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 MAP4K4 9448 broad.mit.edu 37 2 102314997 102314998 + Frame_Shift_Ins INS - - A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr2:102314997_102314998insA ENST00000347699.4 + 2 120_121 c.120_121insA c.(121-123)aagfs p.K41fs MAP4K4_ENST00000456652.1_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000350198.4_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000425019.1_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000324219.4_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000302217.5_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000413150.2_Frame_Shift_Ins_p.K41fs NM_001242559.1|NM_145687.3 NP_001229488.1|NP_663720.1 O95819 M4K4_HUMAN mitogen-activated protein kinase kinase kinase kinase 4 41 GACAAGTCTATAAGGTCGGTGT 0.515000 0 SO:0001589 frameshift_variant ENST00000347699.4 0 1 hg19 CCDS56130.1 TCGA-IB-7889-01A-11D-2154-08 MAP4K4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000339839.1 1 0 0 63 1187 0 227 0 6.222740e-01 0 41 0 227 2 0 0 0 0 0 0 1 1.000000 64 1166 0 224 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 1.985275 0 0.220000 1.900000 0.202454 0.440000 0.340000 0.560000 0.450000 0.453055 0.440000 0 0.390000 0.510000 GOLGA2 2801 broad.mit.edu 37 9 131022880 131022881 + Frame_Shift_Ins INS - - A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr9:131022880_131022881insA ENST00000421699.2 - 17 1552_1553 c.1540_1541insT c.(1540-1542)tggfs p.W514fs AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Frame_Shift_Ins_p.W502fs NM_004486.4 NP_004477.3 Q08379 GOGA2_HUMAN golgin A2 34 CTGCTCCCCCCAGAGCTCGGCC 0.653000 0 SO:0001589 frameshift_variant ENST00000421699.2 0 1 hg19 CCDS6896.2 TCGA-IB-7889-01A-11D-2154-08 GOLGA2-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054358.2 1 0 0 73 1089 0 171 0 6.252918e-01 0 33 0 171 2 0 0 0 0 0 0 1 1.000000 77 1070 0 171 2 0 0 0 0 0 0 -10.635520 1 1 0 0 1 1 2 3 2.022956 0 0.220000 1.900000 0.221712 0.570000 0.450000 0.730000 0.570000 0.581607 0.570000 0 0.500000 0.640000 PRKG1 5592 broad.mit.edu 37 10 53564378 53564378 + Missense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr10:53564378G>A ENST00000401604.2 + 4 775 c.581G>A c.(580-582)cGa>cAa p.R194Q PRKG1_ENST00000373980.4_Missense_Mutation_p.R209Q|PRKG1_ENST00000373985.1_Missense_Mutation_p.R182Q Q13976 KGP1_HUMAN protein kinase, cGMP-dependent, type I 53 all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173) GCCATTGATCGACAATGTTTT 0.338000 0 SO:0001583 missense ENST00000401604.2 1 1 hg19 CCDS44399.1 . . . . . . . . . . G 34 5.387931 0.95988 . . ENSG00000185532 ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976 D;D;D;D 0.97378 -4.36;-4.36;-2.08;-2.08 5.42 5.42 0.78866 Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3); 0.000000 0.64402 D 0.000003 D 0.98516 0.9505 M 0.85099 2.735 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.997 D 0.99327 1.0908 10 0.72032 D 0.01 -5.7115 17.0633 0.86553 0.0:0.0:1.0:0.0 . 209;194 Q13976-2;Q13976 .;KGP1_HUMAN Q 194;182;209;67 ENSP00000384200:R194Q;ENSP00000363097:R182Q;ENSP00000363092:R209Q;ENSP00000363087:R67Q ENSP00000363087:R67Q R + 2 0 PRKG1 53234384 1.000000 0.71417 1.000000 0.80357 0.911000 0.54048 9.386000 0.97228 2.698000 0.92095 0.591000 0.81541 CGA TCGA-IB-7889-01A-11D-2154-08 PRKG1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 31 267 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 1.000000 31 263 0 43 2 0 0 0 0 43 2 -11.831130 1 1 0 0 1 1 2 3 2.107221 0 0.220000 1.900000 0.238430 0.990000 0.690000 1.000000 1.000000 0.937497 0.990000 1 0.830000 1.000000 MYOZ1 58529 broad.mit.edu 37 10 75391860 75391860 + Missense_Mutation SNP G G T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr10:75391860G>T ENST00000359322.4 - 6 1092 c.728C>A c.(727-729)cCc>cAc p.P243H RP11-464F9.22_ENST00000609434.1_lincRNA NM_021245.3 NP_067068.1 myozenin 1 12 Prostate(51;0.0112) GTCAAACTTGGGCATCTGGAA 0.493000 0 SO:0001583 missense ENST00000359322.4 1 1 hg19 CCDS7330.1 . . . . . . . . . . G 21.6 4.170256 0.78452 . . ENSG00000177791 ENST00000359322 T 0.70631 -0.5 5.63 5.63 0.86233 . 0.000000 0.85682 D 0.000000 D 0.86104 0.5853 M 0.83384 2.64 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 D 0.87452 0.2402 10 0.87932 D 0 -11.7099 19.6772 0.95941 0.0:0.0:1.0:0.0 . 243 Q9NP98 MYOZ1_HUMAN H 243 ENSP00000352272:P243H ENSP00000352272:P243H P - 2 0 MYOZ1 75061866 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.558000 0.82253 2.656000 0.90262 0.655000 0.94253 CCC TCGA-IB-7889-01A-11D-2154-08 MYOZ1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048654.1 0 0 0 14 342 0 49 0 2.513233e-01 0 23 0 49 2 0 0 0 0 0 2 1 0.999749 13 339 0 49 2 0 0 0 0 49 2 -3.125343 1 1 0 0 1 1 2 3 2.107221 0 0.220000 1.900000 0.238430 0.390000 0.210000 1.000000 0.370000 0.486804 0.390000 0 0.290000 1.000000 MYOZ1 58529 broad.mit.edu 37 10 75391861 75391861 + Missense_Mutation SNP G G T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr10:75391861G>T ENST00000359322.4 - 6 1091 c.727C>A c.(727-729)Ccc>Acc p.P243T RP11-464F9.22_ENST00000609434.1_lincRNA NM_021245.3 NP_067068.1 myozenin 1 12 Prostate(51;0.0112) TCAAACTTGGGCATCTGGAAG 0.488000 0 SO:0001583 missense ENST00000359322.4 1 1 hg19 CCDS7330.1 . . . . . . . . . . G 21.4 4.136416 0.77662 . . ENSG00000177791 ENST00000359322 T 0.70164 -0.46 5.63 5.63 0.86233 . 0.000000 0.85682 D 0.000000 D 0.84065 0.5390 M 0.83384 2.64 0.80722 D 1 D 0.89917 1.0 D 0.79784 0.993 D 0.85787 0.1365 10 0.87932 D 0 -11.7099 19.6772 0.95941 0.0:0.0:1.0:0.0 . 243 Q9NP98 MYOZ1_HUMAN T 243 ENSP00000352272:P243T ENSP00000352272:P243T P - 1 0 MYOZ1 75061867 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.563000 0.82314 2.656000 0.90262 0.655000 0.94253 CCC TCGA-IB-7889-01A-11D-2154-08 MYOZ1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048654.1 0 0 0 14 337 0 48 0 2.407919e-01 0 22 0 48 2 0 0 0 0 0 2 1 0.999749 13 334 0 48 2 0 0 0 0 48 2 -4.170522 1 1 0 0 1 1 2 3 2.107221 0 0.220000 1.900000 0.238430 0.400000 0.220000 1.000000 0.370000 0.491344 0.400000 0 0.290000 1.000000 OR10Q1 219960 broad.mit.edu 37 11 57995470 57995470 + Missense_Mutation SNP A A G TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr11:57995470A>G ENST00000316770.2 - 1 920 c.878T>C c.(877-879)tTg>tCg p.L293S NM_001004471.2 NP_001004471.1 Q8NGQ4 O10Q1_HUMAN olfactory receptor, family 10, subfamily Q, member 1 35 Breast(21;0.0589) GCTGTAAAGCAAAGGGTTGAG 0.547000 0 SO:0001583 missense ENST00000316770.2 1 1 hg19 CCDS31547.1 . . . . . . . . . . A 15.25 2.778355 0.49786 . . ENSG00000180475 ENST00000316770 T 0.46451 0.87 5.07 5.07 0.68467 GPCR, rhodopsin-like superfamily (1); 0.000000 0.34362 N 0.004034 T 0.62913 0.2467 M 0.79926 2.475 0.32070 N 0.594593 D 0.65815 0.995 P 0.61800 0.894 T 0.74481 -0.3651 10 0.87932 D 0 . 13.8047 0.63223 1.0:0.0:0.0:0.0 . 293 Q8NGQ4 O10Q1_HUMAN S 293 ENSP00000314324:L293S ENSP00000314324:L293S L - 2 0 OR10Q1 57752046 0.712000 0.27916 0.775000 0.31657 0.195000 0.23768 5.574000 0.67424 2.132000 0.65825 0.528000 0.53228 TTG TCGA-IB-7889-01A-11D-2154-08 OR10Q1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394706.1 1 0 0 51 692 0 143 0 0 0 0 143 2 0 0 0 0 0 2 1 1.000000 51 687 0 142 2 0 0 0 0 143 2 -10.818930 1 1 0 0 1 1 2 3 2.035080 0 0.220000 1.900000 0.224267 0.630000 0.470000 1.000000 0.620000 0.648913 0.630000 0 0.540000 0.730000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc 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-IB-7889-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 13 72 0 17 1 1.279220e-01 3 1 0 17 2 1 9.996229e-01 8 75 0 403 2 1 0.999679 13 72 0 17 2 1 1 1878 6141 0 17 2 -9.865792 1 1 0 0 1 0 3 3 2.089326 1 0.220000 1.900000 0.253660 0.990000 0.870000 1.000000 1.000000 0.992446 0.990000 1 0.990000 1.000000 GPR182 11318 broad.mit.edu 37 12 57389416 57389416 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr12:57389416C>T ENST00000300098.1 + 2 642 c.423C>T c.(421-423)atC>atT p.I141I HBCBP_ENST00000600202.1_5'Flank|RP11-474N8.5_ENST00000556850.1_RNA NM_007264.3 NP_009195.1 O15218 GP182_HUMAN G protein-coupled receptor 182 15 ATAGCAGCATCTTCTTCCTGG 0.592000 0 SO:0001819 synonymous_variant ENST00000300098.1 1 1 hg19 CCDS8927.1 TCGA-IB-7889-01A-11D-2154-08 GPR182-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411212.1 1 0 0 35 320 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 34 317 0 44 2 0 0 0 0 44 2 -20.000000 1 1 0 0 1 1 2 3 2.079019 0 0.220000 1.900000 0.253660 0.990000 0.680000 1.000000 1.000000 0.931965 0.990000 1 0.820000 1.000000 HSP90AA1 3320 broad.mit.edu 37 14 102551163 102551163 + Missense_Mutation SNP T T A rs55793809 byFrequency TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr14:102551163T>A ENST00000216281.8 - 5 1041 c.836A>T c.