68 0 2.937825e-01 0 27 0 68 2 0 0 0 0 0 2 1 0.999997 21 522 0 66 2 -3.498016 1 1 0 0 1 2 2 4 2.331064 1 0.200000 1.880000 0.306759 0.470000 0.280000 1.000000 0.430000 0.551637 0.470000 0 0.370000 1.000000 CRNN 49860 broad.mit.edu 37 1 152382385 152382385 + Missense_Mutation SNP G G T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:152382385G>T ENST00000271835.3 - 3 1235 c.1173C>A c.(1171-1173)agC>agA p.S391R RP1-91G5.3_ENST00000411804.1_RNA NM_016190.2 NP_057274.1 Q9UBG3 CRNN_HUMAN cornulin 35 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) CCTCAGGGTTGCTCACTTGCA 0.602000 0 SO:0001583 missense ENST00000271835.3 1 1 hg19 CCDS1010.1 . . . . . . . . . . G 11.93 1.785870 0.31593 . . ENSG00000143536 ENST00000271835 T 0.04970 3.52 4.5 1.36 0.22044 . 0.199037 0.36066 N 0.002802 T 0.04588 0.0125 L 0.50333 1.59 0.09310 N 1 D 0.71674 0.998 P 0.58721 0.844 T 0.26430 -1.0103 10 0.72032 D 0.01 . 2.4183 0.04441 0.1093:0.2065:0.4987:0.1855 . 391 Q9UBG3 CRNN_HUMAN R 391 ENSP00000271835:S391R ENSP00000271835:S391R S - 3 2 CRNN 150649009 0.069000 0.21087 0.062000 0.19696 0.038000 0.13279 0.607000 0.24209 0.495000 0.27882 0.585000 0.79938 AGC TCGA-2J-AABK-01A-31D-A40W-08 CRNN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034503.1 1 0 0 42 514 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 1.000000 41 503 0 64 2 -10.330540 1 1 0 0 1 2 2 4 2.331064 1 0.200000 1.880000 0.306759 0.900000 0.650000 1.000000 1.000000 0.892555 0.900000 1 0.760000 1.000000 HMCN1 83872 broad.mit.edu 37 1 186147896 186147896 + Missense_Mutation SNP T T C TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:186147896T>C ENST00000271588.4 + 104 16521 c.16292T>C c.(16291-16293)gTa>gCa p.V5431A HMCN1_ENST00000367492.2_Intron|GS1-174L6.4_ENST00000428391.1_RNA NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 GACACATGTGTAGGTAAATGT 0.428000 0 SO:0001583 missense ENST00000271588.4 0 1 hg19 CCDS30956.1 . . . . . . . . . . T 13.38 2.221260 0.39201 . . ENSG00000143341 ENST00000271588 D 0.87966 -2.32 5.56 5.56 0.83823 Growth factor, receptor (1); 0.187626 0.47455 D 0.000237 D 0.83101 0.5181 L 0.48174 1.505 0.80722 D 1 B 0.31625 0.332 B 0.27380 0.079 T 0.82808 -0.0274 10 0.56958 D 0.05 . 14.5915 0.68368 0.0:0.0:0.0:1.0 . 5431 Q96RW7 HMCN1_HUMAN A 5431 ENSP00000271588:V5431A ENSP00000271588:V5431A V + 2 0 HMCN1 184414519 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 6.614000 0.74197 2.240000 0.73641 0.533000 0.62120 GTA TCGA-2J-AABK-01A-31D-A40W-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 0 0 0 16 345 1 40 0 2.084493e-02 0 5 1 40 2 0 0 0 0 0 2 0 0.050196 15 340 1 37 27 -17.090710 1 1 0 0 1 2 2 4 2.362231 1 0.200000 1.880000 0.316239 0.550000 0.310000 1.000000 0.520000 0.598668 0.550000 0 0.420000 0.780000 CACNA1S 779 broad.mit.edu 37 1 201079379 201079379 + Missense_Mutation SNP G G C TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:201079379G>C ENST00000362061.3 - 2 397 c.171C>G c.(169-171)atC>atG p.I57M CACNA1S_ENST00000367338.3_Missense_Mutation_p.I57M NM_000069.2 NP_000060.2 Q13698 CAC1S_HUMAN calcium channel, voltage-dependent, L type, alpha 1S subunit 102 Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) TGGTGAGCAAGATGATCGTCT 0.577000 0 SO:0001583 missense ENST00000362061.3 1 1 hg19 CCDS1407.1 . . . . . . . . . . G 18.39 3.614339 0.66672 . . ENSG00000081248 ENST00000362061;ENST00000367338 T;T 0.71698 -0.59;-0.59 4.86 4.86 0.63082 . 0.000000 0.85682 D 0.000000 D 0.86306 0.5901 M 0.92555 3.32 0.47862 D 0.999533 D 0.89917 1.0 D 0.91635 0.999 D 0.88364 0.2990 10 0.59425 D 0.04 . 11.4934 0.50394 0.0841:0.0:0.9159:0.0 . 57 Q13698 CAC1S_HUMAN M 57 ENSP00000355192:I57M;ENSP00000356307:I57M ENSP00000355192:I57M I - 3 3 CACNA1S 199346002 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 4.482000 0.60257 2.388000 0.81334 0.561000 0.74099 ATC TCGA-2J-AABK-01A-31D-A40W-08 CACNA1S-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087049.1 1 0 1 38 292 0 40 1 1.411050e-02 2 0 0 40 2 0 0 0 0 0 2 1 1.000000 38 290 0 39 2 -20.000000 1 1 0 0 1 2 2 4 2.199606 1 0.200000 1.880000 0.266055 0.990000 0.930000 1.000000 1.000000 0.996158 0.990000 1 0.990000 1.000000 EPHB2 2048 broad.mit.edu 37 1 23111370 23111370 + Silent SNP C C A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:23111370C>A ENST00000400191.3 + 3 630 c.612C>A c.(610-612)ggC>ggA p.G204G EPHB2_ENST00000374630.3_Silent_p.G204G|EPHB2_ENST00000374632.3_Silent_p.G204G|EPHB2_ENST00000544305.1_Silent_p.G204G|EPHB2_ENST00000374627.1_Silent_p.G198G NM_004442.6|NM_017449.3 NP_004433.2|NP_059145.2 P29323 EPHB2_HUMAN EPH receptor B2 56 Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258) TCCAGAATGGCGCCATCTTCC 0.627000 0 SO:0001819 synonymous_variant ENST00000400191.3 1 1 hg19 TCGA-2J-AABK-01A-31D-A40W-08 EPHB2-001 KNOWN basic protein_coding protein_coding OTTHUMT00000008060.2 1 0 1 27 149 0 39 1 7.295226e-01 3 13 0 39 2 0 0 0 0 0 2 1 1.000000 26 146 0 39 2 -20.000000 1 1 0 0 1 0 2 2 1.957755 1 0.200000 1.880000 0.200000 0.990000 0.990000 1.000000 1.000000 0.999237 0.990000 1 0.990000 1.000000 RYR2 6262 broad.mit.edu 37 1 237948081 237948081 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:237948081G>A ENST00000366574.2 + 90 13386 c.13069G>A c.(13069-13071)Gcc>Acc p.A4357T RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.A4341T|RYR2_ENST00000360064.6_Missense_Mutation_p.A4363T NM_001035.2 NP_001026.2 Q92736 RYR2_HUMAN ryanodine receptor 2 (cardiac) p.A4355T(1) 586 Ovarian(103;0.103) all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225) OV - Ovarian serous cystadenocarcinoma(106;0.00606) CCTGGAAGCCGCCCTGCCCTC 0.532000 1 Substitution - Missense(1) SO:0001583 missense ENST00000366574.2 1 1 hg19 CCDS55691.1 . . . . . . . . . . G 6.908 0.537143 0.13188 . . ENSG00000198626 ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288 D;D;D 0.93659 -3.26;-3.26;-3.26 5.32 1.05 0.20165 Ryanodine Receptor TM 4-6 (1); 0.568755 0.15572 N 0.255407 T 0.80613 0.4656 N 0.08118 0 0.36787 D 0.884646 B;B 0.32071 0.102;0.355 B;B 0.26614 0.028;0.071 T 0.71310 -0.4631 10 0.14252 T 0.57 -1.744 7.2896 0.26358 0.1498:0.2567:0.5934:0.0 . 