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 COPS7B 64708 broad.mit.edu 37 2 232672287 232672288 + Frame_Shift_Ins INS - - A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr2:232672287_232672288insA ENST00000350033.3 + 7 868_869 c.727_728insA c.(727-729)cacfs p.H243fs COPS7B_ENST00000409091.1_Frame_Shift_Ins_p.H136fs|COPS7B_ENST00000373608.3_Frame_Shift_Ins_p.T261fs|COPS7B_ENST00000409295.1_Frame_Shift_Ins_p.H209fs|COPS7B_ENST00000410024.1_Frame_Shift_Ins_p.H243fs|RP11-690I21.2_ENST00000563949.1_RNA|COPS7B_ENST00000410017.1_Frame_Shift_Ins_p.T266fs NM_001282949.1|NM_022730.1 NP_001269878.1|NP_073567.1 Q9H9Q2 CSN7B_HUMAN COP9 signalosome subunit 7B 8 all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025) GTGTCCCCCTCACGCTGAGCAG 0.614000 0 SO:0001589 frameshift_variant ENST00000350033.3 0 1 hg19 CCDS2488.1 TCGA-HZ-8001-01A-11D-2201-08 COPS7B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256964.2 1 0 0 10 104 0 19 0 9.885156e-01 0 84 0 19 2 0 0 0 0 0 0 1 0.997849 13 106 0 20 2 0 0 0 0 0 0 -15.830590 1 1 0 0 1 0 1 1 2.007643 0 0.150000 1.920000 0.145514 0.990000 0.600000 1.000000 1.000000 0.945801 0.990000 1 8.500000e-01 1 MTUS1 57509 broad.mit.edu 37 8 17612188 17612192 + Frame_Shift_Del DEL TGTCT TGTCT - TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr8:17612188_17612192delTGTCT ENST00000262102.6 - 2 1349_1353 c.1125_1129delAGACA c.(1123-1131)gaagacacafs p.EDT375fs MTUS1_ENST00000519263.1_Frame_Shift_Del_p.EDT375fs|MTUS1_ENST00000381862.3_Frame_Shift_Del_p.EDT375fs|MTUS1_ENST00000381869.3_Frame_Shift_Del_p.EDT375fs NM_001001924.2 NP_001001924.1 Q9ULD2 MTUS1_HUMAN microtubule associated tumor suppressor 1 36 ACCATTTGTGTGTCTTCAGTCTCAG 0.444000 0 SO:0001589 frameshift_variant ENST00000262102.6 0 1 hg19 CCDS43717.1 TCGA-HZ-8001-01A-11D-2201-08 MTUS1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000375247.1 1 0 0 16 279 0 61 0 1.903069e-02 0 4 0 61 2 0 0 0 0 0 0 0 0.201038 19 277 2 63 22 0 0 0 0 0 0 -18.354210 1 1 0 0 1 1 2 3 2.045816 0 0.150000 1.920000 0.160701 0.770000 0.450000 1.000000 1.000000 0.782545 0.770000 0 5.900000e-01 1 COL13A1 1305 broad.mit.edu 37 10 71683572 71683572 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr10:71683572C>T ENST00000398978.3 + 23 1704 c.1212C>T c.(1210-1212)gtC>gtT p.V404V COL13A1_ENST00000398969.3_Silent_p.V347V|COL13A1_ENST00000357811.3_Silent_p.V382V|COL13A1_ENST00000520267.1_Silent_p.V347V|COL13A1_ENST00000398966.3_Silent_p.V382V|COL13A1_ENST00000398974.3_Silent_p.V392V|COL13A1_ENST00000398968.3_Silent_p.V385V|COL13A1_ENST00000354547.3_Silent_p.V382V|COL13A1_ENST00000522165.1_Silent_p.V385V|COL13A1_ENST00000398964.3_Silent_p.V375V|COL13A1_ENST00000398973.3_Silent_p.V404V|COL13A1_ENST00000398972.3_Silent_p.V404V|COL13A1_ENST00000398971.3_Silent_p.V404V|COL13A1_ENST00000517713.1_Silent_p.V382V|COL13A1_ENST00000356340.3_Silent_p.V404V|COL13A1_ENST00000520133.1_Silent_p.V353V NM_001130103.1 NP_001123575.1 collagen, type XIII, alpha 1 28 AAGCAGGTGTCGATGGCCAGG 0.592000 0 SO:0001819 synonymous_variant ENST00000398978.3 0 1 hg19 CCDS44419.1 TCGA-HZ-8001-01A-11D-2201-08 COL13A1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000048468.1 1 0 0 7 102 0 17 0 4.396492e-01 0 20 0 17 2 0 0 0 0 0 2 1 0.979820 6 100 0 17 2 0 0 0 0 17 2 -11.104030 1 1 120912 2 21 1 0 0 0 1.965170 0 0.150000 1.920000 0.126413 0.830000 0.380000 1.000000 1.000000 0.805576 0.830000 0 5.800000e-01 1 ABCC8 6833 broad.mit.edu 37 11 17415843 17415843 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr11:17415843G>A ENST00000389817.3 - 37 4583 c.4515C>T c.(4513-4515)gaC>gaT p.D1505D ABCC8_ENST00000302539.4_Silent_p.D1506D Q09428 ABCC8_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 8 67 Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124) CCGTGGCCTCGTCCATGATGA 0.577000 0 SO:0001819 synonymous_variant ENST00000389817.3 1 1 hg19 CCDS31437.1 TCGA-HZ-8001-01A-11D-2201-08 ABCC8-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000389093.1 0 0 0 24 583 0 104 0 9.999999e-01 0 691 0 104 2 0 0 0 0 0 2 1 1.000000 23 577 0 103 2 0 0 0 0 104 2 -4.356419 1 1 121412 5 41 1 1 2 3 2.041610 0 0.150000 1.920000 0.159456 0.550000 0.350000 1.000000 0.530000 0.602299 0.550000 0 4.400000e-01 7.400000e-01 OR5L2 26338 broad.mit.edu 37 11 55595169 55595169 + Missense_Mutation SNP C C A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr11:55595169C>A ENST00000378397.1 + 1 475 c.475C>A c.(475-477)Cac>Aac p.H159N NM_001004739.1 NP_001004739.1 Q8NGL0 OR5L2_HUMAN olfactory receptor, family 5, subfamily L, member 2 59 all_epithelial(135;0.208) TTCTCTGATTCACTCGTCCTT 0.483000 HNSCC(27;0.073) 0 SO:0001583 missense ENST00000378397.1 1 1 hg19 CCDS31511.1 . . . . . . . . . . . 10.30 1.310982 0.23821 . . ENSG00000205030 ENST00000378397 T 0.00262 8.4 5.18 5.18 0.71444 GPCR, rhodopsin-like superfamily (1); 0.000000 0.56097 D 0.000039 T 0.00496 0.0016 M 0.68593 2.085 0.09310 N 1 D 0.89917 1.0 D 0.97110 1.0 T 0.56062 -0.8041 10 0.59425 D 0.04 -34.9027 12.8637 0.57928 0.163:0.837:0.0:0.0 . 159 Q8NGL0 OR5L2_HUMAN N 159 ENSP00000367650:H159N ENSP00000367650:H159N H + 1 0 OR5L2 55351745 0.000000 0.05858 0.124000 0.21820 0.008000 0.06430 0.901000 0.28445 2.613000 0.88420 0.626000 0.83405 CAC TCGA-HZ-8001-01A-11D-2201-08 OR5L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391516.1 0 0 0 95 1074 1 202 0 0 0 1 202 2 0 0 0 0 0 2 1 1.000000 94 1065 1 200 20 0 0 0 1 202 2 -19.893610 1 1 0 0 1 1 2 3 2.041610 0 0.150000 1.920000 0.159456 0.990000 0.890000 1.000000 1.000000 0.991695 0.990000 1 9.900000e-01 1 IRF7 3665 broad.mit.edu 37 11 613476 613476 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr11:613476C>T ENST00000397574.2 - 9 1336 c.967G>A c.(967-969)Gcc>Acc p.A323T IRF7_ENST00000525445.1_Missense_Mutation_p.A217T|IRF7_ENST00000397570.1_Missense_Mutation_p.A294T|IRF7_ENST00000397562.3_Missense_Mutation_p.A30T|IRF7_ENST00000348655.6_Missense_Mutation_p.A294T|IRF7_ENST00000397566.1_Missense_Mutation_p.A336T|IRF7_ENST00000330243.5_Missense_Mutation_p.A336T NM_001572.3 NP_001563.2 Q92985 IRF7_HUMAN interferon regulatory factor 7 8 all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136) GGGTCTGTGGCCCGGACAGCT 0.672000 0 SO:0001583 missense ENST00000397574.2 1 1 hg19 CCDS7703.1 . . . . . . . . . . C 6.185 0.402214 0.11696 . . ENSG00000185507 ENST00000525445;ENST00000348655;ENST00000397570;ENST00000397566;ENST00000397574;ENST00000397562;ENST00000330243 T;T;T;T;T;T;T 0.55760 0.5;0.5;0.5;0.5;0.5;0.5;0.5 3.84 -0.911 0.10507 SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1); 1.324750 0.05437 N 0.547019 T 0.31482 0.0798 N 0.19112 0.55 0.09310 N 1 B;B;B;B 0.29955 0.263;0.029;0.248;0.208 B;B;B;B 0.31614 0.133;0.02;0.112;0.068 T 0.12218 -1.0556 10 0.16420 T 0.52 -2.4318 1.6157 0.02703 0.1576:0.3487:0.3081:0.1857 . 217;294;323;336 E9PSE3;Q92985-2;Q92985;Q92985-4 .;.;IRF7_HUMAN;. T 217;294;294;336;323;30;336 ENSP00000434009:A217T;ENSP00000331803:A294T;ENSP00000380700:A294T;ENSP00000380697:A336T;ENSP00000380704:A323T;ENSP00000380693:A30T;ENSP00000329411:A336T ENSP00000329411:A336T A - 1 0 IRF7 603476 0.003000 0.15002 0.000000 0.03702 0.002000 0.02628 1.084000 0.30828 -0.269000 0.09298 0.561000 0.74099 GCC TCGA-HZ-8001-01A-11D-2201-08 IRF7-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000255026.1 1 0 0 30 503 0 96 1 8.131308e-01 4 50 0 96 2 0 0 0 0 0 2 1 1.000000 30 492 0 96 2 0 0 0 0 96 2 -3.318794 1 1 0 0 1 1 2 3 2.041610 0 0.150000 1.920000 0.159456 0.780000 0.530000 1.000000 1.000000 0.797124 0.780000 0 6.400000e-01 1 LHX5 64211 broad.mit.edu 37 12 113905137 113905137 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr12:113905137C>T ENST00000261731.3 - 4 1338 c.765G>A c.(763-765)ccG>ccA p.P255P NM_022363.2 NP_071758.1 Q9H2C1 LHX5_HUMAN LIM homeobox 5 10 GCATGCGCCGCGGACTCCGGA 0.657000 0 SO:0001819 synonymous_variant ENST00000261731.3 0 1 hg19 CCDS9171.1 TCGA-HZ-8001-01A-11D-2201-08 LHX5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404788.3 0 0 0 4 63 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 0.877405 4 59 0 19 2 0 0 0 0 19 2 -8.450150 1 1 0 0 1 0 0 0 1.987763 0 0.150000 1.920000 0.135740 0.800000 0.280000 1.000000 1.000000 0.769019 0.800000 0 5.000000e-01 1 DNAH10 196385 broad.mit.edu 37 12 124352474 124352474 + Missense_Mutation SNP G G T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr12:124352474G>T ENST00000409039.3 + 42 6998 c.6973G>T c.(6973-6975)Gat>Tat p.D2325Y NM_207437.3 NP_997320.2 Q8IVF4 DYH10_HUMAN dynein, axonemal, heavy chain 10 52 all_neural(191;0.101)|Medulloblastoma(191;0.163) CAAGATGTTGGATGCGTTGCT 0.512000 0 SO:0001583 missense ENST00000409039.3 1 1 hg19 CCDS9255.2 . . . . . . . . . . G 19.28 3.797647 0.70567 . . ENSG00000197653 ENST00000409039 D 0.92595 -3.07 5.34 5.34 0.76211 . 0.168199 0.39687 U 0.001293 D 0.96836 0.8967 M 0.91972 3.26 0.80722 D 1 D 0.76494 0.999 D 0.66196 0.942 D 0.97569 1.0103 10 0.87932 D 0 . 19.0351 0.92974 0.0:0.0:1.0:0.0 . 