(835-837)aAg>aTg p.K279M HSP90AA1_ENST00000334701.7_Missense_Mutation_p.K401M|HSP90AA1_ENST00000441629.2_Missense_Mutation_p.K100M NM_005348.3 NP_005339.3 P07900 HS90A_HUMAN heat shock protein 90kDa alpha (cytosolic), class A member 1 28 Nedocromil(DB00716)|Rifabutin(DB00615) ttccttaatcttcttcttctt 0.393000 0 SO:0001583 missense ENST00000216281.8 1 0 hg19 CCDS9967.1 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 t 18.27 3.588032 0.66105 0.002043 8.14E-4 ENSG00000080824 ENST00000216281;ENST00000334701;ENST00000441629 T;T;T 0.13538 2.58;2.58;2.58 4.47 4.47 0.54385 . 0.338820 0.24182 U 0.040783 T 0.55305 0.1912 H 0.98701 4.305 0.80722 D 1 D;D;D 0.89917 0.999;1.0;0.999 D;D;D 0.87578 0.996;0.998;0.996 T 0.74372 -0.3687 10 0.87932 D 0 -21.8453 13.7315 0.62789 0.0:0.0:0.0:1.0 rs55793809 100;401;279 Q86U12;P07900-2;P07900 .;.;HS90A_HUMAN M 279;401;100 ENSP00000216281:K279M;ENSP00000335153:K401M;ENSP00000396189:K100M ENSP00000216281:K279M K - 2 0 HSP90AA1 101620916 1.000000 0.71417 1.000000 0.80357 0.960000 0.62799 6.016000 0.70798 1.786000 0.52430 0.533000 0.62120 AAG TCGA-IB-7889-01A-11D-2154-08 HSP90AA1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414952.2 1 0 1 31 175 0 43 1 1 661 437 0 43 2 0 0 0 0 0 2 1 1.000000 29 174 0 42 2 0 0 0 0 43 2 -1.749966 0 1 121306 164 52 1 0 2 2 1.976087 1 0.220000 1.900000 0.220000 0.990000 0.970000 1.000000 1.000000 0.997684 0.990000 1 0.990000 1.000000 FOXA1 3169 broad.mit.edu 37 14 38061592 38061592 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr14:38061592C>T ENST00000250448.2 - 2 458 c.397G>A c.(397-399)Gcc>Acc p.A133T FOXA1_ENST00000545425.2_5'UTR|FOXA1_ENST00000540786.1_Missense_Mutation_p.A100T NM_004496.3 NP_004487.2 P55317 FOXA1_HUMAN forkhead box A1 19 Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213) Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239) GGGTTCATGGCGGCCGCGTAG 0.736000 0 SO:0001583 missense ENST00000250448.2 0 1 hg19 CCDS9665.1 . . . . . . . . . . C 4.498 0.092298 0.08632 . . ENSG00000129514 ENST00000250448;ENST00000540786 T;T 0.18502 2.21;2.21 3.99 1.91 0.25777 Fork-head N-terminal (1); 0.667620 0.14434 N 0.319836 T 0.05868 0.0153 N 0.03608 -0.345 0.22954 N 0.998514 B 0.27997 0.197 B 0.23150 0.044 T 0.40308 -0.9570 10 0.10902 T 0.67 . 8.1718 0.31260 0.4693:0.5307:0.0:0.0 . 133 P55317 FOXA1_HUMAN T 133;100 ENSP00000250448:A133T;ENSP00000440178:A100T ENSP00000250448:A133T A - 1 0 FOXA1 37131343 0.000000 0.05858 0.991000 0.47740 0.985000 0.73830 -0.572000 0.05881 0.869000 0.35703 0.505000 0.49811 GCC TCGA-IB-7889-01A-11D-2154-08 FOXA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276735.1 1 0 0 8 121 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 0.989095 8 118 0 16 2 0 0 0 0 18 2 -12.521950 1 1 0 0 1 0 2 2 1.976087 1 0.220000 1.900000 0.220000 0.610000 0.280000 1.000000 1.000000 0.653599 0.610000 0 0.420000 0.990000 PLA2G4E 123745 broad.mit.edu 37 15 42276761 42276761 + Silent SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr15:42276761G>A ENST00000399518.3 - 19 2745 c.2259C>T c.(2257-2259)taC>taT p.Y753Y CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Silent_p.Y724Y NM_001206670.1 NP_001193599.1 Q3MJ16 PA24E_HUMAN phospholipase A2, group IVE 16 all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273) CTGGCAGCTCGTATTTGGGGA 0.522000 0 SO:0001819 synonymous_variant ENST00000399518.3 1 1 hg19 CCDS55962.1 TCGA-IB-7889-01A-11D-2154-08 PLA2G4E-001 NOVEL not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252738.2 0 0 0 11 241 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 0.998330 11 238 0 41 2 0 0 0 0 41 2 -3.229017 1 1 120874 6 38 1 1 2 3 2.104604 0 0.220000 1.900000 0.237611 0.440000 0.220000 1.000000 0.400000 0.523035 0.440000 0 0.320000 0.840000 SECISBP2L 9728 broad.mit.edu 37 15 49288724 49288724 + Missense_Mutation SNP C C A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr15:49288724C>A ENST00000559471.1 - 17 2726 c.2463G>T c.(2461-2463)atG>atT p.M821I SECISBP2L_ENST00000261847.3_Missense_Mutation_p.M776I|Y_RNA_ENST00000384377.1_RNA NM_001193489.1 NP_001180418.1 Q93073 SBP2L_HUMAN SECIS binding protein 2-like 46 TTGCTGCAACCATATCTTTAT 0.408000 0 SO:0001583 missense ENST00000559471.1 1 1 hg19 CCDS53942.1 . . . . . . . . . . C 26.5 4.747448 0.89663 . . ENSG00000138593 ENST00000261847;ENST00000380927 D 0.91843 -2.92 4.94 4.94 0.65067 . 0.000000 0.85682 D 0.000000 D 0.90109 0.6910 L 0.29908 0.895 0.58432 D 0.999997 D;P 0.54207 0.965;0.94 B;P 0.47402 0.344;0.546 D 0.91643 0.5328 10 0.72032 D 0.01 . 18.3573 0.90362 0.0:1.0:0.0:0.0 . 821;776 Q93073;Q93073-2 SBP2L_HUMAN;. I 776;821 ENSP00000261847:M776I ENSP00000261847:M776I M - 3 0 SECISBP2L 47076016 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 7.300000 0.78841 2.569000 0.86673 0.650000 0.86243 ATG TCGA-IB-7889-01A-11D-2154-08 SECISBP2L-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417277.1 1 0 0 42 958 0 165 0 7.920589e-02 1 10 0 165 2 0 0 0 0 0 2 1 1.000000 42 943 0 164 2 0 0 0 0 165 2 -3.858861 1 1 0 0 1 1 2 3 2.104604 0 0.220000 1.900000 0.237611 0.400000 0.280000 1.000000 0.390000 0.492732 0.400000 0 0.330000 0.580000 KIAA1199 0 broad.mit.edu 37 15 81201475 81201475 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr15:81201475C>T ENST00000394685.3 + 14 2044 c.1625C>T c.(1624-1626)aCg>aTg p.T542M KIAA1199_ENST00000356249.5_Missense_Mutation_p.T542M|RP11-351M8.2_ENST00000560873.1_RNA|RP11-351M8.1_ENST00000560560.1_Intron|KIAA1199_ENST00000220244.3_Missense_Mutation_p.T542M Q8WUJ3 CEMIP_HUMAN 49 TTGGAGGGCACGGAGCTGAAG 0.552000 0 SO:0001583 missense ENST00000394685.3 1 1 hg19 CCDS10315.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 T 10.26 1.302383 0.23736 . . ENSG00000103888 ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683 T;T;T 0.80123 -1.34;-1.34;-1.34 5.09 5.09 0.68999 Pectin lyase fold/virulence factor (1); 0.291065 0.31177 N 0.008117 T 0.60945 0.2308 N 0.03608 -0.345 0.20307 N 0.999913 B 0.02656 0.0 B 0.01281 0.0 T 0.54043 -0.8352 10 0.54805 T 0.06 -9.3098 10.8753 0.46906 0.0:0.0747:0.0:0.9253 . 542 Q8WUJ3 K1199_HUMAN M 542 ENSP00000220244:T542M;ENSP00000378177:T542M;ENSP00000348583:T542M ENSP00000220244:T542M T + 2 0 KIAA1199 78988530 1.000000 0.71417 0.995000 0.50966 0.215000 0.24574 5.679000 0.68160 0.787000 0.33731 -0.516000 0.04426 ACG TCGA-IB-7889-01A-11D-2154-08 KIAA1199-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000291389.1 1 0 0 16 289 0 47 0 2.430141e-01 1 16 0 47 2 0 0 0 0 0 2 1 0.999934 16 286 0 47 2 0 0 0 0 47 2 -3.324015 1 1 121412 3 34 1 1 2 3 2.100873 0 0.220000 1.900000 0.236791 0.520000 0.300000 1.000000 0.490000 0.583472 0.520000 0 0.390000 0.830000 SLC28A1 9154 broad.mit.edu 37 15 85461805 85461805 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr15:85461805C>T ENST00000286749.3 + 9 936 c.846C>T c.(844-846)caC>caT p.H282H SLC28A1_ENST00000537703.1_Silent_p.H204H|SLC28A1_ENST00000537216.1_Silent_p.H282H|SLC28A1_ENST00000394573.1_Silent_p.H282H|SLC28A1_ENST00000538177.1_Silent_p.H282H|SLC28A1_ENST00000537624.1_Silent_p.H282H O00337 S28A1_HUMAN solute carrier family 28 (concentrative nucleoside transporter), member 1 41 BRCA - Breast invasive adenocarcinoma(143;0.0587) Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495) TTCTCTACCACGTGGGCCTCA 0.562000 0 SO:0001819 synonymous_variant ENST00000286749.3 1 1 hg19 CCDS10334.1 TCGA-IB-7889-01A-11D-2154-08 SLC28A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000308998.2 1 0 0 41 753 0 120 0 0 0 0 120 2 0 0 0 0 0 2 1 1.000000 41 748 0 119 2 0 0 0 0 120 2 -6.248170 1 1 121412 2 39 1 1 2 3 2.100873 0 0.220000 1.900000 0.236791 0.490000 0.350000 1.000000 0.480000 0.565820 0.490000 0 0.410000 0.670000 ST8SIA2 8128 broad.mit.edu 37 15 92981637 92981637 + Silent SNP A A G TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr15:92981637A>G ENST00000268164.3 + 4 582 c.345A>G c.(343-345)ggA>ggG p.G115G ST8SIA2_ENST00000539113.1_Silent_p.G94G NM_006011.3 NP_006002.1 Q92186 SIA8B_HUMAN ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 20 Lung NSC(78;0.0893)|all_lung(78;0.125) BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203) TCCTAAAGGGAACCCTGAAGC 0.473000 0 SO:0001819 synonymous_variant ENST00000268164.3 1 1 hg19 CCDS10372.1 TCGA-IB-7889-01A-11D-2154-08 ST8SIA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313526.1 1 0 1 131 918 0 162 0 0 0 0 162 2 0 0 0 0 0 2 1 1.000000 130 911 0 159 2 0 0 0 0 162 2 -20.000000 1 1 121412 1 26 1 1 2 3 2.100873 0 0.220000 1.900000 0.236791 0.990000 0.980000 1.000000 1.000000 0.998882 0.990000 1 0.990000 1.000000 TEPP 374739 broad.mit.edu 37 16 58010414 58010414 + Silent SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr16:58010414G>A ENST00000441824.2 + 1 76 c.39G>A c.