1331;4357 B4DGV4;Q92736 .;RYR2_HUMAN T 4357;4363;4341;1331 ENSP00000355533:A4357T;ENSP00000353174:A4363T;ENSP00000443798:A4341T ENSP00000353174:A4363T A + 1 0 RYR2 236014704 0.000000 0.05858 0.096000 0.21009 0.123000 0.20343 0.422000 0.21296 0.032000 0.15435 -0.143000 0.13931 GCC TCGA-2J-AABK-01A-31D-A40W-08 RYR2-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095402.2 1 0 1 50 204 0 37 1 4.030885e-02 2 0 0 37 2 0 0 0 0 0 2 1 1.000000 49 198 0 37 2 -3.501750 1 1 120864 27 42 1 0 1 1 2.005712 1 0.200000 1.880000 0.121844 0.990000 0.950000 1.000000 1.000000 0.997632 0.990000 1 0.990000 1.000000 ZC3H12A 80149 broad.mit.edu 37 1 37948837 37948837 + Silent SNP A A T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr1:37948837A>T ENST00000373087.6 + 6 1541 c.1425A>T c.(1423-1425)ggA>ggT p.G475G NM_025079.2 NP_079355.2 zinc finger CCCH-type containing 12A 21 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) GTCCCTATGGATCTGAGCTCC 0.677000 0 SO:0001819 synonymous_variant ENST00000373087.6 1 1 hg19 CCDS417.1 TCGA-2J-AABK-01A-31D-A40W-08 ZC3H12A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012154.2 1 0 1 52 333 0 61 1 9.999934e-01 45 69 0 61 2 0 0 0 0 0 2 1 1.000000 51 325 0 60 2 -20.000000 1 1 0 0 1 0 2 2 1.962099 1 0.200000 1.880000 0.200000 0.990000 0.990000 1.000000 1.000000 0.999458 0.990000 1 0.990000 1.000000 TIAM1 7074 broad.mit.edu 37 21 32499427 32499427 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr21:32499427G>A ENST00000286827.3 - 27 4560 c.4089C>T c.(4087-4089)tcC>tcT p.S1363S TIAM1_ENST00000541036.1_Silent_p.S1303S NM_003253.2 NP_003244.2 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 115 CTTCAGACTCGGATTTTACAT 0.453000 0 SO:0001819 synonymous_variant ENST00000286827.3 1 1 hg19 CCDS13609.1 . . . . . . . . . . G 1.678 -0.507137 0.04231 . . ENSG00000156299 ENST00000423206 . . . 6.17 -12.3 0.00002 . . . . . T 0.30262 0.0759 . . . 0.80722 D 1 . . . . . . T 0.46652 -0.9176 4 . . . . 1.7358 0.02941 0.3065:0.0798:0.2498:0.3639 . . . . L 18 . . P - 2 0 TIAM1 31421298 0.000000 0.05858 0.009000 0.14445 0.276000 0.26787 -4.277000 0.00261 -3.566000 0.00140 -1.869000 0.00555 CCG TCGA-2J-AABK-01A-31D-A40W-08 TIAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192552.1 1 0 0 27 260 0 52 0 6.081076e-01 0 21 0 52 2 0 0 0 0 0 2 1 1.000000 27 255 0 52 2 -2.966611 1 1 121412 9 42 1 0 1 1 1.867336 1 0.200000 1.880000 0.137001 0.860000 0.580000 1.000000 1.000000 0.855636 0.860000 1 0.710000 1.000000 DSCR4 10281 broad.mit.edu 37 21 39493319 39493319 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr21:39493319C>T ENST00000328264.3 - 1 135 c.31G>A c.(31-33)Gaa>Aaa p.E11K DSCR4_ENST00000398948.1_Missense_Mutation_p.E11K|DSCR8_ENST00000400477.3_5'Flank|DSCR8_ENST00000357704.4_5'Flank NM_005867.2 NP_005858.1 P56555 DSCR4_HUMAN Down syndrome critical region gene 4 6 atccggggttcatcatctctc 0.498000 0 SO:0001583 missense ENST00000328264.3 1 1 hg19 CCDS33554.1 . . . . . . . . . . C 9.190 1.025771 0.19512 0.0 1.16E-4 ENSG00000184029 ENST00000398948;ENST00000328264 . . . 0.235 0.235 0.15431 . . . . . T 0.50786 0.1636 . . . 0.09310 N 1 P 0.49696 0.927 P 0.56563 0.801 T 0.40021 -0.9585 6 0.87932 D 0 . . . . . 11 P56555 DSCR4_HUMAN K 11 . ENSP00000328676:E11K E - 1 0 DSCR4 38415189 0.016000 0.18221 0.053000 0.19242 0.053000 0.15095 0.305000 0.19254 0.308000 0.22923 0.313000 0.20887 GAA TCGA-2J-AABK-01A-31D-A40W-08 DSCR4-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000194834.1 1 0 0 16 166 0 26 0 0 0 0 26 2 0 0 0 0 0 2 1 0.999944 16 165 0 26 2 -19.995100 1 1 121412 2 34 1 1 2 3 2.074021 0 0.200000 1.880000 0.211823 0.930000 0.550000 1.000000 1.000000 0.882951 0.930000 1 0.720000 1.000000 TRAPPC10 7109 broad.mit.edu 37 21 45502791 45502791 + Missense_Mutation SNP A A G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr21:45502791A>G ENST00000291574.4 + 14 2021 c.1846A>G c.(1846-1848)Atg>Gtg p.M616V NM_003274.4 NP_003265.3 P48553 TPC10_HUMAN trafficking protein particle complex 10 41 GTACAGCCAGATGCCTGTGCC 0.517000 0 SO:0001583 missense ENST00000291574.4 0 1 hg19 CCDS13704.1 . . . . . . . . . . A 15.54 2.864973 0.51482 . . ENSG00000160218 ENST00000291574 T 0.41400 1.0 5.58 4.39 0.52855 . 0.036580 0.85682 D 0.000000 T 0.31827 0.0809 L 0.29908 0.895 0.43069 D 0.994707 P 0.40431 0.717 B 0.38755 0.281 T 0.06643 -1.0815 10 0.44086 T 0.13 . 12.1873 0.54247 0.8569:0.1431:0.0:0.0 . 616 P48553 TPC10_HUMAN V 616 ENSP00000291574:M616V ENSP00000291574:M616V M + 1 0 TRAPPC10 44327219 1.000000 0.71417 1.000000 0.80357 0.916000 0.54674 5.282000 0.65615 0.894000 0.36317 0.533000 0.62120 ATG TCGA-2J-AABK-01A-31D-A40W-08 TRAPPC10-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000195737.1 0 0 0 6 517 0 118 0 1.007299e-02 0 11 0 118 2 0 0 0 0 0 2 1 0.962561 6 505 0 116 2 -3.076553 1 1 121412 1 33 1 0 1 1 1.851892 1 0.200000 1.880000 0.120879 0.100000 0.040000 0.210000 0.100000 0.119651 0.100000 0 0.070000 0.160000 COL18A1 80781 broad.mit.edu 37 21 46902721 46902721 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr21:46902721G>A ENST00000359759.4 + 14 2953 c.2932G>A c.(2932-2934)Gcc>Acc p.A978T COL18A1_ENST00000355480.5_Missense_Mutation_p.A743T|COL18A1_ENST00000400337.2_Missense_Mutation_p.A563T P39060 COIA1_HUMAN collagen, type XVIII, alpha 1 25 TGAAGCAGGCGCCCCAGGACA 0.592000 0 SO:0001583 missense ENST00000359759.4 1 1 hg19 . . . . . . . . . . G 11.05 1.524339 0.27299 0.0 7.17E-4 ENSG00000182871 ENST00000400337;ENST00000355480;ENST00000359759 D;D;D 0.94232 -3.23;-3.38;-3.38 2.62 -1.63 0.08345 . . . . . D 0.84483 0.5482 L 0.37850 1.14 0.21386 N 0.999707 B;B;B 0.24576 0.106;0.086;0.086 B;B;B 0.13407 0.009;0.005;0.005 T 0.69007 -0.5259 9 0.12766 T 0.61 . 