2325 Q8IVF4 DYH10_HUMAN Y 2325 ENSP00000386770:D2325Y ENSP00000386770:D2325Y D + 1 0 DNAH10 122918427 1.000000 0.71417 0.963000 0.40424 0.510000 0.34073 7.974000 0.88039 2.495000 0.84180 0.467000 0.42956 GAT TCGA-HZ-8001-01A-11D-2201-08 DNAH10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335420.3 1 0 0 8 133 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 0.989108 8 130 0 28 2 0 0 0 0 28 2 -11.540010 1 1 0 0 1 0 0 0 1.987763 0 0.150000 1.920000 0.135740 0.750000 0.360000 1.000000 1.000000 0.755217 0.750000 0 5.300000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 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-HZ-8001-01A-11D-2201-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 10 128 0 30 0 3.540391e-02 1 3 0 30 2 1 9.999985e-01 30 393 0 341 2 1 0.997007 10 126 0 30 2 1 1 1063 6927 0 30 2 -5.801681 1 1 0 0 1 0 0 0 1.987763 0 0.150000 1.920000 0.135740 0.940000 0.490000 1.000000 1.000000 0.878741 0.940000 1 6.900000e-01 1 CNPY2 10330 broad.mit.edu 37 12 56705037 56705037 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr12:56705037G>A ENST00000273308.4 - 4 906 c.366C>T c.(364-366)ggC>ggT p.G122G RP11-977G19.10_ENST00000549318.1_Silent_p.G122G|RP11-977G19.11_ENST00000549860.1_RNA|CNPY2_ENST00000551720.1_5'Flank|RP11-977G19.11_ENST00000549565.1_RNA|RP11-977G19.12_ENST00000546789.1_RNA NM_014255.5 NP_055070.1 Q9Y2B0 CNPY2_HUMAN canopy FGF signaling regulator 2 4 CGATTCGGATGCCTTGTAGGT 0.502000 0 SO:0001819 synonymous_variant ENST00000273308.4 1 1 hg19 CCDS8914.1 TCGA-HZ-8001-01A-11D-2201-08 CNPY2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408546.1 1 0 0 71 1084 0 199 1 1 50 747 0 199 2 0 0 0 0 0 2 1 1.000000 71 1069 0 198 2 0 0 0 0 199 2 -10.675380 1 1 0 0 1 0 0 0 1.987763 0 0.150000 1.920000 0.135740 0.800000 0.630000 0.990000 0.800000 0.810471 0.800000 0 7.100000e-01 9.000000e-01 SLC10A2 6555 broad.mit.edu 37 13 103718456 103718456 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr13:103718456G>A ENST00000245312.3 - 1 740 c.144C>T c.(142-144)tcC>tcT p.S48S NM_000452.2 NP_000443 Q12908 NTCP2_HUMAN solute carrier family 10 (sodium/bile acid cotransporter), member 2 34 all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577) TGCATCCCATGGAGAACATCA 0.493000 0 SO:0001819 synonymous_variant ENST00000245312.3 1 1 hg19 CCDS9506.1 TCGA-HZ-8001-01A-11D-2201-08 SLC10A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045716.1 0 0 0 32 828 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 1.000000 32 820 0 131 2 0 0 0 0 131 2 -2.817278 1 1 0 0 1 1 2 3 2.043056 0 0.150000 1.920000 0.160079 0.510000 0.350000 1.000000 0.500000 0.574602 0.510000 0 4.200000e-01 6.800000e-01 BTBD6 90135 broad.mit.edu 37 14 105716868 105716868 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr14:105716868C>T ENST00000392554.3 + 4 1614 c.1317C>T c.(1315-1317)agC>agT p.S439S BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000392557.4_5'Flank|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000546474.1_Intron|BTBD6_ENST00000327471.3_Silent_p.S364S|BRF1_ENST00000446501.2_5'Flank|BTBD6_ENST00000463376.2_Silent_p.S364S|BTBD6_ENST00000536364.1_Silent_p.S439S Q96KE9 BTBD6_HUMAN BTB (POZ) domain containing 6 4 Melanoma(154;0.226) OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391) TGGACGGCAGCGAACTCAGCT 0.592000 0 SO:0001819 synonymous_variant ENST00000392554.3 1 1 hg19 CCDS10002.2 TCGA-HZ-8001-01A-11D-2201-08 BTBD6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000074556.4 0 0 0 64 622 1 100 0 9.995860e-01 0 313 1 100 12 0 0 0 0 0 2 1 0.999999 62 610 1 100 22 0 0 0 1 100 2 -3.142702 1 1 0 0 1 1 2 3 2.043118 0 0.150000 1.920000 0.160079 0.990000 0.990000 1.000000 1.000000 0.998672 0.990000 1 9.900000e-01 1 MDGA2 161357 broad.mit.edu 37 14 47343307 47343307 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr14:47343307C>T ENST00000399232.2 - 13 2691 c.2327G>A c.(2326-2328)aGa>aAa p.R776K MDGA2_ENST00000357362.3_Missense_Mutation_p.R547K|MDGA2_ENST00000399222.3_5'UTR|MDGA2_ENST00000426342.1_Missense_Mutation_p.R547K|MDGA2_ENST00000439988.3_Missense_Mutation_p.R845K NM_001113498.2 NP_001106970.3 Q7Z553 MDGA2_HUMAN MAM domain containing glycosylphosphatidylinositol anchor 2 76 TTTTGTATTTCTTGTTGCTGT 0.373000 0 SO:0001583 missense ENST00000399232.2 1 1 hg19 . . . . . . . . . . C 29.8 5.041051 0.93685 . . ENSG00000139915 ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362 T;T;T;T 0.02032 4.49;4.49;4.49;4.49 5.37 5.37 0.77165 Concanavalin A-like lectin/glucanase (1);MAM domain (3); 0.000000 0.50627 U 0.000107 T 0.07863 0.0197 L 0.52011 1.625 0.80722 D 1 P;P 0.44877 0.845;0.804 P;P 0.55222 0.458;0.771 T 0.17653 -1.0362 10 0.44086 T 0.13 . 17.6763 0.88232 0.0:1.0:0.0:0.0 . 547;776 F6W3S7;Q7Z553 .;MDGA2_HUMAN K 776;547;845;547 ENSP00000400011:R776K;ENSP00000405456:R547K;ENSP00000382178:R845K;ENSP00000349925:R547K ENSP00000349925:R547K R - 2 0 MDGA2 46413057 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 7.487000 0.81328 2.501000 0.84356 0.467000 0.42956 AGA TCGA-HZ-8001-01A-11D-2201-08 MDGA2-001 KNOWN upstream_ATG|basic|appris_principal protein_coding protein_coding OTTHUMT00000073352.5 0 0 0 23 542 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 0.999999 23 535 0 71 2 0 0 0 0 71 2 -4.065207 1 1 0 0 1 1 2 3 2.043118 0 0.150000 1.920000 0.160079 0.570000 0.360000 1.000000 0.550000 0.620421 0.570000 0 4.500000e-01 7.800000e-01 CASC5 57082 broad.mit.edu 37 15 40898600 40898600 + Missense_Mutation SNP C C G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr15:40898600C>G ENST00000346991.5 + 4 475 c.85C>G c.(85-87)Ccc>Gcc p.P29A CASC5_ENST00000527044.1_Missense_Mutation_p.P29A|CASC5_ENST00000399668.2_Missense_Mutation_p.P29A|snoU13_ENST00000459027.1_RNA Q8NG31 CASC5_HUMAN cancer susceptibility candidate 5 57 all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GATATTGAAACCCCCAAGGAG 0.318000 0 SO:0001583 missense ENST00000346991.5 1 1 hg19 CCDS42023.1 . . . . . . . . . . C 12.01 1.810592 0.32053 . . ENSG00000137812 ENST00000346991;ENST00000260369;ENST00000527044;ENST00000399668 T;T;T 0.22945 1.93;1.93;1.93 4.53 4.53 0.55603 . 0.240709 0.28241 N 0.016077 T 0.33498 0.0865 L 0.42245 1.32 0.27413 N 0.954519 D;D;D 0.60160 0.987;0.987;0.987 P;P;P 0.60236 0.871;0.871;0.871 T 0.08106 -1.0738 10 0.17369 T 0.5 . 10.6218 0.45484 0.0:0.8052:0.1948:0.0 . 29;29;29 Q8NG31-2;Q8NG31;Q8NG31-4 .;CASC5_HUMAN;. A 29 ENSP00000335463:P29A;ENSP00000432654:P29A;ENSP00000382576:P29A ENSP00000260369:P29A P + 1 0 CASC5 38685892 1.000000 0.71417 1.000000 0.80357 0.705000 0.40729 2.404000 0.44539 2.362000 0.80069 0.467000 0.42956 CCC TCGA-HZ-8001-01A-11D-2201-08 CASC5-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000390224.2 0 0 0 8 249 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 0.988998 8 245 0 43 2 0 0 0 0 43 2 -3.199974 1 1 0 0 1 0 0 0 1.958945 0 0.150000 1.920000 0.123711 0.410000 0.190000 0.730000 0.400000 0.437015 0.410000 0 2.900000e-01 5.700000e-01 HS3ST2 9956 broad.mit.edu 37 16 22926868 22926868 + Missense_Mutation SNP C C A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr16:22926868C>A ENST00000261374.3 + 2 1523 c.1089C>A c.(1087-1089)gaC>gaA p.D363E NM_006043.1 NP_006034.1 Q9Y278 HS3S2_HUMAN heparan sulfate (glucosamine) 3-O-sulfotransferase 2 19 TTGGGCAGGACTTCAGGTGGG 0.463000 0 SO:0001583 missense ENST00000261374.3 1 1 hg19 CCDS10606.1 . . . . . . . . . . C 16.36 3.101853 0.56183 . . ENSG00000122254 ENST00000261374 T 0.48522 0.81 5.11 3.15 0.36227 . 0.049322 0.85682 D 0.000000 T 0.47284 0.1437 M 0.66297 2.02 0.58432 D 0.999999 P 0.39748 0.686 B 0.41764 0.366 T 0.49000 -0.8984 10 0.49607 T 0.09 . 9.9236 0.41478 0.0:0.8365:0.0:0.1635 . 363 Q9Y278 HS3S2_HUMAN E 363 ENSP00000261374:D363E ENSP00000261374:D363E D + 3 2 HS3ST2 22834369 1.000000 0.71417 1.000000 0.80357 0.906000 0.53458 2.179000 0.42528 1.149000 0.42402 0.561000 0.74099 GAC TCGA-HZ-8001-01A-11D-2201-08 HS3ST2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211598.1 0 0 0 23 602 0 115 0 7.569960e-01 0 73 0 115 2 0 0 0 0 0 2 1 0.999999 23 592 0 115 2 0 0 0 0 115 2 -19.911270 1 1 0 0 1 1 2 3 2.039274 0 0.150000 1.920000 0.159456 0.510000 0.320000 1.000000 0.500000 0.569752 0.510000 0 4.100000e-01 6.900000e-01 SNX20 124460 broad.mit.edu 37 16 50711341 50711341 + Missense_Mutation SNP C C T rs34428900 TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr16:50711341C>T ENST00000330943.4 - 2 268 c.97G>A c.(97-99)Gac>Aac p.D33N SNX20_ENST00000300590.3_Missense_Mutation_p.D33N|SNX20_ENST00000423026.2_Missense_Mutation_p.D33N NM_182854.2 NP_878274.1 Q7Z614 SNX20_HUMAN sorting nexin 20 15 TGCGGGAGGTCGGGGCCAGTG 0.617000 0 SO:0001583 missense ENST00000330943.4 1 1 hg19 CCDS10745.1 . . . . . . . . . . C 12.37 1.918679 0.33908 2.27E-4 0.0 ENSG00000167208 ENST00000300590;ENST00000423026;ENST00000330943;ENST00000413750 T;T;T 0.52295 0.67;0.72;1.34 4.2 2.21 0.28008 . 