(37-39)ctG>ctA p.L13L TEPP_ENST00000290871.5_Silent_p.L13L NM_199456.2 NP_955535.2 Q6URK8 TEPP_HUMAN testis, prostate and placenta expressed 8 TTATTCTGCTGCTGTCCATAA 0.517000 0 SO:0001819 synonymous_variant ENST00000441824.2 1 1 hg19 CCDS45496.1 TCGA-IB-7889-01A-11D-2154-08 TEPP-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000431966.1 1 0 0 29 423 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 1.000000 29 415 0 87 2 0 0 0 0 87 2 -7.293606 1 1 0 0 1 0 0 0 1.971177 0 0.220000 1.900000 0.197035 0.560000 0.380000 0.780000 0.560000 0.578283 0.560000 0 0.470000 0.680000 ADAMTS18 170692 broad.mit.edu 37 16 77353780 77353780 + Missense_Mutation SNP G G A rs147816593 TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr16:77353780G>A ENST00000282849.5 - 16 2916 c.2498C>T c.(2497-2499)gCg>gTg p.A833V NM_199355.2 NP_955387.1 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 18 118 GGGCCCTGGCGCGTACAGACG 0.542000 0 SO:0001583 missense ENST00000282849.5 1 1 hg19 CCDS10926.1 . . . . . . . . . . G 21.4 4.141924 0.77775 2.27E-4 0.0 ENSG00000140873 ENST00000282849 T 0.56941 0.43 5.54 5.54 0.83059 ADAM-TS Spacer 1 (1); 0.000000 0.85682 D 0.000000 T 0.77336 0.4115 M 0.87038 2.855 0.80722 D 1 D;D 0.89917 0.997;1.0 P;D 0.81914 0.897;0.995 T 0.81191 -0.1045 10 0.87932 D 0 . 18.4764 0.90793 0.0:0.0:1.0:0.0 . 833;833 Q8TE60-2;Q8TE60 .;ATS18_HUMAN V 833 ENSP00000282849:A833V ENSP00000282849:A833V A - 2 0 ADAMTS18 75911281 1.000000 0.71417 0.242000 0.24170 0.254000 0.26022 9.378000 0.97191 2.618000 0.88619 0.563000 0.77884 GCG TCGA-IB-7889-01A-11D-2154-08 ADAMTS18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269037.1 1 0 0 28 461 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 28 457 0 74 2 0 0 0 0 74 2 -20.000000 1 1 121412 4 36 1 0 0 0 1.971177 0 0.220000 1.900000 0.197035 0.500000 0.340000 0.700000 0.500000 0.517243 0.500000 0 0.410000 0.610000 DRG2 1819 broad.mit.edu 37 17 18003681 18003681 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr17:18003681C>T ENST00000225729.3 + 6 610 c.472C>T c.(472-474)Ctg>Ttg p.L158L DRG2_ENST00000583355.1_Intron|DRG2_ENST00000395726.4_Silent_p.L158L NM_001388.4 NP_001379.1 P55039 DRG2_HUMAN developmentally regulated GTP binding protein 2 14 all_neural(463;0.228) TCCTAGGTCTCTGCTGGAGAA 0.577000 0 SO:0001819 synonymous_variant ENST00000225729.3 1 1 hg19 CCDS11191.1 TCGA-IB-7889-01A-11D-2154-08 DRG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132075.3 1 0 0 66 703 0 111 1 9.998704e-01 27 110 0 111 2 0 0 0 0 0 2 1 1.000000 66 698 0 110 2 0 0 0 0 111 2 -3.318794 1 1 121412 14 44 1 1 5 6 2.880456 1 0.220000 1.900000 0.443016 0.990000 0.850000 1.000000 1.000000 0.986362 0.990000 1 0.970000 1.000000 NF1 4763 broad.mit.edu 37 17 29576089 29576089 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr17:29576089C>T ENST00000358273.4 + 30 4445 c.4062C>T c.(4060-4062)tcC>tcT p.S1354S NF1_ENST00000356175.3_Silent_p.S1354S NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 p.0?(8)|p.?(4) NF1/ACCN1(2) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) TCAGTTCCTCCTCAGAATTCC 0.398000 D, Mis, N, F, S, O neurofibroma, glioma neurofibroma, glioma Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) yes Rec yes Neurofibromatosis type 1 17 17q12 4763 neurofibromatosis type 1 gene O 12 Whole gene deletion(8)|Unknown(4) SO:0001819 synonymous_variant Familial Cancer Database NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome ENST00000358273.4 1 1 hg19 CCDS42292.1 TCGA-IB-7889-01A-11D-2154-08 NF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256351.2 0 0 0 18 580 0 88 0 1.439571e-02 0 6 0 88 2 0 0 0 0 0 2 1 0.999980 18 571 0 88 2 0 0 0 0 88 2 -2.616949 1 1 0 0 1 1 2 3 2.048456 0 0.220000 1.900000 0.226804 0.280000 0.170000 1.000000 0.270000 0.334518 0.280000 0 0.220000 0.370000 BPTF 2186 broad.mit.edu 37 17 65850550 65850550 + Nonsense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr17:65850550C>T ENST00000321892.4 + 2 1169 c.1108C>T c.(1108-1110)Cag>Tag p.Q370* BPTF_ENST00000335221.5_Nonsense_Mutation_p.Q370*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.Q231*|BPTF_ENST00000306378.6_Nonsense_Mutation_p.Q370* Q12830 BPTF_HUMAN bromodomain PHD finger transcription factor 78 all_cancers(12;6e-11) BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24) TCTAGTCGATCAGTTTCTTAC 0.418000 0 SO:0001587 stop_gained ENST00000321892.4 0 1 hg19 . . . . . . . . . . C 32 5.169246 0.94768 . . ENSG00000171634 ENST00000544491;ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778 . . . 5.62 5.62 0.85841 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.87932 D 0 . 19.6584 0.95853 0.0:1.0:0.0:0.0 . . . . X 275;370;370;370;231 . ENSP00000307208:Q370X Q + 1 0 BPTF 63281012 1.000000 0.71417 0.999000 0.59377 0.406000 0.30931 7.818000 0.86416 2.646000 0.89796 0.655000 0.94253 CAG TCGA-IB-7889-01A-11D-2154-08 BPTF-201 KNOWN basic protein_coding protein_coding 0 0 1 90 693 0 129 1 3.749916e-02 2 1 0 129 2 0 0 0 0 0 2 1 1.000000 90 686 0 128 2 0 0 0 0 129 2 -20.000000 1 1 0 0 1 1 2 3 2.041252 0 0.220000 1.900000 0.225960 0.990000 0.850000 1.000000 1.000000 0.982510 0.990000 1 0.950000 1.000000 TP53 7157 broad.mit.edu 37 17 7577046 7577046 + Nonsense_Mutation SNP C C A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr17:7577046C>A ENST00000269305.4 - 8 1081 c.892G>T c.(892-894)Gag>Tag p.E298* TP53_ENST00000445888.2_Nonsense_Mutation_p.E298*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.E298*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E298*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E298*|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.E298*(49)|p.0?(8)|p.?(2)|p.E298K(1)|p.L299fs*2(1)|p.L265_K305del41(1)|p.E298fs*53(1)|p.G293fs*1(1)|p.E298Q(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGGGGCAGCTCGTGGTGAGGC 0.567000 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 67 Substitution - Nonsense(49)|Whole gene deletion(8)|Deletion - In frame(3)|Unknown(2)|Deletion - Frameshift(2)|Substitution - Missense(2)|Insertion - Frameshift(1) GRCh37 CM031387 TP53 M SO:0001587 stop_gained Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . C 18.34 3.603544 0.66445 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 . . . 5.26 -4.03 0.04021 . 0.553557 0.18174 N 0.149346 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.25106 T 0.35 -12.8318 5.9489 0.19234 0.0:0.2155:0.4162:0.3682 . . . . X 298;298;298;298;298;287;166 . ENSP00000269305:E298X E - 1 0 TP53 7517771 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -0.837000 0.04377 -0.441000 0.07201 -0.218000 0.12543 GAG TCGA-IB-7889-01A-11D-2154-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 36 340 0 64 1 9.965345e-01 2 82 0 64 2 1 9.998332e-01 26 126 2 1162 3 1 1.000000 34 338 0 63 2 0 0 0 0 64 2 -3.221884 1 1 0 0 1 0 1 1 1.882628 1 0.220000 1.900000 0.147820 0.780000 0.560000 1.000000 1.000000 0.797851 0.780000 0 0.670000 0.920000 SMAD4 4089 broad.mit.edu 37 18 48591918 48591918 + Missense_Mutation SNP C C T rs80338963 TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr18:48591918C>T ENST00000342988.3 + 9 1619 c.1081C>T c.(1081-1083)Cgc>Tgc p.R361C SMAD4_ENST00000588745.1_Missense_Mutation_p.R265C|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361C NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.R361C(3)|p.R361S(2)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) TGGAGGAGATCGCTTTTGTTT 0.413000 43 Whole gene deletion(36)|Substitution - Missense(5)|Unknown(2) GRCh37 CM040450|CM041789|CM981228 SMAD4 M rs80338963 SO:0001583 missense ENST00000342988.3 1 1 hg19 CCDS11950.1 . . . . . . . . . . C 27.3 4.820743 0.90873 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 D;D 0.98164 -4.76;-4.76 5.86 5.86 0.93980 SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3); 0.000000 0.85682 D 0.000000 D 0.99275 0.9747 M 0.94021 3.485 0.80722 A 1 D 0.89917 1.0 D 0.97110 1.0 D 0.99157 1.0860 9 0.87932 D 0 . 18.9646 0.92691 0.0:1.0:0.0:0.0 . 361 Q13485 SMAD4_HUMAN C 361 ENSP00000341551:R361C;ENSP00000381452:R361C ENSP00000341551:R361C R + 1 0 SMAD4 46845916 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.718000 0.61930 2.771000 0.95319 0.563000 0.77884 CGC TCGA-IB-7889-01A-11D-2154-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 35 268 0 50 1 8.172738e-01 6 20 0 50 2 1 9.995530e-01 12 80 1 867 2 1 1.000000 34 267 0 50 2 0 0 0 0 50 2 -3.221909 1 1 0 0 1 0 1 1 1.793076 1 0.220000 1.900000 0.128978 0.880000 0.650000 1.000000 1.000000 0.879974 0.880000 1 0.760000 0.990000 CDH20 28316 broad.mit.edu 37 18 59195270 59195270 + Missense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr18:59195270G>A ENST00000262717.4 + 7 1486 c.1088G>A c.