3.4304 0.07426 0.4039:0.205:0.3911:0.0 . 978;743;563 P39060;P39060-1;P39060-2 COIA1_HUMAN;.;. T 563;743;978 ENSP00000383191:A563T;ENSP00000347665:A743T;ENSP00000352798:A978T ENSP00000347665:A743T A + 1 0 COL18A1 45727149 0.002000 0.14202 0.122000 0.21767 0.049000 0.14656 0.305000 0.19254 -0.414000 0.07495 0.549000 0.68633 GCC TCGA-2J-AABK-01A-31D-A40W-08 COL18A1-201 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000206827.1 0 0 0 19 198 0 32 1 9.989867e-01 5 114 0 32 2 0 0 0 0 0 2 1 0.999991 19 194 0 32 2 -3.221877 1 1 120984 43 47 1 0 1 1 1.851892 1 0.200000 1.880000 0.120879 0.770000 0.490000 1.000000 1.000000 0.780327 0.770000 0 0.620000 0.940000 PICK1 9463 broad.mit.edu 37 22 38470363 38470363 + Missense_Mutation SNP G G C TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr22:38470363G>C ENST00000404072.3 + 12 1231 c.884G>C c.(883-885)cGc>cCc p.R295P PICK1_ENST00000356976.3_Missense_Mutation_p.R295P|RP5-1039K5.13_ENST00000445483.1_RNA NM_001039583.1|NM_001039584.1 NP_001034672.1|NP_001034673.1 Q9NRD5 PICK1_HUMAN protein interacting with PRKCA 1 13 Melanoma(58;0.045) TATGAGTACCGCCTGATCCTG 0.682000 OREG0026555 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000404072.3 0 1 hg19 CCDS13965.1 . . . . . . . . . . G 32 5.137385 0.94517 . . ENSG00000100151 ENST00000404072;ENST00000356976 T;T 0.80393 -1.37;-1.37 4.57 4.57 0.56435 Arfaptin-like (3); 0.000000 0.85682 D 0.000000 D 0.90669 0.7073 M 0.85299 2.745 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.92404 0.5932 10 0.72032 D 0.01 -16.2978 17.7234 0.88358 0.0:0.0:1.0:0.0 . 295 Q9NRD5 PICK1_HUMAN P 295 ENSP00000385205:R295P;ENSP00000349465:R295P ENSP00000349465:R295P R + 2 0 PICK1 36800309 1.000000 0.71417 1.000000 0.80357 0.979000 0.70002 7.159000 0.77483 2.251000 0.74343 0.563000 0.77884 CGC TCGA-2J-AABK-01A-31D-A40W-08 PICK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321569.2 0 0 0 5 185 0 38 1 7.879793e-01 2 106 0 38 2 0 0 0 0 0 2 1 0.930082 5 176 0 38 2 -6.904693 1 1 0 0 1 0 0 0 2.011383 0 0.200000 1.880000 0.191919 0.280000 0.100000 0.560000 0.250000 0.302552 0.280000 0 0.170000 0.420000 BIRC6 57448 broad.mit.edu 37 2 32774494 32774494 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr2:32774494C>T ENST00000421745.2 + 65 13224 c.13090C>T c.(13090-13092)Ctc>Ttc p.L4364F NM_016252.3 NP_057336 Q9NR09 BIRC6_HUMAN baculoviral IAP repeat containing 6 172 Acute lymphoblastic leukemia(172;0.155) TCTCGAGCTTCTCAGTCAGTC 0.433000 Pancreas(94;175 1509 16028 18060 45422) 0 SO:0001583 missense ENST00000421745.2 1 1 hg19 CCDS33175.2 . . . . . . . . . . C 22.4 4.288897 0.80914 . . ENSG00000115760 ENST00000421745 D 0.84730 -1.89 5.67 5.67 0.87782 . 0.000000 0.85682 D 0.000000 D 0.92231 0.7536 M 0.71581 2.175 0.80722 D 1 D 0.71674 0.998 D 0.78314 0.991 D 0.92385 0.5916 10 0.72032 D 0.01 . 19.7806 0.96414 0.0:1.0:0.0:0.0 . 4364 Q9NR09 BIRC6_HUMAN F 4364 ENSP00000393596:L4364F ENSP00000393596:L4364F L + 1 0 BIRC6 32627998 1.000000 0.71417 0.998000 0.56505 0.524000 0.34500 7.818000 0.86416 2.669000 0.90835 0.650000 0.86243 CTC TCGA-2J-AABK-01A-31D-A40W-08 BIRC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318769.3 1 0 1 43 420 0 74 1 9.821971e-01 15 49 0 74 2 0 0 0 0 0 2 1 1.000000 42 412 0 71 2 -3.318794 1 1 0 0 1 1 2 3 2.028219 0 0.200000 1.880000 0.203187 0.930000 0.690000 1.000000 1.000000 0.913968 0.930000 1 0.800000 1.000000 CEBPZ 10153 broad.mit.edu 37 2 37455921 37455921 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr2:37455921C>T ENST00000234170.5 - 2 560 c.415G>A c.(415-417)Gtg>Atg p.V139M NDUFAF7_ENST00000336237.6_5'Flank|NDUFAF7_ENST00000002125.4_5'Flank NM_005760.2 NP_005751.2 Q03701 CEBPZ_HUMAN CCAAT/enhancer binding protein (C/EBP), zeta 28 all_hematologic(82;0.21) TTATTTTTCACCTTATTAACT 0.313000 0 SO:0001583 missense ENST00000234170.5 1 1 hg19 CCDS1787.1 . . . . . . . . . . C 0.436 -0.901015 0.02472 . . ENSG00000115816 ENST00000234170;ENST00000545744;ENST00000446769 T;T 0.02498 4.27;4.27 5.32 2.46 0.29980 . 1.732560 0.02990 N 0.146738 T 0.04679 0.0127 L 0.54323 1.7 0.09310 N 1 B 0.33073 0.396 B 0.25987 0.065 T 0.42531 -0.9446 10 0.87932 D 0 . 7.308 0.26459 0.0:0.5701:0.0:0.4299 . 139 Q03701 CEBPZ_HUMAN M 139;139;90 ENSP00000234170:V139M;ENSP00000391881:V90M ENSP00000234170:V139M V - 1 0 CEBPZ 37309425 0.000000 0.05858 0.220000 0.23810 0.024000 0.10985 0.321000 0.19558 0.208000 0.20626 0.655000 0.94253 GTG TCGA-2J-AABK-01A-31D-A40W-08 CEBPZ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000218569.2 1 0 0 38 469 0 121 1 5.066188e-01 2 20 0 121 2 0 0 0 0 0 2 1 1.000000 37 465 0 119 2 -9.910969 1 1 0 0 1 1 2 3 2.028219 0 0.200000 1.880000 0.203187 0.750000 0.540000 1.000000 0.750000 0.768619 0.750000 0 0.640000 0.890000 USP39 10713 broad.mit.edu 37 2 85857980 85857980 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr2:85857980C>T ENST00000323701.6 + 6 870 c.860C>T c.(859-861)cCt>cTt p.P287L USP39_ENST00000409766.3_Missense_Mutation_p.P287L|USP39_ENST00000450066.2_Missense_Mutation_p.P184L|USP39_ENST00000409470.1_Missense_Mutation_p.P287L|USP39_ENST00000409025.1_Missense_Mutation_p.P287L|USP39_ENST00000459775.1_3'UTR NM_006590.3 NP_006581.2 Q53GS9 SNUT2_HUMAN ubiquitin specific peptidase 39 19 CTCTGGAACCCTCGAAATTTC 0.438000 0 SO:0001583 missense ENST00000323701.6 1 1 hg19 CCDS33234.1 . . . . . . . . . . C 32 5.190236 0.94923 . . ENSG00000168883 ENST00000450066;ENST00000409268;ENST00000409025;ENST00000409470;ENST00000323701;ENST00000409766 T;T;T;T;T 0.30182 1.54;1.54;1.54;1.54;1.54 5.97 5.97 0.96955 Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2); 0.000000 0.85682 D 0.000000 T 0.68100 0.2964 H 0.94734 3.575 0.80722 D 1 D;P;D;D;D;D 0.89917 0.986;0.954;0.998;0.999;1.0;0.993 P;D;D;D;D;D 0.79784 0.898;0.934;0.971;0.991;0.993;0.943 T 0.76337 -0.2996 10 0.72032 D 0.01 -7.7009 17.9074 0.88923 0.0:1.0:0.0:0.0 . 