1.051240 0.07436 N 0.896485 T 0.48840 0.1522 L 0.27053 0.805 0.09310 N 1 D;P;D 0.71674 0.998;0.553;0.989 P;B;P 0.59948 0.866;0.059;0.727 T 0.35076 -0.9803 10 0.45353 T 0.12 -29.3821 6.0059 0.19547 0.0:0.7056:0.1911:0.1033 rs34428900 33;33;33 Q7Z614-3;Q7Z614;Q7Z614-4 .;SNX20_HUMAN;. N 33 ENSP00000300590:D33N;ENSP00000388875:D33N;ENSP00000332062:D33N ENSP00000300590:D33N D - 1 0 SNX20 49268842 0.114000 0.22134 0.008000 0.14137 0.008000 0.06430 0.376000 0.20535 0.692000 0.31613 -0.369000 0.07265 GAC TCGA-HZ-8001-01A-11D-2201-08 SNX20-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256879.2 1 0 0 54 549 0 97 0 3.986477e-01 0 14 0 97 2 0 0 0 0 0 2 1 1.000000 49 505 0 90 2 0 0 0 0 97 2 -15.256040 1 1 121412 12 44 1 1 2 3 2.039274 0 0.150000 1.920000 0.159456 0.990000 0.920000 1.000000 1.000000 0.995852 0.990000 1 9.900000e-01 1 TMEM231 79583 broad.mit.edu 37 16 75579249 75579249 + Splice_Site SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr16:75579249C>T ENST00000258173.6 - 4 659 c.e4+1 TMEM231_ENST00000568377.1_Splice_Site|RP11-77K12.7_ENST00000460606.1_Splice_Site|TMEM231_ENST00000569294.1_Splice_Site|RP11-77K12.8_ENST00000564489.1_RNA|TMEM231_ENST00000565067.1_Intron NM_001077418.1 NP_001070886.1 Q9H6L2 TM231_HUMAN transmembrane protein 231 5 AGCGCTCTTACGTTGTATCGG 0.507000 0 SO:0001630 splice_region_variant ENST00000258173.6 1 1 hg19 CCDS45530.1 . . . . . . . . . . C 7.772 0.707761 0.15239 . . ENSG00000205084 ENST00000258173;ENST00000398114 . . . 4.19 3.23 0.37069 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 11.3979 0.49854 0.0:0.9078:0.0:0.0922 . . . . . -1 . . . - . . TMEM231 74136750 1.000000 0.71417 0.962000 0.40283 0.003000 0.03518 7.478000 0.81082 1.072000 0.40860 -0.384000 0.06662 . TCGA-HZ-8001-01A-11D-2201-08 TMEM231-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000435481.2 0 0 0 21 988 0 170 0 0 0 0 170 2 0 0 0 0 0 2 1 0.999997 21 971 0 171 2 0 0 0 0 170 2 -2.819521 1 1 120914 2 37 1 1 2 3 2.043611 0 0.150000 1.920000 0.160079 0.290000 0.180000 1.000000 0.280000 0.381116 0.290000 0 2.300000e-01 4.100000e-01 GPR179 440435 broad.mit.edu 37 17 36499508 36499508 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr17:36499508C>T ENST00000342292.4 - 1 185 c.165G>A c.(163-165)ggG>ggA p.G55G NM_001004334.2 NP_001004334.2 Q6PRD1 GP179_HUMAN G protein-coupled receptor 179 60 Breast(7;2.97e-12) Breast(25;0.0101)|Ovarian(249;0.15) CGGCCTCGGCCCCCTCTAGGG 0.637000 0 SO:0001819 synonymous_variant ENST00000342292.4 1 1 hg19 CCDS42308.1 TCGA-HZ-8001-01A-11D-2201-08 GPR179-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255329.2 0 0 0 14 414 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 0.999734 14 407 0 91 2 0 0 0 0 92 2 -13.383130 1 1 0 0 1 1 2 3 2.019752 0 0.150000 1.920000 0.155070 0.450000 0.250000 1.000000 0.440000 0.496573 0.450000 0 3.400000e-01 6.200000e-01 SMARCE1 6605 broad.mit.edu 37 17 38792702 38792702 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr17:38792702C>T ENST00000348513.6 - 6 1094 c.314G>A c.(313-315)cGa>cAa p.R105Q SMARCE1_ENST00000578044.1_Missense_Mutation_p.R35Q|SMARCE1_ENST00000544009.1_Missense_Mutation_p.R35Q|SMARCE1_ENST00000377808.4_Missense_Mutation_p.R70Q|KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Missense_Mutation_p.R70Q|SMARCE1_ENST00000400122.3_Missense_Mutation_p.R35Q|SMARCE1_ENST00000431889.2_Missense_Mutation_p.R87Q NM_003079.4 NP_003070.3 Q969G3 SMCE1_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 1 Breast(137;0.000812) AGTGAGATCTCGCCACATGCC 0.408000 0 SO:0001583 missense ENST00000348513.6 1 1 hg19 CCDS11370.1 . . . . . . . . . . C 19.99 3.929060 0.73327 . . ENSG00000073584 ENST00000348513;ENST00000544009;ENST00000431889;ENST00000377808 D;D;D;D 0.98164 -4.76;-4.76;-4.76;-4.76 5.74 5.74 0.90152 High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4); 0.000000 0.85682 D 0.000000 D 0.96639 0.8903 L 0.49640 1.575 0.80722 D 1 P;B;P;B 0.39157 0.662;0.279;0.662;0.279 B;B;B;B 0.33620 0.167;0.027;0.098;0.027 D 0.96341 0.9251 10 0.54805 T 0.06 . 20.2825 0.98528 0.0:1.0:0.0:0.0 . 70;87;70;105 C0IMW5;B4DGM3;C0IMW4;Q969G3 .;.;.;SMCE1_HUMAN Q 105;35;87;70 ENSP00000323967:R105Q;ENSP00000441857:R35Q;ENSP00000445370:R87Q;ENSP00000367039:R70Q ENSP00000323967:R105Q R - 2 0 SMARCE1 36046228 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.701000 0.84566 2.873000 0.98535 0.561000 0.74099 CGA TCGA-HZ-8001-01A-11D-2201-08 SMARCE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257203.1 1 0 0 50 552 0 133 1 1 22 271 0 133 2 0 0 0 0 0 2 1 1.000000 48 543 0 133 2 0 0 0 0 133 2 -3.318794 1 1 0 0 1 1 2 3 2.019752 0 0.150000 1.920000 0.155070 0.990000 0.840000 1.000000 1.000000 0.984929 0.990000 1 9.700000e-01 1 TRIM37 4591 broad.mit.edu 37 17 57093064 57093064 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr17:57093064C>T ENST00000262294.7 - 21 2742 c.2483G>A c.(2482-2484)cGg>cAg p.R828Q TRIM37_ENST00000376149.3_Missense_Mutation_p.R706Q|TRIM37_ENST00000393065.2_Missense_Mutation_p.R794Q|TRIM37_ENST00000393066.3_Missense_Mutation_p.R828Q NM_015294.3 NP_056109.1 O94972 TRI37_HUMAN tripartite motif containing 37 37 Medulloblastoma(34;0.0922)|all_neural(34;0.101) TTTACACTGCCGGTCTTCAGT 0.502000 Mulibrey Nanism 0 SO:0001583 missense Familial Cancer Database Perheentupa syndrome ENST00000262294.7 1 1 hg19 CCDS32694.1 . . . . . . . . . . C 17.02 3.280964 0.59758 0.0 1.16E-4 ENSG00000108395 ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065 T;T;T;T 0.31769 1.48;1.48;1.48;1.48 4.93 2.91 0.33838 . 0.162035 0.41500 N 0.000869 T 0.18002 0.0432 L 0.29908 0.895 0.39748 D 0.971849 P;P;P 0.50819 0.939;0.622;0.488 B;B;B 0.37508 0.252;0.186;0.091 T 0.03981 -1.0987 10 0.66056 D 0.02 -1.8697 7.1336 0.25515 0.1695:0.7407:0.0:0.0897 . 794;706;828 F8WEE6;O94972-2;O94972 .;.;TRI37_HUMAN Q 828;828;706;794 ENSP00000376785:R828Q;ENSP00000262294:R828Q;ENSP00000365319:R706Q;ENSP00000376784:R794Q ENSP00000262294:R828Q R - 2 0 TRIM37 54447846 0.717000 0.27966 1.000000 0.80357 0.931000 0.56810 0.594000 0.24014 0.476000 0.27440 0.313000 0.20887 CGG TCGA-HZ-8001-01A-11D-2201-08 TRIM37-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445930.1 0 0 0 29 708 0 131 0 3.146748e-01 1 27 0 131 2 0 0 0 0 0 2 1 1.000000 30 683 0 124 2 0 0 0 0 131 2 -2.576094 1 1 121412 2 36 1 1 2 3 2.019752 0 0.150000 1.920000 0.155070 0.530000 0.360000 1.000000 0.520000 0.570060 0.530000 0 4.400000e-01 6.700000e-01 TP53 7157 broad.mit.edu 37 17 7577538 7577538 + Missense_Mutation SNP C C T rs11540652 TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr17:7577538C>T ENST00000269305.4 - 7 932 c.743G>A c.(742-744)cGg>cAg p.R248Q TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q 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.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GATGGGCCTCCGGTTCATGCC 0.572000 R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 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 725 Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1) GRCh37 CM920675 TP53 M rs11540652 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 27.3 4.822907 0.90873 0.0 1.16E-4 ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99864 -7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28 4.62 3.65 0.41850 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99840 0.9927 M 0.88640 2.97 0.58432 A 0.999994 D;D;D;D;D;D 0.89917 1.0;0.994;1.0;1.0;1.0;1.0 D;P;D;D;D;D 0.91635 0.996;0.882;0.999;0.995;0.996;0.995 D 0.96819 0.9602 9 0.72032 D 0.01 -9.5643 10.6687 0.45745 0.0:0.9059:0.0:0.0941 rs11540652;rs11540652 248;248;155;248;248;248 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. Q 248;248;248;248;248;248;237;155;116;155 ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q ENSP00000269305:R248Q R - 2 0 TP53 7518263 1.000000 0.71417 1.000000 0.80357 0.887000 0.51463 5.884000 0.69729 1.305000 0.44909 0.462000 0.41574 CGG TCGA-HZ-8001-01A-11D-2201-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 33 351 0 67 1 9.987399e-01 20 90 0 67 2 1 1 68 740 0 813 2 1 1.000000 33 346 0 67 2 0 0 0 0 67 2 -2.578431 1 1 121412 7 38 1 0 1 1 1.870738 1 0.150000 1.920000 0.081081 0.900000 0.680000 1.000000 0.990000 0.892024 0.900000 1 8.000000e-01 9.800000e-01 GPI 2821 broad.mit.edu 37 19 34868485 34868485 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr19:34868485C>T ENST00000356487.5 + 5 721 c.480C>T c.(478-480)tcC>tcT p.S160S GPI_ENST00000415930.3_Intron|GPI_ENST00000586425.1_Silent_p.S160S NM_000175.3 NP_000166.2 P06744 G6PI_HUMAN glucose-6-phosphate isomerase 25 Esophageal squamous(110;0.162) TTGGCGGCTCCGACCTGGTGA 0.597000 0 SO:0001819 synonymous_variant ENST00000356487.5 1 1 hg19 CCDS12437.1 TCGA-HZ-8001-01A-11D-2201-08 GPI-006 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451693.3 1 0 0 24 449 0 79 1 1 50 971 0 79 2 0 0 0 0 0 2 1 1.000000 23 443 0 78 2 0 0 0 0 79 2 -2.600954 1 1 121412 1 27 1 1 2 3 2.177207 1 0.150000 1.920000 0.209302 0.730000 0.480000 1.000000 1.000000 0.744463 0.730000 0 5.900000e-01 8.900000e-01 MAP3K10 4294 broad.mit.edu 37 19 40711866 40711866 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr19:40711866C>T ENST00000253055.3 + 5 1525 c.1237C>T c.(1237-1239)Cgc>Tgc p.R413C AC118344.1_ENST00000408124.1_RNA NM_002446.3 NP_002437.2 Q02779 M3K10_HUMAN mitogen-activated protein kinase kinase kinase 10 24 ACAGGAGCAGCGCTTCCAGGA 0.672000 0 SO:0001583 missense ENST00000253055.3 0 1 hg19 CCDS12549.1 . . . . . . . . . . C 22.4 4.287897 0.80803 . . ENSG00000130758 ENST00000253055 T 0.75477 -0.94 4.43 3.26 0.37387 . 0.117141 0.52532 D 0.000071 T 0.77545 0.4146 M 0.64404 1.975 0.80722 D 1 D 0.69078 0.997 P 0.55455 0.776 T 0.79193 -0.1904 10 0.72032 D 0.01 . 8.8376 0.35121 0.3823:0.6177:0.0:0.0 . 