(1087-1089)cGt>cAt p.R363H CDH20_ENST00000538374.1_Missense_Mutation_p.R363H|CDH20_ENST00000536675.2_Missense_Mutation_p.R363H Q9HBT6 CAD20_HUMAN cadherin 20, type 2 61 Colorectal(73;0.186) CTAGAGATGCGTTTTCTGAAC 0.473000 0 SO:0001583 missense ENST00000262717.4 1 1 hg19 CCDS11977.1 . . . . . . . . . . G 15.33 2.800571 0.50315 . . ENSG00000101542 ENST00000536675;ENST00000538374;ENST00000262717 T;T;T 0.38401 1.14;1.14;1.14 5.88 5.01 0.66863 Cadherin (4);Cadherin-like (1); 0.352394 0.34110 N 0.004250 T 0.44307 0.1287 M 0.79805 2.47 0.39023 D 0.959782 B 0.21905 0.062 B 0.22601 0.04 T 0.48127 -0.9062 10 0.54805 T 0.06 . 14.9937 0.71412 0.0683:0.0:0.9317:0.0 . 363 Q9HBT6 CAD20_HUMAN H 363 ENSP00000444767:R363H;ENSP00000442226:R363H;ENSP00000262717:R363H ENSP00000262717:R363H R + 2 0 CDH20 57346250 0.997000 0.39634 1.000000 0.80357 0.991000 0.79684 1.798000 0.38814 1.492000 0.48499 0.650000 0.86243 CGT TCGA-IB-7889-01A-11D-2154-08 CDH20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256141.2 1 0 0 34 321 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1.000000 34 318 0 65 2 0 0 0 0 66 2 -20.000000 1 1 121412 4 36 1 0 1 1 1.793076 1 0.220000 1.900000 0.128978 0.760000 0.540000 0.990000 0.770000 0.775037 0.760000 0 0.650000 0.890000 CYP4F22 126410 broad.mit.edu 37 19 15662205 15662205 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr19:15662205C>T ENST00000269703.3 + 14 1718 c.1519C>T c.(1519-1521)Cgg>Tgg p.R507W CYP4F22_ENST00000601005.2_Missense_Mutation_p.R507W NM_173483.3 NP_775754.2 Q6NT55 CP4FN_HUMAN cytochrome P450, family 4, subfamily F, polypeptide 22 37 GCGCAAGGTGCGGCGGAAGCC 0.672000 0 SO:0001583 missense ENST00000269703.3 0 1 hg19 CCDS12331.1 . . . . . . . . . . C 24.8 4.566553 0.86439 . . ENSG00000171954 ENST00000269703 T 0.69040 -0.37 4.6 4.6 0.57074 . 0.125575 0.53938 D 0.000052 T 0.82006 0.4943 M 0.82823 2.61 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.82500 -0.0426 10 0.37606 T 0.19 . 15.245 0.73499 0.0:1.0:0.0:0.0 . 507 Q6NT55 CP4FN_HUMAN W 507 ENSP00000269703:R507W ENSP00000269703:R507W R + 1 2 CYP4F22 15523205 1.000000 0.71417 1.000000 0.80357 0.935000 0.57460 6.527000 0.73803 2.247000 0.74100 0.455000 0.32223 CGG TCGA-IB-7889-01A-11D-2154-08 CYP4F22-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461338.2 1 0 0 5 75 0 14 0 0 0 1 0 14 2 0 0 0 0 0 2 1 0.939603 5 75 0 14 2 0 0 0 0 14 2 -9.210014 1 0 0 0 1 0 0 0 2.005031 0 0.220000 1.900000 0.211325 0.590000 0.230000 1.000000 1.000000 0.615780 0.590000 0 0.380000 0.860000 GRIN2D 2906 broad.mit.edu 37 19 48919318 48919318 + Silent SNP C C T rs148340456 byFrequency TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr19:48919318C>T ENST00000263269.3 + 7 1729 c.1641C>T c.(1639-1641)tcC>tcT p.S547S NM_000836.2 NP_000827.2 O15399 NMDE4_HUMAN glutamate receptor, ionotropic, N-methyl D-aspartate 2D 37 all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203) Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418) AGGAGCGCTCCGAGATCGTGG 0.662000 0 SO:0001819 synonymous_variant ENST00000263269.3 1 1 hg19 CCDS12719.1 TCGA-IB-7889-01A-11D-2154-08 GRIN2D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466121.1 1 0 0 26 429 0 86 0 9.648041e-02 0 9 0 86 2 0 0 0 0 0 2 1 1.000000 25 424 0 85 2 0 0 0 0 86 2 -2.690484 1 1 121412 16 50 1 0 1 1 2.013467 0 0.220000 1.900000 0.215686 0.510000 0.340000 0.720000 0.510000 0.529886 0.510000 0 0.420000 0.620000 TPM3P9 147804 broad.mit.edu 37 19 53950474 53950474 + RNA SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr19:53950474C>T ENST00000424846.3 + 0 2920 ZNF761_ENST00000454407.1_RNA NR_003148.3 tropomyosin 3 pseudogene 9 ACTCTTGGTACGTGAGGAAGA 0.433000 0 ENST00000424846.3 0 1 hg19 TCGA-IB-7889-01A-11D-2154-08 TPM3P9-002 KNOWN basic processed_transcript pseudogene OTTHUMT00000347070.1 0 0 0 21 341 0 71 0 1.210399e-01 0 10 0 71 2 0 0 0 0 0 2 1 0.999997 19 330 0 69 2 0 0 0 0 71 2 -5.232620 1 1 121408 7 33 1 0 1 1 2.013467 0 0.220000 1.900000 0.215686 0.520000 0.330000 0.760000 0.510000 0.540943 0.520000 0 0.420000 0.650000 MUC16 94025 broad.mit.edu 37 19 9071237 9071237 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr19:9071237C>T ENST00000397910.4 - 3 16412 c.16209G>A c.(16207-16209)ccG>ccA p.P5403P NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated p.P5403P(2)|p.P1036P(1) 590 TGTAAGTGGCCGGTCTCTCAT 0.502000 3 Substitution - coding silent(3) SO:0001819 synonymous_variant ENST00000397910.4 1 1 hg19 CCDS54212.1 TCGA-IB-7889-01A-11D-2154-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 1 0 0 85 1563 0 298 0 7.947024e-03 0 3 0 298 2 0 0 0 0 0 2 1 1.000000 84 1535 0 295 2 0 0 0 0 298 2 -7.962869 1 1 121062 6 44 1 0 0 0 2.005031 0 0.220000 1.900000 0.211325 0.460000 0.360000 0.560000 0.460000 0.467558 0.460000 0 0.410000 0.520000 AMPD1 270 broad.mit.edu 37 1 115216697 115216697 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:115216697C>T ENST00000520113.2 - 14 1921 c.1906G>A c.(1906-1908)Gtg>Atg p.V636M AMPD1_ENST00000353928.6_Missense_Mutation_p.V603M|AMPD1_ENST00000369538.3_Missense_Mutation_p.V632M P23109 AMPD1_HUMAN adenosine monophosphate deaminase 1 45 all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211) all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Adenosine monophosphate(DB00131) TACTGTAGCACGGGACTCTGA 0.353000 0 SO:0001583 missense ENST00000520113.2 1 1 hg19 CCDS876.2 . . . . . . . . . . C 25.5 4.647876 0.87958 . . ENSG00000116748 ENST00000520113;ENST00000369538;ENST00000353928 D;D;D 0.95554 -3.74;-3.74;-3.74 5.96 5.96 0.96718 Adenosine/AMP deaminase (1); 0.052104 0.85682 D 0.000000 D 0.97923 0.9317 M 0.82923 2.615 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.988;0.996 D 0.98016 1.0368 10 0.87932 D 0 -21.0775 20.4008 0.98991 0.0:1.0:0.0:0.0 . 632;603 Q5TF02;P23109 .;AMPD1_HUMAN M 636;632;603 ENSP00000430075:V636M;ENSP00000358551:V632M;ENSP00000316520:V603M ENSP00000316520:V603M V - 1 0 AMPD1 115018220 1.000000 0.71417 1.000000 0.80357 0.925000 0.55904 7.818000 0.86416 2.826000 0.97356 0.655000 0.94253 GTG TCGA-IB-7889-01A-11D-2154-08 AMPD1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000032860.4 1 0 0 9 164 0 37 0 3.113139e-02 0 5 0 37 2 0 0 0 0 0 2 1 0.994302 9 162 0 36 2 0 0 0 0 37 2 -3.318794 1 1 121378 2 34 1 0 0 0 1.888448 1 0.220000 1.900000 0.162910 0.440000 0.220000 0.760000 0.430000 0.469668 0.440000 0 0.320000 0.610000 ADAMTSL4 54507 broad.mit.edu 37 1 150529196 150529196 + Missense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:150529196G>A ENST00000369038.2 + 8 1877 c.1676G>A c.(1675-1677)cGt>cAt p.R559H ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.R582H|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.R559H|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.R559H Q6UY14 ATL4_HUMAN ADAMTS-like 4 32 all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206) CGATATAACCGTCCTCCCAGG 0.647000 0 SO:0001583 missense ENST00000369038.2 1 1 hg19 CCDS955.1 . . . . . . . . . . G 16.85 3.235869 0.58886 . . ENSG00000143382 ENST00000369041;ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038 T;T;T;T 0.55413 0.52;0.52;0.52;0.52 4.54 4.54 0.55810 ADAM-TS Spacer 1 (1); . . . . T 0.65852 0.2731 M 0.85777 2.775 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.83275 0.996;0.995;0.993;0.988 T 0.70992 -0.4721 9 0.72032 D 0.01 . 8.4206 0.32698 0.1047:0.0:0.8953:0.0 . 582;582;559;559 B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2 .;.;ATL4_HUMAN;. H 559;559;97;582;559 ENSP00000358037:R559H;ENSP00000271643:R559H;ENSP00000358035:R582H;ENSP00000358034:R559H ENSP00000271643:R559H R + 2 0 ADAMTSL4 148795820 0.988000 0.35896 0.629000 0.29254 0.140000 0.21249 5.061000 0.64319 2.346000 0.79739 0.462000 0.41574 CGT TCGA-IB-7889-01A-11D-2154-08 ADAMTSL4-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084395.4 1 0 0 51 1047 0 163 0 2.991740e-02 0 6 0 163 2 0 0 0 0 0 2 1 0.999803 48 1032 1 162 22 0 0 0 0 163 2 -5.477019 1 1 121412 1 37 1 0 3 3 2.120537 1 0.220000 1.900000 0.277242 0.470000 0.340000 1.000000 0.460000 0.566720 0.470000 0 0.400000 1.000000 RIT1 6016 broad.mit.edu 37 1 155880296 155880296 + Splice_Site SNP G G T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:155880296G>T ENST00000368323.3 - 3 312 c.108C>A c.(106-108)gcC>gcA p.A36A RIT1_ENST00000368322.3_Splice_Site_p.A53A|RIT1_ENST00000539040.1_5'UTR NM_006912.5 NP_008843.1 Q92963 RIT1_HUMAN Ras-like without CAAX 1 19 Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195) OV - Ovarian serous cystadenocarcinoma(3;1.79e-05) GCATGGTCATGGCTTCAAAAG 0.393000 0 SO:0001630 splice_region_variant ENST00000368323.3 1 0 hg19 CCDS1123.1 TCGA-IB-7889-01A-11D-2154-08 RIT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039593.1 1 0 1 50 275 0 47 1 9.965648e-01 16 34 0 47 2 0 0 0 0 0 2 1 1.000000 49 274 0 47 2 0 0 0 0 47 2 -3.150828 1 1 0 0 1 0 3 3 2.120537 1 0.220000 1.900000 0.277242 0.990000 0.990000 1.000000 1.000000 0.999941 0.990000 1 0.990000 1.000000 CADM3 57863 broad.mit.edu 37 1 159163257 159163257 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:159163257C>T ENST00000368125.4 + 4 584 c.427C>T c.