184;209;287;287;287;287 B4DHT4;B7Z7L9;G5E9H0;B3KM40;B9A018;Q53GS9 .;.;.;.;.;SNUT2_HUMAN L 184;287;287;287;287;287 ENSP00000396133:P184L;ENSP00000386572:P287L;ENSP00000386864:P287L;ENSP00000312981:P287L;ENSP00000386803:P287L ENSP00000312981:P287L P + 2 0 USP39 85711491 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 7.390000 0.79816 2.835000 0.97688 0.591000 0.81541 CCT TCGA-2J-AABK-01A-31D-A40W-08 USP39-009 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329892.1 1 0 1 41 555 0 137 1 9.807415e-01 18 68 0 137 2 0 0 0 0 0 2 1 1.000000 41 550 0 137 2 -2.920851 1 1 0 0 1 1 2 3 2.028219 0 0.200000 1.880000 0.203187 0.690000 0.500000 1.000000 0.690000 0.708958 0.690000 0 0.590000 0.820000 COL6A6 131873 broad.mit.edu 37 3 130354557 130354557 + Silent SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr3:130354557C>T ENST00000358511.6 + 27 5074 c.5043C>T c.(5041-5043)gaC>gaT p.D1681D COL6A6_ENST00000453409.2_Silent_p.D1681D NM_001102608.1 NP_001096078.1 A6NMZ7 CO6A6_HUMAN collagen, type VI, alpha 6 134 AGATTGGGGACCCTGGTGGTC 0.373000 0 SO:0001819 synonymous_variant ENST00000358511.6 0 1 hg19 CCDS46911.1 TCGA-2J-AABK-01A-31D-A40W-08 COL6A6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000356705.5 1 0 0 9 141 0 17 0 0 0 0 17 2 0 0 0 0 0 2 1 0.994502 9 140 0 17 2 -12.771620 1 1 0 0 1 0 0 0 1.976050 0 0.200000 1.880000 0.178645 0.590000 0.290000 1.000000 1.000000 0.617686 0.590000 0 0.420000 0.800000 NBEAL2 23218 broad.mit.edu 37 3 47041634 47041634 + Missense_Mutation SNP C C G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr3:47041634C>G ENST00000450053.3 + 27 4224 c.4045C>G c.(4045-4047)Ctc>Gtc p.L1349V NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Intron NM_015175.2 NP_055990.1 Q6ZNJ1 NBEL2_HUMAN neurobeachin-like 2 51 Acute lymphoblastic leukemia(5;0.0534) TTACCATGCTCTCTCCCCATT 0.607000 0 SO:0001583 missense ENST00000450053.3 1 1 hg19 CCDS46817.1 . . . . . . . . . . C 21.4 4.150562 0.78001 . . ENSG00000160796 ENST00000450053 T 0.57436 0.4 5.48 4.61 0.57282 . . . . . T 0.44393 0.1291 L 0.55481 1.735 0.80722 D 1 P 0.48764 0.915 B 0.36959 0.237 T 0.46317 -0.9200 9 0.46703 T 0.11 . 11.9191 0.52781 0.0:0.9153:0.0:0.0847 . 1349 Q6ZNJ1 NBEL2_HUMAN V 1349 ENSP00000415034:L1349V ENSP00000415034:L1349V L + 1 0 NBEAL2 47016638 0.957000 0.32711 0.784000 0.31847 0.955000 0.61496 2.363000 0.44178 1.320000 0.45209 0.561000 0.74099 CTC TCGA-2J-AABK-01A-31D-A40W-08 NBEAL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344363.3 1 0 1 25 553 0 120 1 8.044325e-01 9 60 0 120 2 0 0 0 0 0 2 1 1.000000 25 543 0 117 2 -3.234949 1 1 121090 1 33 1 0 0 0 1.918343 0 0.200000 1.880000 0.152542 0.400000 0.270000 0.580000 0.410000 0.419112 0.400000 0 0.330000 0.500000 WDR6 11180 broad.mit.edu 37 3 49049685 49049685 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr3:49049685G>A ENST00000608424.1 + 2 757 c.718G>A c.(718-720)Gac>Aac p.D240N WDR6_ENST00000415265.2_Intron|WDR6_ENST00000489684.1_3'UTR|WDR6_ENST00000395474.3_Missense_Mutation_p.D270N|WDR6_ENST00000448293.1_Missense_Mutation_p.D189N Q9NNW5 WDR6_HUMAN WD repeat domain 6 26 GAAGGTGGGCGACCTGCGAGT 0.552000 0 SO:0001583 missense ENST00000608424.1 1 1 hg19 . . . . . . . . . . G 14.29 2.491437 0.44249 . . ENSG00000178252 ENST00000395474;ENST00000448293 T;D 0.93953 -0.13;-3.32 5.32 5.32 0.75619 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.190971 0.47455 D 0.000227 D 0.85279 0.5660 L 0.38531 1.155 0.35719 D 0.817028 P;P;B 0.40107 0.703;0.703;0.266 B;B;B 0.20384 0.029;0.029;0.019 D 0.86499 0.1802 10 0.17369 T 0.5 -34.5279 12.2959 0.54847 0.0827:0.0:0.9173:0.0 . 111;240;189 B4DK45;Q9NNW5;E9PDU5 .;WDR6_HUMAN;. N 270;189 ENSP00000378857:D270N;ENSP00000413432:D189N ENSP00000378857:D270N D + 1 0 WDR6 49024689 0.998000 0.40836 0.997000 0.53966 0.973000 0.67179 3.303000 0.51858 2.650000 0.89964 0.561000 0.74099 GAC TCGA-2J-AABK-01A-31D-A40W-08 WDR6-024 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000471652.1 1 0 1 53 432 0 78 1 9.999159e-01 6 107 0 78 2 0 0 0 0 0 2 1 1.000000 52 430 0 74 2 -18.181600 1 1 0 0 1 0 0 0 1.918343 0 0.200000 1.880000 0.152542 0.990000 0.780000 1.000000 1.000000 0.963261 0.990000 1 0.890000 1.000000 WNT5A 7474 broad.mit.edu 37 3 55508430 55508430 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr3:55508430C>T ENST00000474267.1 - 5 1140 c.619G>A c.(619-621)Gcc>Acc p.A207T WNT5A_ENST00000264634.4_Missense_Mutation_p.A207T|WNT5A_ENST00000497027.1_Missense_Mutation_p.A192T P41221 WNT5A_HUMAN wingless-type MMTV integration site family, member 5A 13 GAGCCCTTGGCGTGGATGCGC 0.682000 0 SO:0001583 missense ENST00000474267.1 0 1 hg19 CCDS46850.1 . . . . . . . . . . C 16.77 3.216001 0.58452 . . ENSG00000114251 ENST00000474267;ENST00000264634;ENST00000536765;ENST00000497027;ENST00000482079 T;T;T;D 0.84660 -1.03;-1.03;-1.02;-1.88 4.84 3.82 0.43975 . 0.329686 0.32987 N 0.005409 T 0.74053 0.3666 L 0.38838 1.175 0.31722 N 0.6382 B 0.06786 0.001 B 0.06405 0.002 T 0.66097 -0.6008 10 0.18710 T 0.47 . 7.1809 0.25772 0.203:0.4728:0.3242:0.0 . 207 P41221 WNT5A_HUMAN T 207;207;118;192;192 ENSP00000417310:A207T;ENSP00000264634:A207T;ENSP00000420104:A192T;ENSP00000418184:A192T ENSP00000264634:A207T A - 1 0 WNT5A 55483470 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 3.044000 0.49830 2.387000 0.81309 0.557000 0.71058 GCC TCGA-2J-AABK-01A-31D-A40W-08 WNT5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350793.3 0 0 0 4 124 0 16 0 5.097955e-03 0 3 0 16 2 0 0 0 0 0 2 1 0.887835 4 122 0 15 2 -6.866657 1 1 0 0 1 0 0 0 1.918343 0 0.200000 1.880000 0.152542 0.310000 0.100000 0.660000 0.280000 0.347378 0.310000 0 0.190000 0.490000 KIAA1211 57482 broad.mit.edu 37 4 57193838 57193838 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr4:57193838G>A ENST00000504228.1 + 9 3675 c.3570G>A c.