413 Q02779 M3K10_HUMAN C 413 ENSP00000253055:R413C ENSP00000253055:R413C R + 1 0 MAP3K10 45403706 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 5.598000 0.67585 2.143000 0.66587 0.491000 0.48974 CGC TCGA-HZ-8001-01A-11D-2201-08 MAP3K10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462552.1 0 0 0 4 58 0 24 0 5.860611e-01 1 26 0 24 2 0 0 0 0 0 2 1 0.876248 4 54 0 21 2 0 0 0 0 24 2 -8.612478 1 1 0 0 1 1 2 3 2.177207 1 0.150000 1.920000 0.209302 0.980000 0.350000 1.000000 1.000000 0.852075 0.980000 1 6.100000e-01 1 NLRP5 126206 broad.mit.edu 37 19 56545008 56545008 + Missense_Mutation SNP A A C TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr19:56545008A>C ENST00000390649.3 + 9 2548 c.2548A>C c.(2548-2550)Aag>Cag p.K850Q NM_153447.4 NP_703148.4 P59047 NALP5_HUMAN NLR family, pyrin domain containing 5 25 Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157) CACCCACCTGAAGGAAGAGGA 0.478000 0 SO:0001583 missense ENST00000390649.3 1 1 hg19 CCDS12938.1 . . . . . . . . . . A 5.972 0.363331 0.11296 . . ENSG00000171487 ENST00000390649 T 0.52754 0.65 3.07 -2.48 0.06423 . 1.303020 0.05712 N 0.596209 T 0.28067 0.0692 N 0.21240 0.645 0.09310 N 1 B 0.33345 0.409 B 0.27715 0.082 T 0.12863 -1.0531 10 0.33141 T 0.24 . 5.8888 0.18896 0.2931:0.5327:0.0:0.1741 . 850 P59047 NALP5_HUMAN Q 850 ENSP00000375063:K850Q ENSP00000375063:K850Q K + 1 0 NLRP5 61236820 0.003000 0.15002 0.000000 0.03702 0.018000 0.09664 0.359000 0.20233 -0.645000 0.05458 0.454000 0.30748 AAG TCGA-HZ-8001-01A-11D-2201-08 NLRP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313735.1 1 0 0 96 1116 0 230 0 0 0 0 230 2 0 0 0 0 0 2 1 1.000000 93 1104 0 229 2 0 0 0 0 230 2 -19.698570 1 1 0 0 1 1 2 3 2.161279 1 0.150000 1.920000 0.209302 0.990000 0.920000 1.000000 1.000000 0.995308 0.990000 1 9.900000e-01 1 LAMC1 3915 broad.mit.edu 37 1 182992997 182992997 + Missense_Mutation SNP G G T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:182992997G>T ENST00000258341.4 + 1 403 c.146G>T c.(145-147)cGc>cTc p.R49L NM_002293.3 NP_002284.3 P11047 LAMC1_HUMAN laminin, gamma 1 (formerly LAMB2) 76 CGGCCGCAGCGCTGCATGCCC 0.721000 0 SO:0001583 missense ENST00000258341.4 1 1 hg19 CCDS1351.1 . . . . . . . . . . G 31 5.096975 0.94197 . . ENSG00000135862 ENST00000258341 T 0.32988 1.43 4.23 4.23 0.50019 Laminin, N-terminal (2); 0.142328 0.47093 U 0.000252 T 0.45175 0.1329 M 0.78456 2.415 0.80722 D 1 P;P 0.46784 0.515;0.884 B;P 0.47573 0.141;0.55 T 0.55198 -0.8178 10 0.56958 D 0.05 . 16.6058 0.84828 0.0:0.0:1.0:0.0 . 49;49 P11047;Q6NVY8 LAMC1_HUMAN;. L 49 ENSP00000258341:R49L ENSP00000258341:R49L R + 2 0 LAMC1 181259620 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.254000 0.65457 1.857000 0.53885 0.591000 0.81541 CGC TCGA-HZ-8001-01A-11D-2201-08 LAMC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085954.2 1 0 0 15 176 0 38 0 2.045256e-02 0 3 0 38 2 0 0 0 0 0 2 1 0.999879 14 174 0 37 2 0 0 0 0 38 2 -19.711590 1 1 0 0 1 1 2 3 2.061797 0 0.150000 1.920000 0.163797 0.990000 0.640000 1.000000 1.000000 0.949271 0.990000 1 8.500000e-01 1 LRRN2 10446 broad.mit.edu 37 1 204588995 204588995 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:204588995C>T ENST00000367175.1 - 1 2338 c.126G>A c.(124-126)acG>acA p.T42T LRRN2_ENST00000367177.3_Silent_p.T42T|LRRN2_ENST00000367176.3_Silent_p.T42T|LRRN2_ENST00000496057.1_5'Flank O75325 LRRN2_HUMAN leucine rich repeat neuronal 2 38 all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19) KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143) ACGAGCGGGGCGTATACCAGG 0.667000 0 SO:0001819 synonymous_variant ENST00000367175.1 1 1 hg19 CCDS1448.1 TCGA-HZ-8001-01A-11D-2201-08 LRRN2-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000089894.1 1 0 0 13 229 0 48 0 5.716737e-01 0 34 0 48 2 0 0 0 0 0 2 1 0.999512 13 224 0 47 2 0 0 0 0 48 2 -15.735880 1 1 121408 3 31 1 1 2 3 2.061797 0 0.150000 1.920000 0.163797 0.780000 0.420000 1.000000 1.000000 0.788469 0.780000 0 5.800000e-01 1 OBSCN 84033 broad.mit.edu 37 1 228467880 228467880 + Splice_Site SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:228467880C>T ENST00000422127.1 + 29 7708 c.7664C>T c.(7663-7665)gCg>gTg p.A2555V OBSCN_ENST00000284548.11_Splice_Site_p.A2555V|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Splice_Site_p.A2984V|OBSCN_ENST00000359599.6_Splice_Site_p.A1402V|OBSCN_ENST00000366709.4_5'UTR NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) TCTCTTGCAGCGCGGGAGGTG 0.642000 0 SO:0001630 splice_region_variant ENST00000422127.1 1 0 hg19 CCDS58065.1 . . . . . . . . . . c 7.233 0.599675 0.13939 . . ENSG00000154358 ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706 T;T;T 0.40756 1.02;1.02;1.02 5.35 1.32 0.21799 Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.418879 0.23291 N 0.049783 T 0.44871 0.1314 L 0.37507 1.11 0.80722 D 1 P;B;D 0.89917 0.836;0.023;1.0 B;B;D 0.68765 0.2;0.002;0.96 T 0.26121 -1.0112 9 . . . . 5.3495 0.16028 0.2442:0.5533:0.0:0.2025 . 2555;2555;2555 Q5VST9;Q5VST9-2;Q5VST9-3 OBSCN_HUMAN;.;. V 2555;2555;1402;254 ENSP00000284548:A2555V;ENSP00000409493:A2555V;ENSP00000352613:A1402V . A + 2 0 OBSCN 226534503 0.040000 0.19996 0.012000 0.15200 0.314000 0.28054 0.351000 0.20096 -0.000000 0.14550 0.550000 0.68814 GCG TCGA-HZ-8001-01A-11D-2201-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 1 0 0 43 415 0 67 0 9.296560e-03 0 2 0 67 2 0 0 0 0 0 2 1 1.000000 43 407 0 65 2 0 0 0 0 67 2 -13.803670 1 1 121170 3 37 1 1 2 3 2.061797 0 0.150000 1.920000 0.163797 0.990000 0.950000 1.000000 1.000000 0.997099 0.990000 1 9.900000e-01 1 ARID1A 8289 broad.mit.edu 37 1 27106228 27106228 + Nonsense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:27106228C>T ENST00000324856.7 + 20 6210 c.5839C>T c.(5839-5841)Cag>Tag p.Q1947* ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q1564*|ARID1A_ENST00000540690.1_Nonsense_Mutation_p.Q275*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q1730* NM_006015.4 NP_006006.3 O14497 ARI1A_HUMAN AT rich interactive domain 1A (SWI-like) ARID1A/MAST2_ENST00000361297(2) 411 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) TAGCCCAGCACAGAGCCACCG 0.532000 Mis, N, F, S, D clear cell ovarian carcinoma, RCC Rec yes 1 1p35.3 8289 AT rich interactive domain 1A (SWI-like) E 0 SO:0001587 stop_gained ENST00000324856.7 0 1 hg19 CCDS285.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 43|43 9.895876|9.895876 0.99290|0.99290 .|. .|. ENSG00000117713|ENSG00000117713 ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690|ENST00000430799 .|. .|. .|. 5.02|5.02 5.02|5.02 0.67125|0.67125 .|. 0.263023|. 0.39687|. N|. 0.001300|. .|T .|0.70527 .|0.3234 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.68300 .|-0.5445 .|4 0.02654|. T|. 1|. -6.3757|-6.3757 14.6091|14.6091 0.68504|0.68504 0.1463:0.8537:0.0:0.0|0.1463:0.8537:0.0:0.0 .|. .|. .|. .|. X|I 1947;1730;1564;275|843 .|. ENSP00000320485:Q1947X|. Q|T +|+ 1|2 0|0 ARID1A|ARID1A 26978815|26978815 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.981000|0.981000 0.71138|0.71138 3.660000|3.660000 0.54496|0.54496 2.769000|2.769000 0.95229|0.95229 0.491000|0.491000 0.48974|0.48974 CAG|ACA TCGA-HZ-8001-01A-11D-2201-08 ARID1A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000011437.2 0 0 0 39 944 0 181 1 8.347515e-01 5 76 0 181 2 1 9.999763e-01 11 365 0 360 2 1 1.000000 38 935 0 180 2 0 0 0 0 181 2 -4.523382 1 1 0 0 1 0 0 0 1.972451 0 0.150000 1.920000 0.129098 0.510000 0.370000 0.680000 0.520000 0.524837 0.510000 0 4.300000e-01 6.000000e-01 BAI2 576 broad.mit.edu 37 1 32222194 32222194 + Missense_Mutation SNP G G C TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:32222194G>C ENST00000373658.3 - 4 585 c.244C>G c.(244-246)Cgc>Ggc p.R82G BAI2_ENST00000257070.4_Missense_Mutation_p.R82G|BAI2_ENST00000398542.1_Missense_Mutation_p.R70G|MIR4254_ENST00000581063.1_RNA|BAI2_ENST00000398556.3_Missense_Mutation_p.R85G|BAI2_ENST00000398547.1_Missense_Mutation_p.R70G|BAI2_ENST00000527361.1_Missense_Mutation_p.R82G|BAI2_ENST00000398538.1_Missense_Mutation_p.R70G|BAI2_ENST00000373655.2_Missense_Mutation_p.R82G NM_001703.2 NP_001694.2 O60241 BAI2_HUMAN brain-specific angiogenesis inhibitor 2 55 Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174) CGGTTGAAGCGCAGGTAGAGG 0.647000 0 SO:0001583 missense ENST00000373658.3 1 1 hg19 CCDS346.2 . . . . . . . . . . G 17.20 3.328325 0.60743 . . ENSG00000121753 ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000398538;ENST00000420125;ENST00000533175 T;T;T;T;T;T;T;T;T;T 0.53857 1.25;1.45;0.65;0.65;1.62;0.6;0.6;0.68;1.22;1.09 5.04 5.04 0.67666 . 0.000000 0.43579 D 0.000544 T 0.61652 0.2364 L 0.43152 1.355 0.80722 D 1 B;D;D;D;P;P 0.71674 0.015;0.998;0.965;0.995;0.831;0.941 B;D;P;P;P;P 0.65874 0.011;0.939;0.777;0.756;0.54;0.501 T 0.63967 -0.6517 10 0.87932 D 0 . 11.3219 0.49428 0.0:0.0:0.7086:0.2914 . 