(427-429)Cgg>Tgg p.R143W CADM3_ENST00000368124.4_Missense_Mutation_p.R177W|CTA-134P22.2_ENST00000415675.2_RNA NM_001127173.1 NP_001120645.1 Q8N126 CADM3_HUMAN cell adhesion molecule 3 55 all_hematologic(112;0.0429) ATCTTCATTACGGGAAAAAGA 0.532000 0 SO:0001583 missense ENST00000368125.4 1 1 hg19 CCDS44251.1 . . . . . . . . . . C 18.15 3.559293 0.65538 . . ENSG00000162706 ENST00000368124;ENST00000368125;ENST00000416746 T;T;T 0.76060 -0.99;-0.99;-0.99 5.13 5.13 0.70059 Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.372580 0.26514 N 0.023944 T 0.73418 0.3584 L 0.39245 1.2 0.36569 D 0.872888 P;D;D 0.76494 0.863;0.999;0.998 D;D;P 0.66979 0.913;0.948;0.787 T 0.77275 -0.2648 10 0.66056 D 0.02 . 11.0641 0.47966 0.1847:0.8152:0.0:0.0 . 143;143;177 Q8N126-3;Q8N126;Q8N126-2 .;CADM3_HUMAN;. W 177;143;143 ENSP00000357106:R177W;ENSP00000357107:R143W;ENSP00000387802:R143W ENSP00000357106:R177W R + 1 2 CADM3 157429881 0.004000 0.15560 1.000000 0.80357 0.953000 0.61014 -0.061000 0.11693 2.655000 0.90218 0.655000 0.94253 CGG TCGA-IB-7889-01A-11D-2154-08 CADM3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000090330.1 1 0 1 84 345 0 73 0 2.575212e-01 0 5 0 73 2 0 0 0 0 0 2 1 1.000000 85 341 0 73 2 0 0 0 0 73 2 -3.322064 1 1 0 0 1 0 3 3 2.161655 1 0.220000 1.900000 0.281636 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 IGSF9 57549 broad.mit.edu 37 1 159900160 159900160 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:159900160C>T ENST00000368094.1 - 15 2080 c.1883G>A c.(1882-1884)cGg>cAg p.R628Q IGSF9_ENST00000361509.3_Missense_Mutation_p.R612Q|IGSF9_ENST00000493195.1_5'UTR NM_001135050.1 NP_001128522.1 Q9P2J2 TUTLA_HUMAN immunoglobulin superfamily, member 9 p.R612L(1) 56 all_hematologic(112;0.0597) Breast(1374;0.000126) BRCA - Breast invasive adenocarcinoma(70;0.111) CACCAGACCCCGCGGAGGGGA 0.652000 1 Substitution - Missense(1) SO:0001583 missense ENST00000368094.1 1 1 hg19 CCDS44254.1 . . . . . . . . . . C 15.97 2.988769 0.53934 . . ENSG00000085552 ENST00000361509;ENST00000368094 T;T 0.53640 0.61;0.61 5.17 5.17 0.71159 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.37012 N 0.002287 T 0.27489 0.0675 L 0.50333 1.59 0.42485 D 0.992879 P 0.41232 0.743 B 0.33750 0.169 T 0.10941 -1.0608 9 . . . -8.1725 16.1513 0.81624 0.0:1.0:0.0:0.0 . 628 Q9P2J2 TUTLA_HUMAN Q 612;628 ENSP00000355049:R612Q;ENSP00000357073:R628Q . R - 2 0 IGSF9 158166784 0.010000 0.17322 0.694000 0.30210 0.512000 0.34134 1.424000 0.34848 2.396000 0.81511 0.455000 0.32223 CGG TCGA-IB-7889-01A-11D-2154-08 IGSF9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059115.1 1 0 1 137 528 0 103 1 9.975707e-01 26 11 0 103 2 0 0 0 0 0 2 1 1.000000 133 520 0 103 2 0 0 0 0 103 2 -2.963670 1 1 0 0 1 0 3 3 2.161655 1 0.220000 1.900000 0.281636 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PAPPA2 60676 broad.mit.edu 37 1 176709307 176709307 + Missense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:176709307G>A ENST00000367662.3 + 14 5290 c.4126G>A c.(4126-4128)Gag>Aag p.E1376K NM_020318.2 NP_064714.2 Q9BXP8 PAPP2_HUMAN pappalysin 2 226 CTCAGAGGACGAGGGGCAGAA 0.483000 0 SO:0001583 missense ENST00000367662.3 1 1 hg19 CCDS41438.1 . . . . . . . . . . G 9.393 1.075892 0.20227 . . ENSG00000116183 ENST00000367662 T 0.01745 4.66 5.3 -2.21 0.06973 . 0.849038 0.10709 N 0.643103 T 0.01976 0.0062 L 0.49256 1.55 0.24431 N 0.994576 B 0.18461 0.028 B 0.13407 0.009 T 0.39941 -0.9589 10 0.54805 T 0.06 -0.3589 4.9535 0.14027 0.3507:0.2614:0.3879:0.0 . 1376 Q9BXP8 PAPP2_HUMAN K 1376 ENSP00000356634:E1376K ENSP00000356634:E1376K E + 1 0 PAPPA2 174975930 0.973000 0.33851 0.000000 0.03702 0.021000 0.10359 1.361000 0.34136 -0.798000 0.04444 -0.345000 0.07892 GAG TCGA-IB-7889-01A-11D-2154-08 PAPPA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084763.1 1 0 1 29 279 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 28 275 0 37 2 0 0 0 0 38 2 -2.920854 1 1 120896 3 40 1 0 3 3 2.161655 1 0.220000 1.900000 0.281636 0.970000 0.650000 1.000000 1.000000 0.919572 0.970000 1 0.790000 1.000000 H6PD 9563 broad.mit.edu 37 1 9324398 9324398 + Missense_Mutation SNP C C A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr1:9324398C>A ENST00000377403.2 + 5 2148 c.1846C>A c.(1846-1848)Ctg>Atg p.L616M H6PD_ENST00000602477.1_Missense_Mutation_p.L627M NM_001282587.1|NM_004285.3 NP_001269516.1|NP_004276.2 O95479 G6PE_HUMAN hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase) 23 all_lung(157;0.23) all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) CCACACGCACCTGTGGCTGGT 0.682000 0 SO:0001583 missense ENST00000377403.2 1 1 hg19 CCDS101.1 . . . . . . . . . . C 16.77 3.213707 0.58452 . . ENSG00000049239 ENST00000377403 T 0.49139 0.79 5.4 5.4 0.78164 Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1); 0.230625 0.37715 N 0.001970 T 0.66703 0.2816 M 0.88570 2.965 0.39055 D 0.960407 D 0.54397 0.966 P 0.58331 0.837 T 0.74262 -0.3722 10 0.72032 D 0.01 -23.0015 8.9799 0.35959 0.0:0.7713:0.1498:0.0789 . 616 O95479 G6PE_HUMAN M 616 ENSP00000366620:L616M ENSP00000366620:L616M L + 1 2 H6PD 9246985 0.995000 0.38212 1.000000 0.80357 0.975000 0.68041 0.536000 0.23129 2.536000 0.85505 0.561000 0.74099 CTG TCGA-IB-7889-01A-11D-2154-08 H6PD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000004928.2 1 0 0 7 159 0 30 0 1.463060e-01 1 13 0 30 2 0 0 0 0 0 2 1 0.980043 7 156 0 28 2 0 0 0 0 30 2 -10.008620 1 1 0 0 1 0 0 0 1.905531 0 0.220000 1.900000 0.168798 0.370000 0.160000 0.670000 0.350000 0.394234 0.370000 0 0.250000 0.520000 TSHZ2 128553 broad.mit.edu 37 20 51872260 51872260 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr20:51872260C>T ENST00000371497.5 + 2 3150 c.2263C>T c.(2263-2265)Cgc>Tgc p.R755C TSHZ2_ENST00000603338.2_Missense_Mutation_p.R752C|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R752C|RP4-678D15.1_ENST00000606932.1_RNA NM_001193421.1|NM_173485.5 NP_001180350.1|NP_775756.3 Q9NRE2 TSH2_HUMAN teashirt zinc finger homeobox 2 84 STAD - Stomach adenocarcinoma(23;0.1) CGTGTCCAGGCGCTACCTGTT 0.512000 0 SO:0001583 missense ENST00000371497.5 1 1 hg19 CCDS33490.1 . . . . . . . . . . C 12.62 1.992826 0.35131 . . ENSG00000182463 ENST00000371497;ENST00000329613;ENST00000450262 T;T 0.50277 0.75;0.75 5.23 5.23 0.72850 . 0.475787 0.23196 N 0.050846 T 0.43144 0.1234 M 0.68317 2.08 0.34997 D 0.755567 P 0.49358 0.923 B 0.34452 0.183 T 0.65709 -0.6102 10 0.87932 D 0 -5.9641 13.7395 0.62838 0.1538:0.8461:0.0:0.0 . 755 Q9NRE2 TSH2_HUMAN C 755;752;281 ENSP00000360552:R755C;ENSP00000333114:R752C ENSP00000333114:R752C R + 1 0 TSHZ2 51305667 1.000000 0.71417 1.000000 0.80357 0.872000 0.50106 3.499000 0.53310 2.438000 0.82558 0.579000 0.79373 CGC TCGA-IB-7889-01A-11D-2154-08 TSHZ2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080398.6 1 0 0 33 462 0 80 1 1.721122e-01 2 9 0 80 2 0 0 0 0 0 2 1 1.000000 33 446 0 78 2 0 0 0 0 80 2 -8.215395 1 1 121410 1 41 1 0 0 0 1.980412 0 0.220000 1.900000 0.200656 0.590000 0.410000 0.790000 0.590000 0.601979 0.590000 0 0.490000 0.700000 TMX4 56255 broad.mit.edu 37 20 7963022 7963022 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr20:7963022C>T ENST00000246024.2 - 8 1141 c.926G>A c.(925-927)cGg>cAg p.R309Q NM_021156.2 NP_066979.2 Q9H1E5 TMX4_HUMAN thioredoxin-related transmembrane protein 4 17 TACTTCCTCCCGGGTCACACC 0.582000 0 SO:0001583 missense ENST00000246024.2 1 1 hg19 CCDS13101.1 . . . . . . . . . . C 10.44 1.350863 0.24512 . . ENSG00000125827 ENST00000246024 T 0.09350 2.99 5.54 -7.71 0.01254 . 2.465280 0.01182 N 0.007100 T 0.02888 0.0086 N 0.02011 -0.69 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.35276 -0.9795 10 0.23891 T 0.37 2.3619 0.5542 0.00668 0.2156:0.2763:0.232:0.276 . 309 Q9H1E5 TMX4_HUMAN Q 309 ENSP00000246024:R309Q ENSP00000246024:R309Q R - 2 0 TMX4 7911022 0.000000 0.05858 0.000000 0.03702 0.011000 0.07611 -1.154000 0.03166 -1.638000 0.01529 -0.455000 0.05494 CGG TCGA-IB-7889-01A-11D-2154-08 TMX4-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000077928.2 1 0 0 22 456 0 76 1 9.696323e-01 6 114 0 76 2 0 0 0 0 0 2 1 0.999999 21 451 0 73 2 0 0 0 0 76 2 -2.247832 0 1 0 0 1 0 0 0 1.980412 0 0.220000 1.900000 0.200656 0.410000 0.260000 0.590000 0.410000 0.421529 0.410000 0 0.330000 0.500000 NCAM2 4685 broad.mit.edu 37 21 22656721 22656721 + Splice_Site SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr21:22656721G>A ENST00000400546.1 + 3 586 c.e3+1 NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000535285.1_Splice_Site|NCAM2_ENST00000486367.1_Splice_Site NM_004540.3 NP_004531.2 O15394 NCAM2_HUMAN neural cell adhesion molecule 2 p.?(1) 108 Lung NSC(9;0.195) GAAATTTACCGTAAGTAATGT 0.294000 1 Unknown(1) SO:0001630 splice_region_variant ENST00000400546.1 0 1 hg19 CCDS42910.1 . . . . . . . . . . G 19.70 3.876114 0.72180 . . ENSG00000154654 ENST00000400546;ENST00000535285 . . . 