(3568-3570)gcG>gcA p.A1190A KIAA1211_ENST00000264229.6_Silent_p.A1190A|KIAA1211_ENST00000541073.1_Silent_p.A1183A Q6ZU35 K1211_HUMAN KIAA1211 65 Glioma(25;0.08)|all_neural(26;0.101) CTCCCCCAGCGCCGCTGGTAA 0.483000 0 SO:0001819 synonymous_variant ENST00000504228.1 0 1 hg19 CCDS43230.1 TCGA-2J-AABK-01A-31D-A40W-08 KIAA1211-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362097.2 0 0 0 9 759 0 99 0 2.400753e-02 0 18 0 99 2 0 0 0 0 0 2 1 0.993665 9 743 0 99 2 -2.598773 1 1 120800 2 35 1 0 0 0 1.949948 0 0.200000 1.880000 0.166667 0.110000 0.050000 0.200000 0.110000 0.123867 0.110000 0 0.080000 0.160000 CRMP1 1400 broad.mit.edu 37 4 5837708 5837708 + Silent SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr4:5837708C>T ENST00000397890.2 - 11 1429 c.1215G>A c.(1213-1215)tcG>tcA p.S405S CRMP1_ENST00000512574.1_Silent_p.S403S|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Silent_p.S519S NM_001313.3 NP_001304.1 Q14194 DPYL1_HUMAN collapsin response mediator protein 1 p.S519S(1) 36 CGTCGGCATCCGAGCCCACGG 0.522000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000397890.2 0 1 hg19 CCDS43207.1 TCGA-2J-AABK-01A-31D-A40W-08 CRMP1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358871.1 0 0 0 5 524 0 110 0 4.643201e-02 0 29 0 110 2 0 0 0 0 0 2 1 0.932291 6 506 0 105 2 -2.496906 0 1 0 0 1 0 0 0 1.949948 0 0.200000 1.880000 0.166667 0.090000 0.030000 0.200000 0.090000 0.107454 0.090000 0 0.050000 0.150000 PCDHGA8 9708 broad.mit.edu 37 5 140773115 140773115 + Silent SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr5:140773115G>A ENST00000398604.2 + 1 735 c.735G>A c.(733-735)ccG>ccA p.P245P PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron NM_032088.1 NP_114477.1 Q9Y5G5 PCDG8_HUMAN protocadherin gamma subfamily A, 8 51 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TTCCTCACCCGATTTACCGAG 0.567000 0 SO:0001819 synonymous_variant ENST00000398604.2 0 1 hg19 CCDS47291.1 TCGA-2J-AABK-01A-31D-A40W-08 PCDHGA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376972.1 0 0 0 10 582 0 116 0 0 0 0 116 2 0 0 0 0 0 2 1 0.996672 10 573 0 112 2 -2.500870 1 1 0 0 1 0 0 0 1.949583 0 0.200000 1.880000 0.166667 0.160000 0.080000 0.280000 0.160000 0.176282 0.160000 0 0.110000 0.230000 PROP1 5626 broad.mit.edu 37 5 177421284 177421284 + Missense_Mutation SNP C C A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr5:177421284C>A ENST00000308304.2 - 2 473 c.165G>T c.(163-165)agG>agT p.R55S NM_006261.4 NP_006252 O75360 PROP1_HUMAN PROP paired-like homeobox 1 13 all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GCGGGGAGAACCTTGATCTCC 0.662000 0 SO:0001583 missense ENST00000308304.2 0 1 hg19 CCDS4430.1 . . . . . . . . . . . 7.946 0.743725 0.15642 . . ENSG00000175325 ENST00000308304 D 0.89123 -2.47 2.49 -1.51 0.08664 Homeodomain-related (1); 0.319443 0.22765 N 0.055904 T 0.69860 0.3158 L 0.29908 0.895 0.09310 N 1 P 0.39480 0.675 B 0.28553 0.091 T 0.66380 -0.5938 10 0.10377 T 0.69 -4.9502 2.364 0.04314 0.2286:0.369:0.0:0.4024 . 55 O75360 PROP1_HUMAN S 55 ENSP00000311290:R55S ENSP00000311290:R55S R - 3 2 PROP1 177353890 0.000000 0.05858 0.001000 0.08648 0.209000 0.24338 0.413000 0.21148 -0.354000 0.08212 0.306000 0.20318 AGG TCGA-2J-AABK-01A-31D-A40W-08 PROP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253472.1 1 0 0 12 91 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 0.999220 11 90 0 14 2 -19.550380 1 1 0 0 1 0 0 0 1.949583 0 0.200000 1.880000 0.166667 0.990000 0.610000 1.000000 1.000000 0.939087 0.990000 1 0.820000 1.000000 ANKRD34B 340120 broad.mit.edu 37 5 79854551 79854551 + Nonsense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr5:79854551G>A ENST00000338682.3 - 5 1960 c.1288C>T c.(1288-1290)Cga>Tga p.R430* NM_001004441.2 NP_001004441.2 A5PLL1 AN34B_HUMAN ankyrin repeat domain 34B 28 Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113) CCTGAACCTCGCCTTTCTAAA 0.468000 0 SO:0001587 stop_gained ENST00000338682.3 0 1 hg19 CCDS34194.1 . . . . . . . . . . G 40 8.135039 0.98670 . . ENSG00000189127 ENST00000338682 . . . 6.04 6.04 0.98038 . 0.000000 0.64402 D 0.000006 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -15.0151 15.5464 0.76104 0.0:0.1383:0.8617:0.0 . . . . X 430 . ENSP00000339802:R430X R - 1 2 ANKRD34B 79890307 1.000000 0.71417 0.998000 0.56505 0.154000 0.21943 2.812000 0.47994 2.873000 0.98535 0.563000 0.77884 CGA TCGA-2J-AABK-01A-31D-A40W-08 ANKRD34B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369475.1 0 0 0 16 424 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 0.999927 16 418 0 93 2 -3.132744 1 1 0 0 1 0 0 0 1.949583 0 0.200000 1.880000 0.166667 0.350000 0.200000 0.540000 0.340000 0.365047 0.350000 0 0.270000 0.450000 VARS 7407 broad.mit.edu 37 6 31752372 31752372 + Splice_Site SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr6:31752372C>T ENST00000375663.3 - 11 1907 c.1467G>A c.(1465-1467)gaG>gaA p.E489E VARS_ENST00000482996.1_5'Flank|VARS_ENST00000444930.2_Splice_Site_p.E194E NM_006295.2 NP_006286.1 P26640 SYVC_HUMAN valyl-tRNA synthetase 30 L-Valine(DB00161) GGGGGCGCACCTCAATGTCAG 0.582000 0 SO:0001630 splice_region_variant ENST00000375663.3 1 0 hg19 CCDS34412.1 TCGA-2J-AABK-01A-31D-A40W-08 VARS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076619.2 1 0 0 13 269 0 46 1 8.789927e-01 5 75 0 46 2 0 0 0 0 0 2 1 0.999464 13 261 0 46 2 -3.705078 1 1 121292 1 33 1 0 0 0 1.941004 0 0.200000 1.880000 0.163180 0.440000 0.250000 0.700000 0.440000 0.462719 0.440000 0 0.330000 0.580000 PBX2 5089 broad.mit.edu 37 6 32157563 32157563 + Missense_Mutation SNP C C A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr6:32157563C>A ENST00000375050.4 - 1 400 c.130G>T c.