70;82;70;70;82;82 A2A3C3;O60241-4;O60241-3;A2A3C1;O60241-2;O60241 .;.;.;.;.;BAI2_HUMAN G 85;70;82;82;70;82;82;70;75;116 ENSP00000381564:R85G;ENSP00000381555:R70G;ENSP00000362762:R82G;ENSP00000362759:R82G;ENSP00000381550:R70G;ENSP00000257070:R82G;ENSP00000435397:R82G;ENSP00000381548:R70G;ENSP00000410921:R75G;ENSP00000437219:R116G ENSP00000257070:R82G R - 1 0 BAI2 31994781 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 2.598000 0.46223 2.506000 0.84524 0.462000 0.41574 CGC TCGA-HZ-8001-01A-11D-2201-08 BAI2-015 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000381838.1 1 0 0 9 99 0 32 0 4.666519e-02 0 4 0 32 2 0 0 0 0 0 2 1 0.993893 9 95 0 31 2 0 0 0 0 32 2 -14.118600 1 1 0 0 1 0 0 0 1.972451 0 0.150000 1.920000 0.129098 0.990000 0.540000 1.000000 1.000000 0.917215 0.990000 1 7.700000e-01 1 CCDC28B 79140 broad.mit.edu 37 1 32669888 32669888 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:32669888G>A ENST00000373602.5 + 4 780 c.433G>A c.(433-435)Gat>Aat p.D145N IQCC_ENST00000291358.6_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA|CCDC28B_ENST00000483009.1_Intron|CCDC28B_ENST00000421922.2_Missense_Mutation_p.D145N|RP4-622L5.7_ENST00000373604.4_RNA|IQCC_ENST00000537469.1_5'Flank NM_024296.3 NP_077272.2 Q9BUN5 CC28B_HUMAN coiled-coil domain containing 28B 10 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174) GGAGGAGGACGATGAAGAGGA 0.577000 0 SO:0001583 missense ENST00000373602.5 1 1 hg19 CCDS354.2 . . . . . . . . . . G 11.04 1.520724 0.27211 . . ENSG00000160050 ENST00000373602;ENST00000421922 T;T 0.44881 0.99;0.91 4.5 4.5 0.54988 . 0.918054 0.09119 N 0.845946 T 0.27241 0.0668 N 0.08118 0 0.26056 N 0.981417 B 0.09022 0.002 B 0.01281 0.0 T 0.08722 -1.0708 10 0.49607 T 0.09 -26.5204 12.8892 0.58061 0.0:0.0:1.0:0.0 . 145 Q9BUN5 CC28B_HUMAN N 145 ENSP00000362704:D145N;ENSP00000413017:D145N ENSP00000362704:D145N D + 1 0 CCDC28B 32442475 0.999000 0.42202 0.824000 0.32777 0.940000 0.58332 0.923000 0.28757 2.504000 0.84457 0.561000 0.74099 GAT TCGA-HZ-8001-01A-11D-2201-08 CCDC28B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000015723.4 1 0 0 23 421 0 67 1 9.774913e-01 5 109 0 67 2 0 0 0 0 0 2 1 0.999999 23 412 0 67 2 0 0 0 0 67 2 -3.318794 1 1 0 0 1 0 0 0 1.972451 0 0.150000 1.920000 0.129098 0.670000 0.440000 0.960000 0.660000 0.688438 0.670000 0 5.400000e-01 8.200000e-01 ATPAF1 64756 broad.mit.edu 37 1 47123857 47123857 + Missense_Mutation SNP A A T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr1:47123857A>T ENST00000371937.4 - 4 535 c.431T>A c.(430-432)cTc>cAc p.L144H ATPAF1_ENST00000574428.1_Missense_Mutation_p.L144H|ATPAF1_ENST00000532925.1_Missense_Mutation_p.L56H|ATPAF1_ENST00000542495.1_5'UTR|ATPAF1_ENST00000525633.1_5'Flank|ATPAF1_ENST00000576409.1_Missense_Mutation_p.L167H|ATPAF1_ENST00000329231.4_Missense_Mutation_p.L167H NM_022745.4 NP_073582.3 Q5TC12 ATPF1_HUMAN ATP synthase mitochondrial F1 complex assembly factor 1 8 Acute lymphoblastic leukemia(166;0.155) GATTGAACTGAGAGTCTTGAA 0.323000 Melanoma(138;107 1777 21672 30337 52312) 0 SO:0001583 missense ENST00000371937.4 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 20.7|20.7 4.040846|4.040846 0.75732|0.75732 .|. .|. ENSG00000123472|ENSG00000123472 ENST00000371937;ENST00000526821;ENST00000329231;ENST00000532925|ENST00000534216 D|. 0.85258|. -1.96|. 5.44|5.44 5.44|5.44 0.79542|0.79542 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.80297|0.80297 0.4597|0.4597 M|M 0.90082|0.90082 3.085|3.085 0.80722|0.80722 D|D 1|1 D;D;D|. 0.89917|. 1.0;1.0;1.0|. D;D;D|. 0.97110|. 1.0;1.0;1.0|. D|D 0.84033|0.84033 0.0360|0.0360 10|5 0.87932|. D|. 0|. -11.4791|-11.4791 13.1214|13.1214 0.59329|0.59329 1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0 .|. 56;144;144|. B7Z7I6;A8MRA7;Q5TC12|. .;.;ATPF1_HUMAN|. H|T 144;58;144;56|16 ENSP00000361005:L144H|. ENSP00000330685:L144H|. L|S -|- 2|1 0|0 ATPAF1|ATPAF1 46896444|46896444 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.987000|0.987000 0.75469|0.75469 4.986000|4.986000 0.63851|0.63851 2.285000|2.285000 0.76669|0.76669 0.533000|0.533000 0.62120|0.62120 CTC|TCA TCGA-HZ-8001-01A-11D-2201-08 ATPAF1-201 KNOWN basic protein_coding protein_coding 0 0 0 17 187 0 43 1 9.897741e-01 13 72 0 43 2 0 0 0 0 0 2 1 0.999965 17 182 0 43 2 0 0 0 0 43 2 -19.999650 1 1 0 0 1 0 0 0 1.972451 0 0.150000 1.920000 0.129098 0.990000 0.660000 1.000000 1.000000 0.946115 0.990000 1 8.400000e-01 1 PTGIS 5740 broad.mit.edu 37 20 48130848 48130848 + Missense_Mutation SNP C C T rs13306027 TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr20:48130848C>T ENST00000244043.4 - 7 969 c.940G>A c.(940-942)Gag>Aag p.E314K PTGIS_ENST00000478971.1_5'UTR NM_000961.3 NP_000952.1 Q16647 PTGIS_HUMAN prostaglandin I2 (prostacyclin) synthase 27 BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166) Epoprostenol(DB01240)|Phenylbutazone(DB00812) AGGATACTCTCGAGCTCTCCG 0.587000 0 SO:0001583 missense ENST00000244043.4 1 1 hg19 CCDS13419.1 . . . . . . . . . . C 10.71 1.425967 0.25726 . . ENSG00000124212 ENST00000244043 T 0.67698 -0.28 4.1 2.07 0.26955 . 0.753921 0.12015 N 0.507523 T 0.52741 0.1753 L 0.55213 1.73 0.09310 N 1 B 0.31705 0.336 B 0.30646 0.118 T 0.40194 -0.9576 10 0.05959 T 0.93 -9.1386 6.6996 0.23217 0.0:0.7109:0.1818:0.1073 . 314 Q16647 PTGIS_HUMAN K 314 ENSP00000244043:E314K ENSP00000244043:E314K E - 1 0 PTGIS 47564255 0.014000 0.17966 0.018000 0.16275 0.060000 0.15804 0.192000 0.17096 0.282000 0.22254 -0.305000 0.09177 GAG TCGA-HZ-8001-01A-11D-2201-08 PTGIS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080496.2 1 0 1 38 345 0 66 0 9.999358e-01 1 132 0 66 2 0 0 0 0 0 2 1 1.000000 38 343 0 66 2 0 0 0 0 66 2 -3.142702 1 1 121412 9 42 1 1 2 3 2.036933 0 0.150000 1.920000 0.158832 0.990000 0.970000 1.000000 1.000000 0.997941 0.990000 1 9.900000e-01 1 ADAMTS5 11096 broad.mit.edu 37 21 28338459 28338459 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr21:28338459G>A ENST00000284987.5 - 1 373 c.252C>T c.(250-252)ggC>ggT p.G84G NM_007038.3 NP_008969.2 Q9UNA0 ATS5_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 5 72 CCACCTTGCCGCCGCCGGAGT 0.697000 Esophageal Squamous(53;683 1080 10100 14424 45938) 0 SO:0001819 synonymous_variant ENST00000284987.5 1 1 hg19 CCDS13579.1 TCGA-HZ-8001-01A-11D-2201-08 ADAMTS5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171648.1 1 0 0 23 510 0 109 0 0 0 1 0 109 2 0 0 0 0 0 2 1 0.999999 21 503 0 106 2 0 0 0 0 109 2 -3.279060 1 1 0 0 1 0 0 0 1.958296 0 0.150000 1.920000 0.122354 0.550000 0.360000 0.790000 0.550000 0.571477 0.550000 0 4.500000e-01 6.800000e-01 TTN 7273 broad.mit.edu 37 2 179574354 179574354 + Nonsense_Mutation SNP G G T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr2:179574354G>T ENST00000591111.1 - 97 27965 c.27741C>A c.(27739-27741)taC>taA p.Y9247* TTN_ENST00000342992.6_Nonsense_Mutation_p.Y8320*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Nonsense_Mutation_p.Y9564*|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTTTGCATGTGTACAAACCAG 0.438000 0 SO:0001587 stop_gained ENST00000591111.1 0 1 hg19 . . . . . . . . . . G 59 39.972864 0.99985 . . ENSG00000155657 ENST00000342992 . . . 5.91 3.13 0.36017 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 . 11.527 0.50586 0.2349:0.0:0.7651:0.0 . . . . X 8320 . ENSP00000343764:Y8320X Y - 3 2 TTN 179282599 1.000000 0.71417 1.000000 0.80357 0.683000 0.39861 1.422000 0.34826 1.508000 0.48769 0.655000 0.94253 TAC TCGA-HZ-8001-01A-11D-2201-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 24 329 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 1.000000 24 328 0 50 2 0 0 0 0 50 2 -7.199919 1 1 0 0 1 0.150000 1.920000 0 0 TRIP12 9320 broad.mit.edu 37 2 230660000 230660000 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr2:230660000G>A ENST00000283943.5 - 25 3816 c.3638C>T c.(3637-3639)gCa>gTa p.A1213V TRIP12_ENST00000389045.3_Missense_Mutation_p.A943V|TRIP12_ENST00000389044.4_Missense_Mutation_p.A1261V NM_001284214.1|NM_004238.1 NP_001271143.1|NP_004229.1 Q14669 TRIPC_HUMAN thyroid hormone receptor interactor 12 87 Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164) CAACAAAGGTGCATTACCCAC 0.408000 0 SO:0001583 missense ENST00000283943.5 1 1 hg19 CCDS33391.1 . . . . . . . . . . G 15.81 2.941825 0.53079 . . ENSG00000153827 ENST00000283943;ENST00000389045;ENST00000389044 T;T;T 0.47177 0.86;1.18;0.85 5.74 5.74 0.90152 . 0.144194 0.64402 D 0.000009 T 0.39253 0.1071 L 0.29908 0.895 0.80722 D 1 B;B;B 0.23058 0.079;0.003;0.079 B;B;B 0.26517 0.07;0.006;0.07 T 0.13791 -1.0496 10 0.35671 T 0.21 . 15.4109 0.74917 0.0:0.1385:0.8615:0.0 . 943;1261;1213 Q14CF1;Q14CA3;Q14669 .;.;TRIPC_HUMAN V 1213;943;1261 ENSP00000283943:A1213V;ENSP00000373697:A943V;ENSP00000373696:A1261V ENSP00000283943:A1213V A - 2 0 TRIP12 230368244 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.541000 0.60670 2.712000 0.92718 0.650000 0.86243 GCA TCGA-HZ-8001-01A-11D-2201-08 TRIP12-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000331861.3 1 0 0 25 300 0 65 1 9.204537e-01 5 49 0 65 2 0 0 0 0 0 2 1 1.000000 25 296 0 65 2 0 0 0 0 65 2 -3.318794 1 1 0 0 1 0 1 1 2.007643 0 0.150000 1.920000 0.145514 0.990000 0.680000 1.000000 1.000000 0.940094 0.990000 1 8.300000e-01 1 GALNT14 79623 broad.mit.edu 37 2 31178784 31178784 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr2:31178784G>A ENST00000349752.5 - 5 1165 c.526C>T c.