5.58 5.58 0.84498 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 18.134 0.89612 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . NCAM2 21578592 1.000000 0.71417 1.000000 0.80357 0.941000 0.58515 8.804000 0.91921 2.632000 0.89209 0.591000 0.81541 . TCGA-IB-7889-01A-11D-2154-08 NCAM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000170915.1 1 0 0 6 121 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 0.966148 6 121 0 19 2 0 0 0 0 19 2 -3.360477 1 1 0 0 1 0 0 0 1.988257 0 0.220000 1.900000 0.204244 0.440000 0.180000 0.820000 0.410000 0.468309 0.440000 0 0.290000 0.630000 GGT1 2678 broad.mit.edu 37 22 25023843 25023843 + Silent SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr22:25023843G>A ENST00000400382.1 + 13 1988 c.1233G>A c.(1231-1233)ccG>ccA p.P411P GGT1_ENST00000403838.1_Silent_p.P67P|GGT1_ENST00000400380.1_Silent_p.P411P|GGT1_ENST00000248923.4_Silent_p.P411P|GGT1_ENST00000401885.1_Silent_p.P67P|GGT1_ENST00000400383.1_Silent_p.P411P|GGT1_ENST00000406383.2_Silent_p.P411P|GGT1_ENST00000404532.1_Silent_p.P67P|GGT1_ENST00000404920.1_Silent_p.P67P|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Silent_p.P67P P19440 GGT1_HUMAN gamma-glutamyltransferase 1 40 Glutathione(DB00143) TCCGCTCCCCGGTCAGCGGGA 0.597000 0 SO:0001819 synonymous_variant ENST00000400382.1 1 1 hg19 CCDS42992.1 TCGA-IB-7889-01A-11D-2154-08 GGT1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250797.1 1 0 0 15 313 0 56 1 9.119113e-01 9 81 0 56 2 0 0 0 0 0 2 1 0.999838 15 300 0 62 2 0 0 0 0 56 2 -2.647879 1 1 121410 8 41 1 0 1 1 2.000519 0 0.220000 1.900000 0.208684 0.410000 0.240000 0.640000 0.400000 0.429460 0.410000 0 0.320000 0.530000 CSNK1E 1454 broad.mit.edu 37 22 38690455 38690455 + Missense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr22:38690455G>A ENST00000396832.1 - 8 1231 c.971C>T c.(970-972)gCg>gTg p.A324V CSNK1E_ENST00000403904.1_Missense_Mutation_p.A324V|CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000400206.2_Missense_Mutation_p.A324V|CSNK1E_ENST00000359867.3_Missense_Mutation_p.A324V NM_152221.2 NP_689407.1 P49674 KC1E_HUMAN casein kinase 1, epsilon 22 Melanoma(58;0.045) GGCTCGGGTCGCGGACCCCCG 0.726000 Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601) 0 SO:0001583 missense ENST00000396832.1 0 1 hg19 CCDS13970.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.49|16.49 3.138626|3.138626 0.56936|0.56936 .|. .|. ENSG00000213923|ENSG00000213923 ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904|ENST00000366216 T;T;T;T|. 0.57107|. 0.42;0.42;0.42;0.42|. 5.56|5.56 4.54|4.54 0.55810|0.55810 .|. 0.436410|. 0.26156|. N|. 0.026018|. T|. 0.61553|. 0.2356|. L|L 0.48642|0.48642 1.525|1.525 0.42079|0.42079 D|D 0.991242|0.991242 B|. 0.13594|. 0.008|. B|. 0.08055|. 0.003|. T|. 0.59836|. -0.7379|. 10|. 0.31617|. T|. 0.26|. .|. 14.7935|14.7935 0.69860|0.69860 0.0699:0.0:0.9301:0.0|0.0699:0.0:0.9301:0.0 .|. 324|. P49674|. KC1E_HUMAN|. V|X 324|27 ENSP00000352929:A324V;ENSP00000380044:A324V;ENSP00000383067:A324V;ENSP00000384074:A324V|. ENSP00000352929:A324V|. A|R -|- 2|1 0|2 CSNK1E|CSNK1E 37020401|37020401 1.000000|1.000000 0.71417|0.71417 0.040000|0.040000 0.18447|0.18447 0.110000|0.110000 0.19582|0.19582 5.714000|5.714000 0.68422|0.68422 1.327000|1.327000 0.45338|0.45338 0.650000|0.650000 0.86243|0.86243 GCG|CGA TCGA-IB-7889-01A-11D-2154-08 CSNK1E-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321462.1 0 0 0 3 27 0 10 1 6.597741e-01 3 17 0 10 2 0 0 0 0 0 2 1 0.812770 3 27 0 9 2 0 0 0 0 10 2 -9.593557 1 1 119040 7 33 1 0 1 1 2.000519 0 0.220000 1.900000 0.208684 0.900000 0.280000 1.000000 1.000000 0.810961 0.900000 1 0.530000 1.000000 LCT 3938 broad.mit.edu 37 2 136564940 136564940 + Nonsense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr2:136564940G>A ENST00000264162.2 - 9 3941 c.3931C>T c.(3931-3933)Cga>Tga p.R1311* Y_RNA_ENST00000363794.1_RNA NM_002299.2 NP_002290.2 P09848 LPH_HUMAN lactase 124 Vitamin C(DB00126) ACATACCCTCGAAGGTCTATA 0.522000 0 SO:0001587 stop_gained ENST00000264162.2 0 1 hg19 CCDS2178.1 . . . . . . . . . . G 38 6.963892 0.97967 . . ENSG00000115850 ENST00000264162;ENST00000455227 . . . 5.87 4.98 0.66077 . 0.165435 0.53938 D 0.000056 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -6.877 13.1749 0.59621 0.0:0.0:0.5643:0.4357 . . . . X 1311;743 . ENSP00000264162:R1311X R - 1 2 LCT 136281410 0.998000 0.40836 1.000000 0.80357 0.748000 0.42578 2.030000 0.41108 1.446000 0.47643 0.655000 0.94253 CGA TCGA-IB-7889-01A-11D-2154-08 LCT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254657.1 1 0 0 36 450 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 1.000000 36 443 0 95 2 0 0 0 0 96 2 -9.381009 1 1 0 0 1 0 0 0 1.985275 0 0.220000 1.900000 0.202454 0.650000 0.470000 0.870000 0.660000 0.668554 0.650000 0 0.550000 0.770000 CXCR4 7852 broad.mit.edu 37 2 136872710 136872710 + Missense_Mutation SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr2:136872710G>A ENST00000241393.3 - 2 892 c.788C>T c.(787-789)tCc>tTc p.S263F CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.S267F NM_003467.2 NP_003458.1 P61073 CXCR4_HUMAN chemokine (C-X-C motif) receptor 4 25 Framycetin(DB00452)|Plerixafor(DB06809) GAGGATGAAGGAGTCGATGCT 0.517000 0 SO:0001583 missense ENST00000241393.3 1 1 hg19 CCDS46420.1 . . . . . . . . . . G 15.06 2.722563 0.48728 . . ENSG00000121966 ENST00000409817;ENST00000241393;ENST00000537957 T;T 0.36699 1.24;1.24 6.17 5.29 0.74685 GPCR, rhodopsin-like superfamily (1); 0.137085 0.64402 D 0.000003 T 0.30634 0.0771 L 0.33189 0.99 0.49483 D 0.99979 P;D 0.57257 0.718;0.979 B;B 0.39503 0.237;0.301 T 0.16719 -1.0393 10 0.87932 D 0 . 17.6818 0.88246 0.0:0.1228:0.8772:0.0 . 263;267 P61073;P61073-2 CXCR4_HUMAN;. F 267;263;133 ENSP00000386884:S267F;ENSP00000241393:S263F ENSP00000241393:S263F S - 2 0 CXCR4 136589180 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 4.050000 0.57404 1.615000 0.50252 0.655000 0.94253 TCC TCGA-IB-7889-01A-11D-2154-08 CXCR4-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000331732.1 0 0 0 13 382 0 76 0 9.999547e-01 1 540 0 76 2 0 0 0 0 0 2 1 0.999504 13 376 0 75 2 0 0 0 0 76 2 -3.592798 1 1 0 0 1 0 0 0 1.985275 0 0.220000 1.900000 0.202454 0.290000 0.160000 0.470000 0.290000 0.310414 0.290000 0 0.220000 0.390000 RNF144A 9781 broad.mit.edu 37 2 7160800 7160800 + Silent SNP C C G TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr2:7160800C>G ENST00000320892.6 + 6 940 c.498C>G c.(496-498)ccC>ccG p.P166P RNF144A_ENST00000467276.1_3'UTR NM_014746.3 NP_055561.2 P50876 R144A_HUMAN ring finger protein 144A 25 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) all_cancers(51;0.226) CCTTCCTCCCCGGGGAGACCA 0.587000 0 SO:0001819 synonymous_variant ENST00000320892.6 1 1 hg19 CCDS1657.1 . . . . . . . . . . C 7.556 0.663657 0.14710 . . ENSG00000151692 ENST00000432850 T 0.30182 1.54 5.42 -5.68 0.02436 . 0.000000 0.85682 D 0.000000 T 0.16938 0.0407 . . . 0.80722 D 1 . . . . . . T 0.17868 -1.0355 7 0.20046 T 0.44 . 2.4736 0.04570 0.3811:0.1371:0.0718:0.41 . . . . R 162 ENSP00000411616:P162R ENSP00000411616:P162R P + 2 0 RNF144A 7078251 0.025000 0.19082 0.602000 0.28890 0.849000 0.48306 -0.908000 0.04063 -1.362000 0.02166 -0.254000 0.11334 CCG TCGA-IB-7889-01A-11D-2154-08 RNF144A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206725.2 1 0 1 59 491 0 92 0 6.145692e-02 0 3 0 92 2 0 0 0 0 0 2 1 1.000000 59 485 0 91 2 0 0 0 0 92 2 -2.429492 0 1 0 0 1 0 0 0 1.983751 0 0.220000 1.900000 0.202454 0.940000 0.730000 1.000000 1.000000 0.929858 0.940000 1 0.830000 1.000000 QTRTD1 79691 broad.mit.edu 37 3 113804663 113804663 + Missense_Mutation SNP A A G TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr3:113804663A>G ENST00000493014.1 + 6 910 c.842A>G c.(841-843)tAc>tGc p.Y281C QTRTD1_ENST00000281273.4_Missense_Mutation_p.Y387C|QTRTD1_ENST00000485050.1_Missense_Mutation_p.Y399C|QTRTD1_ENST00000479882.1_Missense_Mutation_p.Y264C NM_001256836.1 NP_001243765.1 queuine tRNA-ribosyltransferase domain containing 1 10 TTTGAACACTACTTTGGGTTT 0.463000 0 SO:0001583 missense ENST00000493014.1 1 1 hg19 CCDS58845.1 . . . . . . . . . . A 24.4 4.524255 0.85600 . . ENSG00000151576 ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014 . . . 6.08 6.08 0.98989 . 0.000000 0.85682 D 0.000000 D 0.85004 0.5598 M 0.89785 3.06 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.998;1.0 D 0.87953 0.2725 9 0.87932 D 0 -16.4311 15.2149 0.73258 1.0:0.0:0.0:0.0 . 