(130-132)Gtc>Ttc p.V44F NM_002586.4 NP_002577.2 P40425 PBX2_HUMAN pre-B-cell leukemia homeobox 2 p.V44F(2) 14 CCTCCCGGGACCCCCCCGCTA 0.711000 2 Substitution - Missense(2) SO:0001583 missense ENST00000375050.4 0 1 hg19 CCDS4748.1 . . . . . . . . . . C 18.17 3.564390 0.65651 . . ENSG00000204304 ENST00000375050 T 0.80653 -1.4 4.56 4.56 0.56223 . 0.219742 0.22684 N 0.056918 T 0.49098 0.1537 N 0.14661 0.345 0.37506 D 0.916978 B;B 0.30542 0.284;0.176 B;B 0.15052 0.012;0.012 T 0.58999 -0.7536 10 0.52906 T 0.07 -5.1027 10.8156 0.46573 0.0:0.8072:0.1928:0.0 . 44;44 Q7KZE5;P40425 .;PBX2_HUMAN F 44 ENSP00000364190:V44F ENSP00000364190:V44F V - 1 0 PBX2 32265541 0.974000 0.33945 1.000000 0.80357 0.971000 0.66376 1.692000 0.37731 2.062000 0.61559 0.542000 0.68232 GTC TCGA-2J-AABK-01A-31D-A40W-08 PBX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076194.4 0 0 0 5 141 0 24 0 1.698378e-01 0 18 0 24 2 0 0 0 0 0 2 1 0.934002 5 137 0 23 2 -2.326668 0 1 118800 10 33 1 0 0 0 1.941004 0 0.200000 1.880000 0.163180 0.340000 0.130000 0.680000 0.310000 0.373986 0.340000 0 0.220000 0.510000 DOPEY1 23033 broad.mit.edu 37 6 83847927 83847927 + Missense_Mutation SNP A A G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr6:83847927A>G ENST00000349129.2 + 21 4426 c.4166A>G c.(4165-4167)aAa>aGa p.K1389R DOPEY1_ENST00000369739.3_Missense_Mutation_p.K1380R|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000237163.5_Missense_Mutation_p.K1370R NM_015018.3 NP_055833.2 Q5JWR5 DOP1_HUMAN dopey family member 1 67 all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203) TCTGCCATCAAAGCCATCTTG 0.373000 0 SO:0001583 missense ENST00000349129.2 1 1 hg19 CCDS4996.1 . . . . . . . . . . A 10.18 1.278737 0.23307 . . ENSG00000083097 ENST00000349129;ENST00000237163;ENST00000369739 T;T 0.42900 0.96;0.96 6.16 6.16 0.99307 . 0.140329 0.64402 D 0.000004 T 0.20455 0.0492 N 0.25201 0.72 0.80722 D 1 P;P;P 0.50156 0.932;0.791;0.791 P;B;B 0.45310 0.476;0.196;0.196 T 0.03829 -1.1000 10 0.12430 T 0.62 . 16.8061 0.85666 1.0:0.0:0.0:0.0 . 1280;1380;1389 E1P545;B2RWN9;Q5JWR5 .;.;DOP1_HUMAN R 1389;1370;1370 ENSP00000195654:K1389R;ENSP00000237163:K1370R ENSP00000237163:K1370R K + 2 0 DOPEY1 83904646 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 3.770000 0.55310 2.367000 0.80283 0.528000 0.53228 AAA TCGA-2J-AABK-01A-31D-A40W-08 DOPEY1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043785.2 1 0 0 28 536 0 92 0 2.355436e-01 0 18 0 92 2 0 0 0 0 0 2 1 1.000000 28 532 0 91 2 -20.000000 1 1 0 0 1 0 0 0 1.941004 0 0.200000 1.880000 0.163180 0.470000 0.320000 0.660000 0.470000 0.485377 0.470000 0 0.390000 0.570000 BRAF 673 broad.mit.edu 37 7 140481423 140481423 + Missense_Mutation SNP C C G TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr7:140481423C>G ENST00000288602.6 - 11 1445 c.1385G>C c.(1384-1386)aGa>aCa p.R462T NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN B-Raf proto-oncogene, serine/threonine kinase p.R462I(2)|p.R462K(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) 27380 Melanoma(164;0.00956) Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881) AGATCCAATTCTTTGTCCCAC 0.393000 61 Mis, T, O AKAP9, KIAA1549 melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome Colon(40;35 892 2973 5743 27438) Dom yes 7 7q34 673 v-raf murine sarcoma viral oncogene homolog B1 yes E 3 Substitution - Missense(3) SO:0001583 missense Familial Cancer Database CFC, CFCS ENST00000288602.6 1 1 hg19 CCDS5863.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 22.6|22.6 4.309763|4.309763 0.81247|0.81247 .|. .|. ENSG00000157764|ENSG00000157764 ENST00000496384|ENST00000288602 .|D .|0.82167 .|-1.58 5.62|5.62 5.62|5.62 0.85841|0.85841 .|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); .|0.043720 .|0.85682 .|D .|0.000000 T|T 0.78470|0.78470 0.4288|0.4288 L|L 0.39085|0.39085 1.19|1.19 0.80722|0.80722 D|D 1|1 .|B .|0.28026 .|0.198 .|B .|0.26094 .|0.066 T|T 0.77070|0.77070 -0.2724|-0.2724 5|10 .|0.87932 .|D .|0 .|. 17.8428|17.8428 0.88720|0.88720 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|462 .|P15056 .|BRAF_HUMAN Q|T 70|462 .|ENSP00000288602:R462T .|ENSP00000288602:R462T E|R -|- 1|2 0|0 BRAF|BRAF 140127892|140127892 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.995000|0.995000 0.86356|0.86356 6.072000|6.072000 0.71238|0.71238 2.637000|2.637000 0.89404|0.89404 0.585000|0.585000 0.79938|0.79938 GAA|AGA TCGA-2J-AABK-01A-31D-A40W-08 BRAF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348886.1 1 0 1 55 379 0 67 1 5.077965e-01 4 9 0 67 2 0 0 0 0 0 2 1 1.000000 55 373 0 66 2 -19.996730 1 1 0 0 1 1 2 3 2.032002 0 0.200000 1.880000 0.227799 0.990000 0.990000 1.000000 1.000000 0.999246 0.990000 1 0.990000 1.000000 CCL26 10344 broad.mit.edu 37 7 75401253 75401253 + Nonsense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr7:75401253G>A ENST00000394905.2 - 3 399 c.142C>T c.(142-144)Cga>Tga p.R48* CCL26_ENST00000005180.4_Nonsense_Mutation_p.R48* NM_006072.4 NP_006063.1 Q9Y258 CCL26_HUMAN chemokine (C-C motif) ligand 26 3 TCATAGCTTCGCACCCAGGTC 0.527000 0 SO:0001587 stop_gained ENST00000394905.2 0 1 hg19 CCDS5578.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 22.9 4.355434 0.82243 . . ENSG00000006606 ENST00000005180;ENST00000394905 . . . 3.61 0.592 0.17471 . 2.078680 0.02083 N 0.052554 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.16420 T 0.52 . 