(526-528)Cgg>Tgg p.R176W GALNT14_ENST00000324589.5_Missense_Mutation_p.R181W|GALNT14_ENST00000356174.3_Missense_Mutation_p.R143W|GALNT14_ENST00000420311.2_Missense_Mutation_p.R141W|GALNT14_ENST00000486564.1_5'Flank|GALNT14_ENST00000406653.1_Missense_Mutation_p.R156W NM_024572.3 NP_078848.2 Q96FL9 GLT14_HUMAN polypeptide N-acetylgalactosaminyltransferase 14 43 Acute lymphoblastic leukemia(172;0.155) CTACCTTGCCGTTCATTATTG 0.522000 0 SO:0001583 missense ENST00000349752.5 1 0 hg19 CCDS1773.2 . . . . . . . . . . G 19.81 3.896951 0.72639 . . ENSG00000158089 ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311;ENST00000430167 T;T;T;T;T;T 0.60299 0.2;0.2;0.2;0.2;0.2;0.2 5.28 4.38 0.52667 Glycosyl transferase, family 2 (1); 0.000000 0.85682 D 0.000000 D 0.85737 0.5766 H 0.99391 4.545 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;0.999;1.0;1.0;1.0 D 0.90544 0.4504 10 0.87932 D 0 . 12.6946 0.56997 0.0:0.0:0.575:0.425 . 141;141;143;181;176;156 F5H263;B7Z5C5;Q96FL9-2;Q96FL9-3;Q96FL9;B3KV89 .;.;.;.;GLT14_HUMAN;. W 176;181;156;143;141;143 ENSP00000288988:R176W;ENSP00000314500:R181W;ENSP00000385435:R156W;ENSP00000348497:R143W;ENSP00000415514:R141W;ENSP00000406399:R143W ENSP00000314500:R181W R - 1 2 GALNT14 31032288 1.000000 0.71417 0.800000 0.32199 0.939000 0.58152 2.181000 0.42547 1.195000 0.43115 0.561000 0.74099 CGG TCGA-HZ-8001-01A-11D-2201-08 GALNT14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000157264.1 1 0 0 133 1441 0 269 0 5.914075e-01 0 23 0 269 2 0 0 0 0 0 2 1 1.000000 132 1417 0 264 2 0 0 0 0 269 2 -20.000000 1 1 121412 1 36 1 1 2 3 2.032373 0 0.150000 1.920000 0.157582 0.990000 0.960000 1.000000 1.000000 0.997812 0.990000 1 9.900000e-01 1 FSHR 2492 broad.mit.edu 37 2 49190896 49190896 + Missense_Mutation SNP G G T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr2:49190896G>T ENST00000406846.2 - 10 1183 c.1064C>A c.(1063-1065)cCa>cAa p.P355Q FSHR_ENST00000304421.4_Missense_Mutation_p.P329Q|FSHR_ENST00000346173.3_Missense_Mutation_p.P293Q|FSHR_ENST00000541117.1_Missense_Mutation_p.P91Q NM_000145.3 NP_000136.2 P23945 FSHR_HUMAN follicle stimulating hormone receptor 73 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094) ATCTTCACATGGGTTGAATGC 0.453000 Gonadal Dysgenesis, 46 XX 0 SO:0001583 missense Familial Cancer Database ENST00000406846.2 1 1 hg19 CCDS1843.1 . . . . . . . . . . G 20.2 3.945958 0.73672 . . ENSG00000170820 ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117 D;D;D;D 0.91686 -2.89;-2.89;-2.89;-2.89 5.13 5.13 0.70059 . 0.000000 0.85682 D 0.000000 D 0.97470 0.9172 H 0.96048 3.76 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.999;0.999 D 0.98525 1.0625 9 . . . . 17.7464 0.88422 0.0:0.0:1.0:0.0 . 329;293;355 Q05AH0;G5E967;P23945 .;.;FSHR_HUMAN Q 355;293;329;91 ENSP00000384708:P355Q;ENSP00000333908:P293Q;ENSP00000306780:P329Q;ENSP00000444172:P91Q . P - 2 0 FSHR 49044400 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.657000 0.98554 2.673000 0.90976 0.561000 0.74099 CCA TCGA-HZ-8001-01A-11D-2201-08 FSHR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251367.2 1 0 0 41 417 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 1.000000 41 412 0 88 2 0 0 0 0 89 2 -2.402340 0 1 0 0 1 1 2 3 2.032373 0 0.150000 1.920000 0.157582 0.990000 0.880000 1.000000 1.000000 0.992700 0.990000 1 9.900000e-01 1 ACTG2 72 broad.mit.edu 37 2 74135852 74135852 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr2:74135852C>T ENST00000409624.1 + 5 951 c.308C>T c.(307-309)cCc>cTc p.P103L ACTG2_ENST00000345517.3_Missense_Mutation_p.P103L|ACTG2_ENST00000409731.3_Missense_Mutation_p.P60L P63267 ACTH_HUMAN actin, gamma 2, smooth muscle, enteric 18 GAAGAGCACCCCACCCTGCTC 0.527000 0 SO:0001583 missense ENST00000409624.1 1 1 hg19 CCDS1930.1 . . . . . . . . . . C 20.1 3.932979 0.73442 . . ENSG00000163017 ENST00000409731;ENST00000345517;ENST00000442912;ENST00000409624 D;D;D;D 0.97959 -4.63;-4.63;-3.69;-4.63 4.93 4.93 0.64822 . 0.000000 0.85682 D 0.000000 D 0.99302 0.9756 H 0.98370 4.215 0.80722 D 1 D;D 0.89917 0.997;1.0 D;D 0.91635 0.978;0.999 D 0.98494 1.0611 10 0.87932 D 0 . 17.4422 0.87568 0.0:1.0:0.0:0.0 . 60;103 E9PG30;P63267 .;ACTH_HUMAN L 60;103;103;103 ENSP00000386929:P60L;ENSP00000295137:P103L;ENSP00000410020:P103L;ENSP00000386857:P103L ENSP00000295137:P103L P + 2 0 ACTG2 73989360 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 7.651000 0.83577 2.724000 0.93272 0.462000 0.41574 CCC TCGA-HZ-8001-01A-11D-2201-08 ACTG2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328086.1 0 0 0 11 300 0 75 0 9.999084e-01 0 488 0 75 2 0 0 0 0 0 2 1 0.998440 11 301 0 75 2 0 0 0 0 75 2 -2.722986 1 1 0 0 1 1 2 3 2.032373 0 0.150000 1.920000 0.157582 0.500000 0.260000 1.000000 0.470000 0.554462 0.500000 0 3.600000e-01 7.300000e-01 PRR23B 389151 broad.mit.edu 37 3 138738751 138738751 + Silent SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr3:138738751C>T ENST00000329447.5 - 1 1017 c.753G>A c.(751-753)ccG>ccA p.P251P MRPS22_ENST00000495075.1_Intron NM_001013650.2 NP_001013672.1 Q6ZRT6 PR23B_HUMAN proline rich 23B 29 GAGGGCGTTCCGGGAGCGGCG 0.667000 0 SO:0001819 synonymous_variant ENST00000329447.5 1 1 hg19 CCDS33868.1 TCGA-HZ-8001-01A-11D-2201-08 PRR23B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000361501.1 1 0 0 14 223 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 0.999150 13 181 0 44 2 0 0 0 0 56 2 -3.020362 1 1 121012 1 36 1 0 0 0 1.963010 0 0.150000 1.920000 0.125064 0.760000 0.440000 1.000000 1.000000 0.771772 0.760000 0 5.800000e-01 9.700000e-01 ATR 545 broad.mit.edu 37 3 142185227 142185227 + Missense_Mutation SNP T T G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr3:142185227T>G ENST00000350721.4 - 40 6957 c.6836A>C c.(6835-6837)aAc>aCc p.N2279T RP11-383G6.3_ENST00000460977.1_RNA|ATR_ENST00000383101.3_Missense_Mutation_p.N2215T NM_001184.3 NP_001175.2 Q13535 ATR_HUMAN ATR serine/threonine kinase 122 GCTAGCATGGTTAGCATGGGT 0.368000 Other conserved DNA damage response genes 0 SO:0001583 missense ENST00000350721.4 1 1 hg19 CCDS3124.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 17.29|17.29 3.351061|3.351061 0.61183|0.61183 .|. .|. ENSG00000175054|ENSG00000175054 ENST00000350721;ENST00000383101|ENST00000513291 T;T|. 0.80566|. -1.39;-1.39|. 5.43|5.43 5.43|5.43 0.79202|0.79202 Protein kinase-like domain (1);|. 0.188475|. 0.31199|. U|. 0.008062|. T|. 0.58652|. 0.2137|. L|L 0.38175|0.38175 1.15|1.15 0.50039|0.50039 D|D 0.999842|0.999842 B|. 0.19445|. 0.036|. B|. 0.12837|. 0.008|. T|. 0.55509|. -0.8130|. 10|. 0.21540|. T|. 0.41|. -3.5943|-3.5943 15.4542|15.4542 0.75299|0.75299 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. 2279|. Q13535|. ATR_HUMAN|. T|Y 2279;2215|125 ENSP00000343741:N2279T;ENSP00000372581:N2215T|. ENSP00000343741:N2279T|. N|X -|- 2|3 0|2 ATR|ATR 143667917|143667917 1.000000|1.000000 0.71417|0.71417 0.996000|0.996000 0.52242|0.52242 0.969000|0.969000 0.65631|0.65631 7.965000|7.965000 0.87945|0.87945 2.055000|2.055000 0.61198|0.61198 0.477000|0.477000 0.44152|0.44152 AAC|TAA TCGA-HZ-8001-01A-11D-2201-08 ATR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353995.2 1 0 1 45 401 0 81 1 9.303734e-01 2 40 0 81 2 0 0 0 0 0 2 1 1.000000 45 397 0 80 2 0 0 0 0 81 2 -15.411920 1 1 0 0 1 0 0 0 1.963010 0 0.150000 1.920000 0.125064 0.990000 0.960000 1.000000 1.000000 0.997720 0.990000 1 9.900000e-01 1 MED12L 116931 broad.mit.edu 37 3 151129293 151129293 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr3:151129293G>A ENST00000474524.1 + 39 6071 c.6033G>A c.(6031-6033)caG>caA p.Q2011Q MED12L_ENST00000273432.4_Intron NM_053002.4 NP_443728.3 Q86YW9 MD12L_HUMAN mediator complex subunit 12-like 128 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) CTGGCTCTCAGAGGTGATACA 0.478000 0 SO:0001819 synonymous_variant ENST00000474524.1 1 1 hg19 CCDS33876.1 TCGA-HZ-8001-01A-11D-2201-08 MED12L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357707.2 1 0 0 37 399 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1.000000 38 388 0 65 2 0 0 0 0 69 2 -3.318794 1 1 0 0 1 0 0 0 1.963010 0 0.150000 1.920000 0.125064 0.990000 0.780000 1.000000 1.000000 0.973822 0.990000 1 9.300000e-01 1 SFRP2 6423 broad.mit.edu 37 4 154709592 154709592 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:154709592G>A ENST00000274063.4 - 1 680 c.396C>T c.(394-396)ttC>ttT p.F132F NM_003013.2 NP_003004.1 Q96HF1 SFRP2_HUMAN secreted frizzled-related protein 2 16 all_hematologic(180;0.093) Renal(120;0.117) AGGGGAAGCCGAAGGCGGACA 0.662000 0 SO:0001819 synonymous_variant ENST00000274063.4 1 1 hg19 CCDS34082.1 TCGA-HZ-8001-01A-11D-2201-08 SFRP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365296.1 0 0 0 29 682 0 113 1 1 3 7880 0 113 2 0 0 0 0 0 2 1 1.000000 29 671 0 108 2 0 0 0 0 113 2 -20.000000 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.570000 0.380000 1.000000 0.550000 0.631201 0.570000 0 4.700000e-01 8.300000e-01 PGM2 55276 broad.mit.edu 37 4 37863199 37863199 + Missense_Mutation SNP C C A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:37863199C>A ENST00000381967.4 + 14 1905 c.1805C>A c.(1804-1806)cCa>cAa p.P602Q PGM2_ENST00000537241.1_Missense_Mutation_p.P442Q NM_018290.3 NP_060760.2 Q96G03 PGM2_HUMAN phosphoglucomutase 2 19 TTTTTCCAGCCACAGAAGTAC 0.403000 0 SO:0001583 missense ENST00000381967.4 1 1 hg19 CCDS3443.1 . . . . . . . . . . C 32 5.182832 0.94885 . . ENSG00000169299 ENST00000381967;ENST00000537241 T;T 0.47177 0.85;1.71 6.14 6.14 0.99180 . 