281;387 B7Z472;Q9H974 .;QTRD1_HUMAN C 399;387;264;281 . ENSP00000281273:Y387C Y + 2 0 QTRTD1 115287353 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 8.273000 0.89887 2.333000 0.79357 0.533000 0.62120 TAC TCGA-IB-7889-01A-11D-2154-08 QTRTD1-004 PUTATIVE basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000354711.1 1 0 1 30 565 0 97 1 2.395284e-01 8 10 0 97 2 0 0 0 0 0 2 1 1.000000 30 561 0 96 2 0 0 0 0 97 2 -5.601550 1 1 121412 1 21 1 0 0 0 1.985992 0 0.220000 1.900000 0.204244 0.440000 0.300000 0.620000 0.450000 0.459686 0.440000 0 0.370000 0.540000 SYNPO2 171024 broad.mit.edu 37 4 119948009 119948009 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr4:119948009C>T ENST00000429713.2 + 3 667 c.485C>T c.(484-486)cCg>cTg p.P162L SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.P162L|SYNPO2_ENST00000434046.2_Missense_Mutation_p.P162L NM_001128933.1 NP_001122405.1 Q9UMS6 SYNP2_HUMAN synaptopodin 2 64 GAAACAGGCCCGAGCTACCAA 0.547000 0 SO:0001583 missense ENST00000429713.2 1 1 hg19 CCDS47129.1 . . . . . . . . . . C 0.003 -2.429248 0.00184 . . ENSG00000172403 ENST00000307142;ENST00000429713;ENST00000434046 T;T;T 0.06768 3.26;3.26;3.26 4.56 -5.91 0.02269 . 0.414976 0.17348 N 0.177482 T 0.01489 0.0048 N 0.00237 -1.79 0.09310 N 0.999996 B;B;B;B 0.06786 0.001;0.0;0.0;0.0 B;B;B;B 0.04013 0.0;0.001;0.0;0.0 T 0.47774 -0.9091 10 0.31617 T 0.26 0.9506 8.3027 0.32023 0.1979:0.5711:0.0:0.231 . 162;162;162;162 B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6 .;.;.;SYNP2_HUMAN L 162 ENSP00000306015:P162L;ENSP00000395143:P162L;ENSP00000390965:P162L ENSP00000306015:P162L P + 2 0 SYNPO2 120167457 0.001000 0.12720 0.000000 0.03702 0.014000 0.08584 0.077000 0.14738 -0.619000 0.05648 -1.181000 0.01715 CCG TCGA-IB-7889-01A-11D-2154-08 SYNPO2-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000364020.1 1 0 1 38 196 0 42 0 0 0 1 0 42 2 0 0 0 0 0 2 1 1.000000 38 196 0 41 2 0 0 0 0 42 2 -2.957194 1 1 0 0 1 0 0 0 2.008776 0 0.220000 1.900000 0.213075 0.990000 0.990000 1.000000 1.000000 0.999493 0.990000 1 0.990000 1.000000 CCRN4L 25819 broad.mit.edu 37 4 139966043 139966043 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr4:139966043C>T ENST00000280614.2 + 3 904 c.711C>T c.(709-711)gcC>gcT p.A237A ELF2_ENST00000515489.1_Intron NM_012118.2 NP_036250.2 Q9UK39 NOCT_HUMAN CCR4 carbon catabolite repression 4-like (S. cerevisiae) 9 all_hematologic(180;0.162) ATGGTTGTGCCTTATTTTTTC 0.463000 Ovarian(144;566 1842 19130 21379 22209) 0 SO:0001819 synonymous_variant ENST00000280614.2 1 1 hg19 CCDS3743.1 TCGA-IB-7889-01A-11D-2154-08 CCRN4L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257231.3 0 0 0 30 387 0 74 1 2.500807e-01 4 9 0 74 2 0 0 0 0 0 2 1 1.000000 27 384 0 72 2 0 0 0 0 74 2 -2.920856 1 1 0 0 1 0 0 0 2.008776 0 0.220000 1.900000 0.213075 0.640000 0.440000 0.880000 0.640000 0.660609 0.640000 0 0.540000 0.770000 PCDHB13 56123 broad.mit.edu 37 5 140595561 140595561 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr5:140595561C>T ENST00000341948.4 + 1 2053 c.1866C>T c.(1864-1866)ggC>ggT p.G622G NM_018933.2 NP_061756.1 Q9Y5F0 PCDBD_HUMAN protocadherin beta 13 66 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) CGCACAATGGCGAGGTGCGCA 0.701000 0 SO:0001819 synonymous_variant ENST00000341948.4 1 0 hg19 CCDS4255.1 TCGA-IB-7889-01A-11D-2154-08 PCDHB13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251810.1 1 0 0 20 268 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.999934 13 201 0 121 2 0 0 0 0 61 2 -19.999950 1 1 0 0 1 0 0 0 1.998860 0 0.220000 1.900000 0.207800 0.620000 0.390000 0.900000 0.610000 0.639125 0.620000 0 0.500000 0.770000 FOXQ1 94234 broad.mit.edu 37 6 1313384 1313384 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr6:1313384C>T ENST00000296839.2 + 1 710 c.445C>T c.(445-447)Ctc>Ttc p.L149F NM_033260.3 NP_150285.3 Q9C009 FOXQ1_HUMAN forkhead box Q1 2 Ovarian(93;0.0733) Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895) CAACGAGTACCTCATGGGCAA 0.657000 0 SO:0001583 missense ENST00000296839.2 1 1 hg19 CCDS4471.1 . . . . . . . . . . C 15.40 2.821825 0.50633 . . ENSG00000164379 ENST00000296839 D 0.96011 -3.88 3.87 1.9 0.25705 Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4); 0.093430 0.44483 N 0.000458 D 0.91415 0.7291 N 0.25426 0.745 0.45822 D 0.998695 D 0.57571 0.98 P 0.59761 0.863 D 0.90412 0.4410 10 0.66056 D 0.02 . 6.7197 0.23323 0.1739:0.7262:0.0:0.1 . 149 Q9C009 FOXQ1_HUMAN F 149 ENSP00000296839:L149F ENSP00000296839:L149F L + 1 0 FOXQ1 1258384 0.969000 0.33509 0.955000 0.39395 0.340000 0.28889 0.219000 0.17641 0.643000 0.30638 -1.206000 0.01644 CTC TCGA-IB-7889-01A-11D-2154-08 FOXQ1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043410.1 1 0 0 14 264 0 61 1 4.565631e-01 2 27 0 61 2 0 0 0 0 0 2 1 0.999769 14 263 0 61 2 0 0 0 0 61 2 -16.454680 1 1 0 0 1 0 0 0 1.871651 1 0.220000 1.900000 0.154930 0.420000 0.240000 0.660000 0.420000 0.440724 0.420000 0 0.320000 0.550000 ZAN 7455 broad.mit.edu 37 7 100377265 100377265 + RNA SNP A A T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr7:100377265A>T ENST00000348028.3 + 0 6679 ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_RNA Q9Y493 ZAN_HUMAN zonadhesin (gene/pseudogene) 139 Lung NSC(181;0.041)|all_lung(186;0.0581) STAD - Stomach adenocarcinoma(171;0.19) ACCCTCTGTGAGTTCGGAGGT 0.652000 0 ENST00000348028.3 0 1 hg19 . . . . . . . . . . A 8.808 0.934469 0.18206 . . ENSG00000146839 ENST00000546292;ENST00000538115;ENST00000542585 T;T;T 0.77877 -1.13;-1.13;-1.13 4.17 1.81 0.25067 Uncharacterised domain, cysteine-rich (2); 1.310930 0.05416 N 0.543352 D 0.83667 0.5304 . . . 0.34357 D 0.690562 D;D 0.63046 0.99;0.992 P;D 0.63283 0.858;0.913 T 0.73940 -0.3824 9 0.46703 T 0.11 . 5.6012 0.17355 0.7788:0.0:0.2212:0.0 . 2171;2172 F5H0T8;Q9Y493 .;ZAN_HUMAN V 2171 ENSP00000445943:E2171V;ENSP00000445091:E2171V;ENSP00000444427:E2171V ENSP00000445091:E2171V E + 2 0 ZAN 100215201 0.412000 0.25392 0.247000 0.24249 0.095000 0.18619 0.900000 0.28431 0.419000 0.25927 0.456000 0.33151 GAG TCGA-IB-7889-01A-11D-2154-08 ZAN-006 KNOWN basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000347214.1 0 0 0 7 43 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.983297 7 43 0 12 2 0 0 0 0 12 2 -14.445940 1 1 0 0 1 1 2 3 2.094265 0 0.220000 1.900000 0.235968 0.990000 0.620000 1.000000 1.000000 0.962772 0.990000 1 0.940000 1.000000 SPAM1 6677 broad.mit.edu 37 7 123599604 123599604 + Silent SNP C C T rs146075363 TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr7:123599604C>T ENST00000439500.1 + 6 1724 c.1111C>T c.(1111-1113)Cta>Tta p.L371L SPAM1_ENST00000223028.7_Silent_p.L371L|SPAM1_ENST00000460182.1_Silent_p.L371L|SPAM1_ENST00000340011.5_Silent_p.L371L|SPAM1_ENST00000402183.2_Silent_p.L371L NM_001174045.1|NM_001174046.1 NP_001167516.1|NP_001167517.1 P38567 HYALP_HUMAN sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding) 46 CAACGTCACACTAGCAGCCAA 0.378000 0 SO:0001819 synonymous_variant ENST00000439500.1 1 1 hg19 CCDS5791.1 TCGA-IB-7889-01A-11D-2154-08 SPAM1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000348309.1 1 0 1 37 305 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 1.000000 37 302 0 56 2 0 0 0 0 56 2 -14.405540 1 1 121354 1 25 1 1 2 3 2.094265 0 0.220000 1.900000 0.235968 0.990000 0.730000 1.000000 1.000000 0.953776 0.990000 1 0.870000 1.000000 BBS9 27241 broad.mit.edu 37 7 33407475 33407475 + Splice_Site SNP G G A TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr7:33407475G>A ENST00000242067.6 + 17 2310 c.e17+1 BBS9_ENST00000355070.2_Splice_Site|BBS9_ENST00000350941.3_Splice_Site|BBS9_ENST00000354265.4_Splice_Site|BBS9_ENST00000396127.2_Splice_Site NM_198428.2 NP_940820.1 Q3SYG4 PTHB1_HUMAN Bardet-Biedl syndrome 9 BBS9/PKD1L1(2) 50 GBM - Glioblastoma multiforme(11;0.0894) AAAACTTCTCGTAAGTAAAAC 0.373000 Bardet-Biedl syndrome 0 GRCh37 CS055613 BBS9 S SO:0001630 splice_region_variant Familial Cancer Database BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome ENST00000242067.6 1 1 hg19 CCDS43566.1 . . . . . . . . . . G 24.1 4.496770 0.85069 . . ENSG00000122507 ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000434373 . . . 5.48 5.48 0.80851 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 18.9484 0.92630 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . BBS9 33374000 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.787000 0.75099 2.572000 0.86782 0.655000 0.94253 . TCGA-IB-7889-01A-11D-2154-08 BBS9-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000329064.1 1 0 0 14 266 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 0.999769 14 265 0 49 2 0 0 0 0 49 2 -4.463742 1 1 0 0 1 1 3 4 2.330104 1 0.220000 1.900000 0.309612 0.580000 0.310000 1.000000 0.510000 0.649202 0.580000 0 0.420000 1.000000 PRKAR1B 5575 broad.mit.edu 37 7 720280 720280 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr7:720280C>T ENST00000406797.1 - 3 435 c.261G>A c.