4.5482 0.12092 0.1229:0.0:0.5932:0.2838 . . . . X 48 . ENSP00000005180:R48X R - 1 2 CCL26 75239189 0.000000 0.05858 0.000000 0.03702 0.015000 0.08874 -0.693000 0.05121 0.010000 0.14839 0.400000 0.26472 CGA TCGA-2J-AABK-01A-31D-A40W-08 CCL26-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344900.1 1 0 1 37 321 0 38 1 5.876756e-02 2 2 0 38 2 0 0 0 0 0 2 1 1.000000 37 312 0 36 2 -13.416930 1 1 121412 1 29 1 1 2 3 2.085085 0 0.200000 1.880000 0.214145 0.990000 0.760000 1.000000 1.000000 0.968199 0.990000 1 0.910000 1.000000 CPSF1 29894 broad.mit.edu 37 8 145620538 145620538 + Silent SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr8:145620538C>T ENST00000349769.3 - 28 3223 c.3129G>A c.(3127-3129)ccG>ccA p.P1043P MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_5'Flank NM_013291.2 NP_037423.2 Q10570 CPSF1_HUMAN cleavage and polyadenylation specific factor 1, 160kDa 38 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055) TGCGGGCACACGGCGTGTTGG 0.632000 NSCLC(133;1088 1848 27708 34777 35269) 0 SO:0001819 synonymous_variant ENST00000349769.3 0 1 hg19 CCDS34966.1 TCGA-2J-AABK-01A-31D-A40W-08 CPSF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382422.2 1 0 1 13 124 0 17 1 9.999949e-01 48 191 0 17 2 0 0 0 0 0 2 1 0.999581 13 122 0 16 2 -19.156050 1 1 121370 25 40 1 1 2 3 2.057049 0 0.200000 1.880000 0.208704 0.990000 0.550000 1.000000 1.000000 0.905056 0.990000 1 0.750000 1.000000 CLU 1191 broad.mit.edu 37 8 27462692 27462692 + Missense_Mutation SNP T T C TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr8:27462692T>C ENST00000316403.10 - 5 983 c.578A>G c.(577-579)gAc>gGc p.D193G CLU_ENST00000546343.1_Missense_Mutation_p.D204G|CLU_ENST00000405140.3_Missense_Mutation_p.D193G|CLU_ENST00000523500.1_Missense_Mutation_p.D193G|CLU_ENST00000560366.1_Missense_Mutation_p.D245G P10909 CLUS_HUMAN clusterin 21 Ovarian(32;2.61e-05) GAAGAACCTGTCCTGGAAGAG 0.612000 0 SO:0001583 missense ENST00000316403.10 0 1 hg19 CCDS47832.1 . . . . . . . . . . T 11.83 1.754978 0.31046 . . ENSG00000120885 ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012;ENST00000523589;ENST00000520796 T;T;T;T;T 0.25085 1.82;1.82;1.82;1.82;1.82 4.96 1.18 0.20946 Clusterin, N-terminal (1); 0.271710 0.40385 N 0.001116 T 0.29126 0.0724 M 0.79475 2.455 0.39868 D 0.973464 P;P;P;P 0.52316 0.916;0.952;0.873;0.625 B;B;B;B 0.43155 0.41;0.337;0.225;0.192 T 0.21586 -1.0241 10 0.66056 D 0.02 -18.8233 8.6897 0.34260 0.0:0.2008:0.0:0.7992 . 58;245;204;193 E7ETA7;P10909-2;P10909-5;P10909 .;.;.;CLUS_HUMAN G 245;204;193;193;18;58;193;193 ENSP00000446413:D204G;ENSP00000385419:D193G;ENSP00000429620:D193G;ENSP00000431070:D193G;ENSP00000429336:D193G ENSP00000315130:D245G D - 2 0 CLU 27518609 1.000000 0.71417 0.556000 0.28293 0.320000 0.28249 1.512000 0.35812 0.263000 0.21812 0.460000 0.39030 GAC TCGA-2J-AABK-01A-31D-A40W-08 CLU-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219953.3 0 0 0 7 199 0 27 1 1 64 5061 0 27 2 0 0 0 0 0 2 1 0.980817 7 198 0 26 2 -9.191678 1 1 0 0 1 1 2 3 2.057049 0 0.200000 1.880000 0.208704 0.370000 0.160000 1.000000 0.340000 0.436662 0.370000 0 0.250000 0.580000 DENND1A 57706 broad.mit.edu 37 9 126202749 126202749 + Missense_Mutation SNP C C T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr9:126202749C>T ENST00000373624.2 - 19 1579 c.1378G>A c.(1378-1380)Gcc>Acc p.A460T DENND1A_ENST00000542603.1_Missense_Mutation_p.A202T|DENND1A_ENST00000373620.3_Missense_Mutation_p.A460T|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000373618.1_Missense_Mutation_p.A428T|DENND1A_ENST00000394219.3_Missense_Mutation_p.A428T|DENND1A_ENST00000394215.2_Missense_Mutation_p.A430T NM_020946.1 NP_065997.1 Q8TEH3 DEN1A_HUMAN DENN/MADD domain containing 1A 43 GGGGTGGGGGCGCAGCCATTC 0.622000 0 SO:0001583 missense ENST00000373624.2 1 1 hg19 CCDS35133.1 . . . . . . . . . . C 11.98 1.802047 0.31869 . . ENSG00000119522 ENST00000373624;ENST00000542603;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618 T;T;T;T;T;T 0.22945 3.39;1.93;3.26;3.38;3.24;3.25 5.58 2.27 0.28462 . 0.627020 0.17144 N 0.185346 T 0.12305 0.0299 N 0.25647 0.755 0.09310 N 1 B;B;B;B;B;B;B 0.20052 0.02;0.007;0.002;0.014;0.017;0.003;0.041 B;B;B;B;B;B;B 0.12156 0.007;0.006;0.002;0.003;0.004;0.002;0.007 T 0.32666 -0.9898 10 0.07030 T 0.85 -2.3994 4.3489 0.11146 0.1645:0.4533:0.0:0.3822 . 428;418;428;430;460;460;280 Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3;Q9HCG4 .;.;.;.;.;DEN1A_HUMAN;. T 460;202;428;460;430;428 ENSP00000362727:A460T;ENSP00000437457:A202T;ENSP00000377766:A428T;ENSP00000362722:A460T;ENSP00000377763:A430T;ENSP00000362720:A428T ENSP00000362720:A428T A - 1 0 DENND1A 125242570 0.049000 0.20398 0.571000 0.28486 0.558000 0.35554 0.343000 0.19944 0.670000 0.31165 0.655000 0.94253 GCC TCGA-2J-AABK-01A-31D-A40W-08 DENND1A-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053997.1 0 0 0 18 241 1 33 1 5.128095e-02 5 22 1 33 5 0 0 0 0 0 2 1 0.999984 17 240 0 33 2 -19.996590 1 1 121412 1 34 1 1 2 3 2.025733 0 0.200000 1.880000 0.201597 0.700000 0.430000 1.000000 1.000000 0.717160 0.700000 0 0.550000 0.880000 CACNA1B 774 broad.mit.edu 37 9 141012490 141012490 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr9:141012490G>A ENST00000371372.1 + 43 6015 c.5870G>A c.(5869-5871)cGt>cAt p.R1957H CACNA1B_ENST00000277551.2_Missense_Mutation_p.R1957H|CACNA1B_ENST00000277549.5_Missense_Mutation_p.R1151H|CACNA1B_ENST00000371355.4_Missense_Mutation_p.R1958H|CACNA1B_ENST00000371363.1_Missense_Mutation_p.R1955H|CACNA1B_ENST00000371357.1_Missense_Mutation_p.R1956H NM_000718.3|NM_001243812.1 NP_000709.1|NP_001230741.1 Q00975 CAC1B_HUMAN calcium channel, voltage-dependent, N type, alpha 1B subunit 80 all_cancers(76;0.166) Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661) CCCCTGGAGCGTGGCCACTCC 0.617000 0 SO:0001583 missense ENST00000371372.1 0 1 hg19 CCDS59522.1 . . . . . . . . . . G 20.6 4.019883 0.75275 . . ENSG00000148408 ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355 D;D;D;D;D;D 0.97328 -4.07;-4.1;-4.34;-4.08;-4.06;-4.06 4.47 4.47 0.54385 . 