0.047041 0.85682 D 0.000000 T 0.77579 0.4151 M 0.91561 3.22 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 T 0.80692 -0.1269 10 0.87932 D 0 -14.225 20.8597 0.99761 0.0:1.0:0.0:0.0 . 602 Q96G03 PGM2_HUMAN Q 602;442 ENSP00000371393:P602Q;ENSP00000437342:P442Q ENSP00000371393:P602Q P + 2 0 PGM2 37539594 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 7.331000 0.79192 2.937000 0.99478 0.650000 0.86243 CCA TCGA-HZ-8001-01A-11D-2201-08 PGM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215079.2 1 0 1 56 619 0 146 1 9.971442e-01 19 79 0 146 2 0 0 0 0 0 2 1 1.000000 55 589 0 145 2 0 0 0 0 146 2 -2.920853 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.990000 0.860000 1.000000 1.000000 0.989236 0.990000 1 9.900000e-01 1 TLR6 10333 broad.mit.edu 37 4 38830874 38830874 + Missense_Mutation SNP A A G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:38830874A>G ENST00000381950.1 - 1 286 c.221T>C c.(220-222)tTt>tCt p.F74S TLR6_ENST00000436693.2_Missense_Mutation_p.F74S Q9Y2C9 TLR6_HUMAN toll-like receptor 6 22 CTCTGATAGAAAGCTCATGTC 0.378000 0 SO:0001583 missense ENST00000381950.1 1 1 hg19 CCDS3446.1 . . . . . . . . . . A 3.403 -0.121850 0.06838 . . ENSG00000174130 ENST00000436693;ENST00000381950;ENST00000508542;ENST00000508254;ENST00000514655 T;T;T;T 0.02140 4.43;4.43;4.43;4.43 5.55 -1.15 0.09709 . 0.635810 0.15748 N 0.246554 T 0.01061 0.0035 N 0.20483 0.58 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.47484 -0.9114 10 0.05620 T 0.96 . 0.4819 0.00549 0.2689:0.1258:0.2356:0.3697 . 74 Q9Y2C9 TLR6_HUMAN S 74 ENSP00000389600:F74S;ENSP00000371376:F74S;ENSP00000424718:F74S;ENSP00000423326:F74S ENSP00000371376:F74S F - 2 0 TLR6 38507269 0.270000 0.24152 0.480000 0.27341 0.606000 0.37113 0.320000 0.19540 0.034000 0.15491 0.459000 0.35465 TTT TCGA-HZ-8001-01A-11D-2201-08 TLR6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250431.1 1 0 0 21 265 0 74 0 6.079393e-03 0 2 0 74 2 0 0 0 0 0 2 1 0.999998 21 260 0 73 2 0 0 0 0 74 2 -20.000000 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.990000 0.650000 1.000000 1.000000 0.936667 0.990000 1 8.200000e-01 1 ZNF721 170960 broad.mit.edu 37 4 435583 435583 + Missense_Mutation SNP T T G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:435583T>G ENST00000338977.5 - 2 2685 c.2637A>C c.(2635-2637)aaA>aaC p.K879N ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Missense_Mutation_p.K891N Q8TF20 ZN721_HUMAN zinc finger protein 721 33 ACGTGTAGGGTTTCTCTCCAG 0.383000 0 SO:0001583 missense ENST00000338977.5 1 1 hg19 . . . . . . . . . . T 9.545 1.114493 0.20795 . . ENSG00000182903 ENST00000338977;ENST00000511833 T;T 0.26067 1.76;1.76 0.539 0.539 0.17156 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.44871 0.1314 M 0.85710 2.77 0.24306 N 0.995109 D;D;D 0.67145 0.996;0.996;0.995 P;P;P 0.60541 0.828;0.876;0.804 T 0.21793 -1.0235 9 0.62326 D 0.03 . 5.2995 0.15770 0.0:1.0E-4:0.0:0.9999 . 879;891;891 Q8TF20;D9N162;Q8TF20-2 ZN721_HUMAN;.;. N 879;891 ENSP00000340524:K879N;ENSP00000428878:K891N ENSP00000340524:K879N K - 3 2 ZNF721 425583 0.275000 0.24201 0.151000 0.22473 0.126000 0.20510 -0.123000 0.10611 0.440000 0.26502 0.172000 0.16884 AAA TCGA-HZ-8001-01A-11D-2201-08 ZNF721-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000357939.1 0 0 0 8 179 0 33 0 2.208867e-02 0 5 0 33 2 0 0 0 0 0 2 1 0.988901 8 175 0 33 2 0 0 0 0 33 2 -3.861498 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.640000 0.290000 1.000000 1.000000 0.678668 0.640000 0 4.400000e-01 1 C4orf40 0 broad.mit.edu 37 4 71024100 71024100 + Missense_Mutation SNP T T C TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:71024100T>C ENST00000344526.5 + 3 320 c.131T>C c.(130-132)aTa>aCa p.I44T C4orf40_ENST00000502441.2_Intron|C4orf40_ENST00000502294.1_Missense_Mutation_p.I44T NM_214711.3 NP_999876.2 Q6MZM9 PRR27_HUMAN 12 CCTTATGGCATACGGAATTTA 0.438000 0 SO:0001583 missense ENST00000344526.5 1 1 hg19 CCDS3535.1 . . . . . . . . . . T 9.190 1.025685 0.19512 . . ENSG00000187533 ENST00000502294;ENST00000344526 T;T 0.34472 1.36;1.36 1.85 -2.75 0.05914 . . . . . T 0.21022 0.0506 N 0.14661 0.345 0.09310 N 1 P 0.41041 0.736 P 0.47251 0.542 T 0.18366 -1.0339 9 0.08837 T 0.75 2.5581 5.9415 0.19196 0.0:0.5263:0.0:0.4737 . 44 Q6MZM9 CD040_HUMAN T 44 ENSP00000426249:I44T;ENSP00000343172:I44T ENSP00000343172:I44T I + 2 0 C4orf40 71058689 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -2.906000 0.00701 -0.643000 0.05473 -0.363000 0.07495 ATA TCGA-HZ-8001-01A-11D-2201-08 C4orf40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251558.1 1 0 0 49 849 0 161 0 0 0 0 161 2 0 0 0 0 0 2 1 1.000000 48 832 0 161 2 0 0 0 0 161 2 -7.786283 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.760000 0.550000 1.000000 0.740000 0.785400 0.760000 0 6.500000e-01 1 ENAM 10117 broad.mit.edu 37 4 71510452 71510452 + Silent SNP A A G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:71510452A>G ENST00000396073.3 + 9 3590 c.3309A>G c.(3307-3309)gaA>gaG p.E1103E ENAM_ENST00000472903.1_Intron NM_031889.2 NP_114095.2 Q9NRM1 ENAM_HUMAN enamelin 6 Lung(101;0.235) CTACTGAGGAACAATTTAAGA 0.428000 0 SO:0001819 synonymous_variant ENST00000396073.3 1 1 hg19 CCDS3544.2 TCGA-HZ-8001-01A-11D-2201-08 ENAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252166.3 1 0 0 42 421 0 82 0 8.731367e-03 0 2 0 82 2 0 0 0 0 0 2 1 1.000000 41 415 0 82 2 0 0 0 0 82 2 -12.612160 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.990000 0.910000 1.000000 1.000000 0.994900 0.990000 1 9.900000e-01 1 HELQ 113510 broad.mit.edu 37 4 84375061 84375061 + Missense_Mutation SNP T T C TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr4:84375061T>C ENST00000295488.3 - 2 497 c.335A>G c.(334-336)gAt>gGt p.D112G MRPS18C_ENST00000507349.1_5'Flank|MRPS18C_ENST00000295491.4_5'Flank|HELQ_ENST00000510985.1_Missense_Mutation_p.D112G|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000440639.2_5'UTR NM_133636.2 NP_598375 Q8TDG4 HELQ_HUMAN helicase, POLQ-like 38 AGTAAAGCTATCATAGTCACC 0.378000 Other identified genes with known or suspected DNA repair function 0 SO:0001583 missense ENST00000295488.3 1 1 hg19 CCDS3603.1 . . . . . . . . . . T 25.4 4.634374 0.87660 . . ENSG00000163312 ENST00000295488;ENST00000510985 T;T 0.75367 -0.37;-0.93 5.13 5.13 0.70059 . 0.062767 0.64402 D 0.000015 D 0.83982 0.5372 M 0.61703 1.905 0.47476 D 0.999433 D;D;D;D 0.89917 0.994;0.999;1.0;0.982 P;P;D;P 0.79108 0.759;0.846;0.992;0.661 D 0.85759 0.1348 10 0.72032 D 0.01 -26.4433 15.1068 0.72326 0.0:0.0:0.0:1.0 . 112;112;75;112 E3W980;E3W982;Q8TDG4-2;Q8TDG4 .;.;.;HELQ_HUMAN G 112 ENSP00000295488:D112G;ENSP00000424539:D112G ENSP00000295488:D112G D - 2 0 HELQ 84594085 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 4.946000 0.63576 2.149000 0.67028 0.533000 0.62120 GAT TCGA-HZ-8001-01A-11D-2201-08 HELQ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252810.1 1 0 0 42 775 0 193 1 3.791377e-01 2 23 0 193 2 0 0 0 0 0 2 1 1.000000 40 757 0 192 2 0 0 0 0 193 2 -6.502885 1 1 0 0 1 1 2 3 2.055290 0 0.150000 1.920000 0.162562 0.720000 0.510000 1.000000 0.700000 0.750434 0.720000 0 6.000000e-01 9.700000e-01 FBN2 2201 broad.mit.edu 37 5 127866347 127866347 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr5:127866347C>T ENST00000508053.1 - 9 1351 c.377G>A c.(376-378)cGt>cAt p.R126H FBN2_ENST00000262464.4_Missense_Mutation_p.R126H|FBN2_ENST00000508989.1_Intron P35556 FBN2_HUMAN fibrillin 2 197 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) CATGTTAGGACGGGAACAAAA 0.338000 0 SO:0001583 missense ENST00000508053.1 1 1 hg19 CCDS34222.1 . . . . . . . . . . C 19.45 3.829221 0.71258 . . ENSG00000138829 ENST00000262464;ENST00000508053;ENST00000502468 D;D;T 0.85773 -2.03;-2.03;0.12 4.59 3.71 0.42584 . 0.000000 0.64402 D 0.000003 D 0.91102 0.7199 M 0.72118 2.19 0.53005 D 0.999961 D;D 0.89917 1.0;0.995 D;P 0.83275 0.996;0.719 D 0.91917 0.5544 10 0.59425 D 0.04 . 14.6579 0.68847 0.1472:0.8528:0.0:0.0 . 126;126 E9PHW4;P35556 .;FBN2_HUMAN H 126 ENSP00000262464:R126H;ENSP00000424571:R126H;ENSP00000424753:R126H ENSP00000262464:R126H R - 2 0 FBN2 127894246 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.243000 0.78219 1.511000 0.48818 0.655000 0.94253 CGT TCGA-HZ-8001-01A-11D-2201-08 FBN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371618.2 1 0 0 25 309 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 25 305 0 58 2 0 0 0 0 58 2 -8.106028 1 1 121410 14 42 1 1 2 3 2.051179 0 0.150000 1.920000 0.161322 0.990000 0.680000 1.000000 1.000000 0.946249 0.990000 1 8.500000e-01 1 SIM1 6492 broad.mit.edu 37 6 100896021 100896021 + Splice_Site SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr6:100896021C>T ENST00000369208.3 - 8 1633 c.e8+1 SIM1_ENST00000262901.4_Splice_Site P81133 SIM1_HUMAN single-minded family bHLH transcription factor 1 79 all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13) TGGCGCCTTACGCAAATGGTG 0.617000 0 SO:0001630 splice_region_variant ENST00000369208.3 0 1 hg19 CCDS5045.1 . . . . . . . . . . C 11.44 1.640537 0.29157 . . ENSG00000112246 ENST00000369208;ENST00000262901 . . . 