(259-261)ccG>ccA p.P87P PRKAR1B_ENST00000403562.1_Silent_p.P87P|PRKAR1B_ENST00000360274.4_Silent_p.P87P|PRKAR1B_ENST00000537384.1_Silent_p.P87P|PRKAR1B_ENST00000544935.1_Silent_p.P87P NM_001164761.1 NP_001158233.1 P31321 KAP1_HUMAN protein kinase, cAMP-dependent, regulatory, type I, beta 17 Ovarian(82;0.0779) CCACAGGGTTCGGGGGGGTGG 0.622000 0 SO:0001819 synonymous_variant ENST00000406797.1 1 0 hg19 CCDS34579.1 TCGA-IB-7889-01A-11D-2154-08 PRKAR1B-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322525.1 1 0 1 52 431 0 45 0 3.824771e-01 1 11 0 45 2 0 0 0 0 0 2 1 1.000000 52 423 0 42 2 0 0 0 0 45 2 -1.639820 0 1 0 0 1 1 3 4 2.330104 1 0.220000 1.900000 0.309612 0.990000 0.850000 1.000000 1.000000 0.987826 0.990000 1 0.990000 1.000000 RGS22 26166 broad.mit.edu 37 8 101076206 101076206 + Missense_Mutation SNP A A T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr8:101076206A>T ENST00000360863.6 - 8 984 c.790T>A c.(790-792)Ttg>Atg p.L264M RGS22_ENST00000523287.1_Missense_Mutation_p.L83M|RGS22_ENST00000523437.1_Missense_Mutation_p.L252M NM_015668.3 NP_056483.3 Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 RGS22/SYCP1(2) 68 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) TCAGAAATCAATTTGTTGGTT 0.343000 0 SO:0001583 missense ENST00000360863.6 1 1 hg19 CCDS43758.1 . . . . . . . . . . A 14.54 2.564891 0.45694 . . ENSG00000132554 ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437 T;T;T 0.32988 1.45;1.44;1.43 5.45 0.102 0.14522 . 2.260420 0.01579 N 0.020975 T 0.30386 0.0763 L 0.60455 1.87 0.09310 N 1 P;P;B 0.37864 0.61;0.61;0.065 B;B;B 0.39185 0.293;0.293;0.037 T 0.09509 -1.0671 10 0.39692 T 0.17 . 1.6829 0.02835 0.4861:0.1481:0.0809:0.2849 . 252;264;83 A8K944;Q8NE09;G3V112 .;RGS22_HUMAN;. M 264;252;83;252 ENSP00000354109:L264M;ENSP00000429382:L83M;ENSP00000428212:L252M ENSP00000354109:L264M L - 1 2 RGS22 101145382 0.000000 0.05858 0.000000 0.03702 0.337000 0.28794 -0.768000 0.04715 -0.138000 0.11434 0.528000 0.53228 TTG TCGA-IB-7889-01A-11D-2154-08 RGS22-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000380365.1 1 0 0 51 870 0 109 0 0 0 1 0 109 2 0 0 0 0 0 2 1 1.000000 50 858 0 109 2 0 0 0 0 109 2 -20.000000 1 1 0 0 1 1 3 4 2.338081 1 0.220000 1.900000 0.324090 0.600000 0.440000 1.000000 0.580000 0.672623 0.600000 0 0.510000 1.000000 TRPS1 7227 broad.mit.edu 37 8 116616325 116616325 + Missense_Mutation SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr8:116616325C>T ENST00000220888.5 - 3 1991 c.1832G>A c.(1831-1833)cGa>cAa p.R611Q TRPS1_ENST00000520276.1_Missense_Mutation_p.R615Q|TRPS1_ENST00000519076.1_Intron|TRPS1_ENST00000519674.1_Missense_Mutation_p.R611Q|TRPS1_ENST00000395715.3_Missense_Mutation_p.R624Q Q9UHF7 TRPS1_HUMAN trichorhinophalangeal syndrome I 111 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) ATGTTTGACTCGCGAGCTTCC 0.478000 Langer-Giedion syndrome 0 SO:0001583 missense Familial Cancer Database Trichorhinophalangeal syndrome type 2, TRPS II ENST00000220888.5 1 1 hg19 . . . . . . . . . . C 15.09 2.729920 0.48833 . . ENSG00000104447 ENST00000395715;ENST00000220888;ENST00000520276;ENST00000519674 T;T;T;T 0.10960 2.82;2.82;2.82;2.82 5.87 5.87 0.94306 . 0.183848 0.49305 D 0.000160 T 0.23886 0.0578 L 0.27053 0.805 0.40856 D 0.983791 D;D;D 0.69078 0.991;0.994;0.997 P;D;D 0.69479 0.563;0.921;0.964 T 0.00717 -1.1596 10 0.72032 D 0.01 . 20.5827 0.99408 0.0:1.0:0.0:0.0 . 615;611;624 Q9UHF7-3;Q9UHF7;Q9UHF7-2 .;TRPS1_HUMAN;. Q 624;611;615;611 ENSP00000379065:R624Q;ENSP00000220888:R611Q;ENSP00000428680:R615Q;ENSP00000429174:R611Q ENSP00000220888:R611Q R - 2 0 TRPS1 116685500 1.000000 0.71417 0.587000 0.28692 0.015000 0.08874 5.682000 0.68182 2.941000 0.99782 0.655000 0.94253 CGA TCGA-IB-7889-01A-11D-2154-08 TRPS1-002 KNOWN basic protein_coding protein_coding OTTHUMT00000286436.3 1 0 1 56 308 0 46 0 0 0 1 0 46 2 0 0 0 0 0 2 1 1.000000 55 305 0 45 2 0 0 0 0 46 2 -2.926725 1 1 120940 1 30 1 2 2 4 2.208572 1 0.220000 1.900000 0.287411 0.990000 0.990000 1.000000 1.000000 0.999979 0.990000 1 0.990000 1.000000 ASH2L 9070 broad.mit.edu 37 8 37964684 37964684 + Splice_Site SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr8:37964684C>T ENST00000343823.6 + 3 710 c.401C>T c.(400-402)tCa>tTa p.S134L ASH2L_ENST00000428278.2_Splice_Site_p.S40L|ASH2L_ENST00000545394.1_Intron|ASH2L_ENST00000250635.7_Splice_Site_p.S40L|ASH2L_ENST00000521652.1_Splice_Site_p.S40L NM_004674.4 NP_004665.2 Q9UBL3 ASH2L_HUMAN ash2 (absent, small, or homeotic)-like (Drosophila) 19 Colorectal(12;0.000501) Lung NSC(58;0.0295)|all_lung(54;0.0413) ATAGATACCTCGTGAGTACTT 0.408000 0 SO:0001630 splice_region_variant ENST00000343823.6 1 0 hg19 CCDS6101.1 . . . . . . . . . . C 18.82 3.705343 0.68615 . . ENSG00000129691 ENST00000343823;ENST00000250635;ENST00000517719;ENST00000428278;ENST00000521652 T;T;T;T;T 0.19806 2.12;2.12;2.12;2.12;2.12 4.82 4.82 0.62117 . 0.114028 0.64402 D 0.000014 T 0.16214 0.0390 N 0.19112 0.55 0.80722 D 1 B;B 0.27732 0.187;0.061 B;B 0.21151 0.033;0.005 T 0.05468 -1.0883 10 0.62326 D 0.03 . 17.9105 0.88932 0.0:1.0:0.0:0.0 . 40;134 Q9UBL3-2;Q9UBL3 .;ASH2L_HUMAN L 134;40;148;40;40 ENSP00000340896:S134L;ENSP00000250635:S40L;ENSP00000428877:S148L;ENSP00000395310:S40L;ENSP00000430259:S40L ENSP00000250635:S40L S + 2 0 ASH2L 38083841 1.000000 0.71417 1.000000 0.80357 0.924000 0.55760 2.090000 0.41682 2.223000 0.72356 0.557000 0.71058 TCA TCGA-IB-7889-01A-11D-2154-08 ASH2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376749.4 1 0 0 33 454 0 60 1 8.169225e-01 2 43 0 60 2 0 0 0 0 0 2 1 1.000000 33 450 0 60 2 0 0 0 0 60 2 -2.744761 1 1 0 0 1 2 2 4 2.146007 1 0.220000 1.900000 0.268293 0.690000 0.470000 1.000000 0.650000 0.736590 0.690000 0 0.570000 1.000000 WHSC1L1 54904 broad.mit.edu 37 8 38187221 38187221 + Missense_Mutation SNP G G T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr8:38187221G>T ENST00000317025.8 - 6 1773 c.1256C>A c.(1255-1257)aCc>aAc p.T419N WHSC1L1_ENST00000316985.3_Missense_Mutation_p.T419N|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.T419N|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.T419N NM_023034.1 NP_075447.1 Q9BZ95 NSD3_HUMAN Wolf-Hirschhorn syndrome candidate 1-like 1 24 Colorectal(12;0.000442)|Esophageal squamous(3;0.0725) all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065) Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511) TGGTCGTCGGGTTTTTTTAAC 0.433000 T NUP98 AML Dom yes 8 8p12 54904 Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3) L 0 SO:0001583 missense ENST00000317025.8 1 1 hg19 CCDS43729.1 . . . . . . . . . . G 8.652 0.898580 0.17686 . . ENSG00000147548 ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985 D;D;D;T 0.95137 -3.62;-3.62;-3.62;-0.48 5.6 4.65 0.58169 . 0.608282 0.13904 U 0.354722 D 0.82870 0.5131 N 0.02011 -0.69 0.25889 N 0.983491 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.04013 0.0;0.0;0.001;0.0 T 0.68580 -0.5371 10 0.12103 T 0.63 . 11.164 0.48533 0.0:0.0:0.5948:0.4052 . 419;419;419;419 B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95 .;.;.;NSD3_HUMAN N 419;419;356;419;419 ENSP00000393284:T419N;ENSP00000313983:T419N;ENSP00000434730:T419N;ENSP00000313410:T419N ENSP00000313410:T419N T - 2 0 WHSC1L1 38306378 0.785000 0.28726 0.870000 0.34147 0.989000 0.77384 1.199000 0.32235 2.634000 0.89283 0.650000 0.86243 ACC TCGA-IB-7889-01A-11D-2154-08 WHSC1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381924.3 1 0 0 19 429 0 65 1 8.856142e-01 7 81 0 65 2 0 0 0 0 0 2 1 0.999989 19 421 0 63 2 0 0 0 0 65 2 -3.210257 1 1 0 0 1 2 2 4 2.146007 1 0.220000 1.900000 0.268293 0.440000 0.260000 1.000000 0.420000 0.543674 0.440000 0 0.340000 1.000000 PKN3 29941 broad.mit.edu 37 9 131477728 131477728 + Silent SNP C C T TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc g.chr9:131477728C>T ENST00000291906.4 + 15 2190 c.1797C>T c.(1795-1797)gaC>gaT p.D599D PKN3_ENST00000485301.1_Intron NM_013355.3 NP_037487.2 Q6P5Z2 PKN3_HUMAN protein kinase N3 p.D599D(1) 24 TCAGCCGGGACGAGATAGAGA 0.612000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000291906.4 1 1 hg19 CCDS6908.1 TCGA-IB-7889-01A-11D-2154-08 PKN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054487.1 1 0 0 13 255 0 56 1 8.674753e-01 7 66 0 56 2 0 0 0 0 0 2 1 0.999547 12 254 0 56 2 0 0 0 0 56 2 -15.209500 1 1 0 0 1 1 2 3 2.022956 0 0.220000 1.900000 0.221712 0.450000 0.250000 0.760000 0.440000 0.471469 0.450000 0 0.340000 0.590000 CDKN2A 1029 broad.mit.edu 37 9 21971120 21971120 + Nonsense_Mutation SNP G G A rs121913388 TCGA-IB-7889-01A-11D-2154-08 TCGA-IB-7889-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 01ca4fa5-629f-433d-ab6a-e0a8b2417ddc 273e3c23-c89d-4142-a9c3-59c5ec1224dc 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-IB-7889-01A-11D-2154-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 16 117 0 24 0 0 0 0 24 2 1 7.398962e-01 5 16 0 141 2 1 0.999630 14 88 0 21 2 0 0 0 0 24 2 -2.749063 1 1 0 0 1 0 1 1 1.860055 1 0.220000 1.900000 0.134295 0.880000 0.560000 1.000000 1.000000 0.866427 0.880000 1 0.720000 1.000000