1.579960 0.03633 N 0.238175 D 0.96632 0.8901 M 0.73962 2.25 0.80722 D 1 P;P 0.38922 0.651;0.651 B;B 0.35073 0.195;0.139 D 0.86427 0.1758 10 0.21540 T 0.41 . 16.756 0.85499 0.0:0.0:1.0:0.0 . 1956;1955 B1AQK7;B1AQK6 .;. H 1957;1957;1151;1955;1956;1958 ENSP00000360423:R1957H;ENSP00000277551:R1957H;ENSP00000277549:R1151H;ENSP00000360414:R1955H;ENSP00000360408:R1956H;ENSP00000360406:R1958H ENSP00000277549:R1151H R + 2 0 CACNA1B 140132311 0.993000 0.37304 1.000000 0.80357 0.958000 0.62258 0.082000 0.14847 2.036000 0.60181 0.561000 0.74099 CGT TCGA-2J-AABK-01A-31D-A40W-08 CACNA1B-001 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000055380.1 1 0 0 6 59 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 0.962210 6 56 0 12 2 -11.394230 1 1 120776 6 30 1 1 2 3 2.025733 0 0.200000 1.880000 0.201597 0.940000 0.410000 1.000000 1.000000 0.855197 0.940000 1 0.630000 1.000000 CDKN2A 1029 broad.mit.edu 37 9 21971120 21971120 + Nonsense_Mutation SNP G G A rs121913388 TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr9:21971120G>A ENST00000304494.5 - 2 508 c.238C>T c.(238-240)Cga>Tga p.R80* CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29* NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) TGCACGGGTCGGGTGAGAGTG 0.726000 R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1474 Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1) GRCh37 CM014695 CDKN2A M rs121913388 SO:0001587 stop_gained ENST00000304494.5 0 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 39|39 7.328457|7.328457 0.98214|0.98214 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 D;D|. 0.86497|. -2.13;-2.02|. 5.93|5.93 5.01|5.01 0.66863|0.66863 .|. 0.000000|. 0.37136|. N|. 0.002233|. T|. 0.44561|. 0.1299|. L|L 0.36672|0.36672 1.1|1.1 0.47511|0.47511 D|D 0.999443|0.999443 D|. 0.59357|. 0.985|. B|. 0.40602|. 0.334|. T|. 0.34825|. -0.9813|. 10|. 0.13108|0.02654 T|T 0.6|1 -2.989|-2.989 8.7197|8.7197 0.34434|0.34434 0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526 .|. 135|. Q8N726|. CD2A2_HUMAN|. L|X 135;94|80 ENSP00000355153:P135L;ENSP00000432664:P94L|. ENSP00000355153:P135L|ENSP00000307101:R80X P|R -|- 2|1 0|2 CDKN2A|CDKN2A 21961120|21961120 0.995000|0.995000 0.38212|0.38212 1.000000|1.000000 0.80357|0.80357 0.899000|0.899000 0.52679|0.52679 2.363000|2.363000 0.44178|0.44178 1.464000|1.464000 0.47987|0.47987 0.650000|0.650000 0.86243|0.86243 CCG|CGA TCGA-2J-AABK-01A-31D-A40W-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 13 101 0 13 1 9.966490e-01 10 69 0 13 2 1 9.999658e-01 14 143 0 149 2 1 0.999100 13 86 0 12 2 -2.749059 1 1 0 0 1 0 1 1 2.022665 0 0.200000 1.880000 0.198397 0.990000 0.650000 1.000000 1.000000 0.952556 0.990000 1 0.860000 1.000000 LINGO2 158038 broad.mit.edu 37 9 27949709 27949709 + Missense_Mutation SNP G G A TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chr9:27949709G>A ENST00000379992.2 - 6 1410 c.961C>T c.(961-963)Cgc>Tgc p.R321C LINGO2_ENST00000308675.3_Missense_Mutation_p.R321C NM_152570.2 NP_689783.1 Q7L985 LIGO2_HUMAN leucine rich repeat and Ig domain containing 2 44 Melanoma(11;0.242) all_neural(11;2.78e-09) CGTAGGAAGCGGAGCCCTTGG 0.527000 0 SO:0001583 missense ENST00000379992.2 1 1 hg19 CCDS6524.1 . . . . . . . . . . G 14.99 2.699273 0.48307 . . ENSG00000174482 ENST00000379992;ENST00000308675 T;T 0.57907 0.37;0.37 5.95 5.95 0.96441 . 0.116612 0.64402 D 0.000016 T 0.71039 0.3293 M 0.63428 1.95 0.80722 D 1 D 0.89917 1.0 D 0.68621 0.959 T 0.67043 -0.5770 9 . . . . 20.3931 0.98965 0.0:0.0:1.0:0.0 . 321 Q7L985 LIGO2_HUMAN C 321 ENSP00000369328:R321C;ENSP00000310126:R321C . R - 1 0 LINGO2 27939709 1.000000 0.71417 1.000000 0.80357 0.830000 0.47004 3.357000 0.52277 2.824000 0.97209 0.655000 0.94253 CGC TCGA-2J-AABK-01A-31D-A40W-08 LINGO2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051978.2 0 0 0 26 309 0 55 0 7.899213e-02 0 6 0 55 2 0 0 0 0 0 2 1 1.000000 25 307 0 54 2 -2.540642 1 1 121412 12 44 1 0 1 1 2.022665 0 0.200000 1.880000 0.198397 0.770000 0.520000 1.000000 1.000000 0.783530 0.770000 0 0.630000 0.930000 GPR112 139378 broad.mit.edu 37 X 135426583 135426583 + Missense_Mutation SNP A A T TCGA-2J-AABK-01A-31D-A40W-08 TCGA-2J-AABK-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 10fe2e36-6d45-4c97-b4b4-468985c589cd e8152b10-7ebb-4153-9837-dcc6185632c2 g.chrX:135426583A>T ENST00000394143.1 + 6 1009 c.718A>T c.(718-720)Agt>Tgt p.S240C GPR112_ENST00000412101.1_Missense_Mutation_p.S35C|GPR112_ENST00000370652.1_Missense_Mutation_p.S240C|GPR112_ENST00000394141.1_Missense_Mutation_p.S35C|GPR112_ENST00000287534.4_Missense_Mutation_p.S177C NM_153834.3 NP_722576.3 Q8IZF6 GP112_HUMAN G protein-coupled receptor 112 199 Acute lymphoblastic leukemia(192;0.000127) TCAAGAAAAAAGTACAACTGT 0.333000 0 SO:0001583 missense ENST00000394143.1 1 1 hg19 CCDS35409.1 . . . . . . . . . . a 12.04 1.818484 0.32145 . . ENSG00000156920 ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141 T;T;T;T;T 0.41065 1.19;1.19;1.01;1.01;1.01 4.3 4.3 0.51218 . . . . . T 0.48447 0.1500 L 0.27053 0.805 0.09310 N 0.999997 D;D;D 0.89917 1.0;1.0;0.999 D;D;P 0.71414 0.973;0.957;0.907 T 0.30937 -0.9961 9 0.72032 D 0.01 . 9.3376 0.38060 1.0:0.0:0.0:0.0 . 177;35;240 Q8IZF6-2;Q8IZF6-3;Q8IZF6 .;.;GP112_HUMAN C 240;240;35;177;35 ENSP00000377699:S240C;ENSP00000359686:S240C;ENSP00000416526:S35C;ENSP00000287534:S177C;ENSP00000377697:S35C ENSP00000287534:S177C S + 1 0 GPR112 135254249 0.461000 0.25783 0.255000 0.24374 0.024000 0.10985 3.803000 0.55560 1.661000 0.50771 0.414000 0.27820 AGT TCGA-2J-AABK-01A-31D-A40W-08 GPR112-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000286639.1 1 0 1 36 111 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 1.000000 36 108 0 28 2 -20.000000 1 1 0 0 1 0 1 1 0.200000 1.880000 0.200000 0.940000 0.770000 1.000000 0.990000 0.930663 0.940000 1 0.860000 0.990000