5.19 4.31 0.51392 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.0421 0.71799 0.1433:0.8567:0.0:0.0 . . . . . -1 . . . - . . SIM1 101002742 1.000000 0.71417 0.989000 0.46669 0.001000 0.01503 7.487000 0.81328 1.163000 0.42636 -0.181000 0.13052 . TCGA-HZ-8001-01A-11D-2201-08 SIM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041628.3 0 0 0 5 95 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 0.937534 5 94 0 31 2 0 0 0 0 31 2 -8.754000 1 1 0 0 1 0 1 1 1.875206 1 0.150000 1.920000 0.081081 0.580000 0.230000 0.950000 0.560000 0.599108 0.580000 0 3.800000e-01 8.100000e-01 MDGA1 266727 broad.mit.edu 37 6 37631799 37631799 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr6:37631799G>A ENST00000434837.3 - 2 1329 c.151C>T c.(151-153)Cgg>Tgg p.R51W MDGA1_ENST00000297153.7_Missense_Mutation_p.R51W|MDGA1_ENST00000505425.1_Missense_Mutation_p.R51W NM_153487.3 NP_705691.1 Q8NFP4 MDGA1_HUMAN MAM domain containing glycosylphosphatidylinositol anchor 1 38 TCCCCCTCCCGGATGGTGTAG 0.637000 0 SO:0001583 missense ENST00000434837.3 1 1 hg19 CCDS47417.1 . . . . . . . . . . G 20.1 3.935517 0.73442 . . ENSG00000112139 ENST00000434837;ENST00000297153;ENST00000505425 T;T;T 0.49432 0.78;0.78;0.78 5.25 3.45 0.39498 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.160511 0.28796 N 0.014104 T 0.55273 0.1910 M 0.79258 2.445 0.46725 D 0.999177 D 0.89917 1.0 D 0.73380 0.98 T 0.59279 -0.7484 10 0.56958 D 0.05 . 9.6088 0.39650 0.0745:0.0:0.7847:0.1408 . 51 Q8NFP4 MDGA1_HUMAN W 51 ENSP00000402584:R51W;ENSP00000297153:R51W;ENSP00000422042:R51W ENSP00000297153:R51W R - 1 2 MDGA1 37739777 1.000000 0.71417 1.000000 0.80357 0.743000 0.42351 4.461000 0.60115 0.587000 0.29643 -0.150000 0.13652 CGG TCGA-HZ-8001-01A-11D-2201-08 MDGA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040419.3 1 0 0 48 430 0 81 0 1.558782e-01 1 6 0 81 2 0 0 0 0 0 2 1 1.000000 48 423 0 78 2 0 0 0 0 81 2 -2.806910 1 1 121096 2 36 1 0 1 1 1.875206 1 0.150000 1.920000 0.081081 0.940000 0.790000 1.000000 0.990000 0.940224 0.940000 1 8.800000e-01 9.900000e-01 RELN 5649 broad.mit.edu 37 7 103124188 103124188 + Missense_Mutation SNP C C T rs115035120 by1000genomes TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr7:103124188C>T ENST00000428762.1 - 62 10252 c.10093G>A c.(10093-10095)Gtc>Atc p.V3365I RN7SKP86_ENST00000410454.1_RNA|RELN_ENST00000473945.1_5'UTR|RELN_ENST00000424685.2_Missense_Mutation_p.V3365I|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000343529.5_Missense_Mutation_p.V3365I NM_005045.3 NP_005036.2 P78509 RELN_HUMAN reelin p.V3365I(1) 227 CCGTTGTTGACGCTGTATTGC 0.552000 NSCLC(146;835 1944 15585 22231 52158) 1 Substitution - Missense(1) SO:0001583 missense ENST00000428762.1 1 1 hg19 CCDS47680.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 13.12 2.142400 0.37825 0.0 9.3E-4 ENSG00000189056 ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171 T;T;T 0.21932 1.98;1.98;1.98 5.87 3.1 0.35709 . 0.145479 0.45606 N 0.000351 T 0.28400 0.0702 L 0.43152 1.355 0.39557 D 0.969078 B;D 0.67145 0.347;0.996 B;P 0.60415 0.054;0.874 T 0.03597 -1.1021 10 0.22706 T 0.39 . 8.8648 0.35280 0.1229:0.7486:0.0:0.1285 . 3365;3365 P78509-2;P78509 .;RELN_HUMAN I 3365;3365;3365;882;3365 ENSP00000392423:V3365I;ENSP00000345694:V3365I;ENSP00000388446:V3365I ENSP00000345694:V3365I V - 1 0 RELN 102911424 0.747000 0.28283 0.782000 0.31804 0.737000 0.42083 1.384000 0.34396 0.393000 0.25203 0.655000 0.94253 GTC TCGA-HZ-8001-01A-11D-2201-08 RELN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000348148.1 1 0 0 54 908 0 161 0 2.937466e-02 0 5 0 161 2 0 0 0 0 0 2 1 1.000000 52 893 0 160 2 0 0 0 0 161 2 -8.041069 1 1 121412 112 54 1 0.150000 1.920000 0 0 NUP205 23165 broad.mit.edu 37 7 135258466 135258466 + Missense_Mutation SNP G G T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr7:135258466G>T ENST00000285968.6 + 3 262 c.236G>T c.(235-237)gGt>gTt p.G79V NUP205_ENST00000440390.2_5'UTR|NUP205_ENST00000489493.1_3'UTR NM_015135.2 NP_055950 Q92621 NU205_HUMAN nucleoporin 205kDa 93 GCCATTCAGGGTCAACAGGGA 0.398000 0 SO:0001583 missense ENST00000285968.6 1 1 hg19 CCDS34759.1 . . . . . . . . . . G 26.3 4.726728 0.89298 . . ENSG00000155561 ENST00000285968 T 0.33438 1.41 5.1 5.1 0.69264 . 0.096661 0.64402 D 0.000001 T 0.57125 0.2032 M 0.75615 2.305 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.56129 -0.8030 10 0.37606 T 0.19 1.6054 18.4985 0.90874 0.0:0.0:1.0:0.0 . 79 Q92621 NU205_HUMAN V 79 ENSP00000285968:G79V ENSP00000285968:G79V G + 2 0 NUP205 134909006 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 9.571000 0.98176 2.373000 0.80994 0.484000 0.47621 GGT TCGA-HZ-8001-01A-11D-2201-08 NUP205-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340358.1 0 0 0 11 334 0 69 0 3.771939e-03 0 3 0 69 2 0 0 0 0 0 2 1 0.998292 11 330 0 69 2 0 0 0 0 69 2 -3.682763 1 1 0 0 1 0 1 1 2.004344 0 0.150000 1.920000 0.144869 0.430000 0.220000 0.710000 0.420000 0.450490 0.430000 0 3.100000e-01 5.700000e-01 RP1L1 94137 broad.mit.edu 37 8 10468915 10468915 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr8:10468915G>A ENST00000382483.3 - 4 2916 c.2693C>T c.(2692-2694)aCg>aTg p.T898M NM_178857.5 NP_849188.4 Q8IWN7 RP1L1_HUMAN retinitis pigmentosa 1-like 1 148 TGGGGACGGCGTGGGGCCTGG 0.701000 0 SO:0001583 missense ENST00000382483.3 0 1 hg19 CCDS43708.1 . . . . . . . . . . G 13.91 2.378486 0.42207 . . ENSG00000183638 ENST00000382483 T 0.04317 3.65 4.18 -1.81 0.07882 . . . . . T 0.01905 0.0060 N 0.14661 0.345 0.09310 N 1 P 0.39737 0.685 B 0.28011 0.085 T 0.41556 -0.9502 9 0.44086 T 0.13 4.6758 1.1406 0.01765 0.4403:0.1562:0.245:0.1585 . 898 A6NKC6 . M 898 ENSP00000371923:T898M ENSP00000371923:T898M T - 2 0 RP1L1 10506325 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.564000 0.05936 -0.265000 0.09352 -0.379000 0.06801 ACG TCGA-HZ-8001-01A-11D-2201-08 RP1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375673.1 0 0 0 4 72 0 9 0 0 0 0 9 2 0 0 0 0 0 2 1 0.889105 4 71 0 9 2 0 0 0 0 9 2 -8.095815 1 1 0 0 1 1 2 3 2.045816 0 0.150000 1.920000 0.160701 0.820000 0.270000 1.000000 1.000000 0.773359 0.820000 0 4.900000e-01 1 CRB2 286204 broad.mit.edu 37 9 126129592 126129592 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr9:126129592G>A ENST00000373631.3 + 5 897 c.896G>A c.(895-897)cGc>cAc p.R299H CRB2_ENST00000359999.3_Missense_Mutation_p.R299H|CRB2_ENST00000373629.2_5'Flank NM_173689.5 NP_775960.4 Q5IJ48 CRUM2_HUMAN crumbs family member 2 23 TTCAGCTTCCGCCATGCTGCG 0.687000 0 SO:0001583 missense ENST00000373631.3 1 1 hg19 CCDS6852.2 . . . . . . . . . . G 11.90 1.777241 0.31411 . . ENSG00000148204 ENST00000359999;ENST00000373631 D;D 0.91843 -2.92;-2.92 5.1 -0.0543 0.13814 Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1); 0.652576 0.13569 N 0.378198 T 0.81809 0.4901 N 0.19112 0.55 0.09310 N 1 B;B 0.26635 0.096;0.155 B;B 0.19148 0.006;0.024 T 0.69749 -0.5061 10 0.45353 T 0.12 . 5.2636 0.15588 0.3333:0.1413:0.5254:0.0 . 299;299 Q5IJ48;Q5IJ48-2 CRUM2_HUMAN;. H 299 ENSP00000353092:R299H;ENSP00000362734:R299H ENSP00000353092:R299H R + 2 0 CRB2 125169413 0.000000 0.05858 0.103000 0.21229 0.020000 0.10135 0.113000 0.15499 -0.055000 0.13244 -0.777000 0.03380 CGC TCGA-HZ-8001-01A-11D-2201-08 CRB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053990.3 1 0 0 12 223 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 0.999073 12 218 0 65 2 0 0 0 0 67 2 -3.330730 1 1 121282 2 35 1 0 0 0 1.946438 0 0.150000 1.920000 0.116883 0.650000 0.360000 1.000000 1.000000 0.676120 0.650000 0 4.900000e-01 8.500000e-01 STXBP1 6812 broad.mit.edu 37 9 130442473 130442473 + Missense_Mutation SNP C C G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr9:130442473C>G ENST00000373299.1 + 17 1614 c.1499C>G c.(1498-1500)cCt>cGt p.P500R STXBP1_ENST00000373302.3_Missense_Mutation_p.P500R|STXBP1_ENST00000481942.1_Intron NM_001032221.3 NP_001027392.1 P61764 STXB1_HUMAN syntaxin binding protein 1 23 AAACACTACCCTTATATCTCT 0.488000 0 SO:0001583 missense ENST00000373299.1 1 1 hg19 CCDS35146.1 . . . . . . . . . . C 18.34 3.601542 0.66445 . . ENSG00000136854 ENST00000535154;ENST00000373302;ENST00000541198;ENST00000373299 T;T 0.78481 -1.18;-1.18 5.64 5.64 0.86602 . 0.000000 0.85682 D 0.000000 D 0.92024 0.7473 H 0.96301 3.8 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.79784 0.992;0.993 D 0.93931 0.7214 10 0.87932 D 0 -5.0024 17.5557 0.87889 0.0:1.0:0.0:0.0 . 500;500 P61764;P61764-2 STXB1_HUMAN;. R 454;500;332;500 ENSP00000362399:P500R;ENSP00000362396:P500R ENSP00000362396:P500R P + 2 0 STXBP1 129482294 1.000000 0.71417 0.999000 0.59377 0.217000 0.24651 7.648000 0.83479 2.826000 0.97356 0.561000 0.74099 CCT TCGA-HZ-8001-01A-11D-2201-08 STXBP1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054229.1 1 0 0 66 735 0 142 0 9.409564e-01 0 54 0 142 2 0 0 0 0 0 2 1 1.000000 65 723 0 142 2 0 0 0 0 142 2 -3.017764 1 1 0 0 1 0 0 0 1.946438 0 0.150000 1.920000 0.116883 0.990000 0.820000 1.000000 1.000000 0.975945 0.990000 1 9.300000e-01 1 PNPLA7 375775 broad.mit.edu 37 9 140357967 140357967 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr9:140357967G>A ENST00000277531.4 - 28 3354 c.3168C>T c.(3166-3168)taC>taT p.Y1056Y PNPLA7_ENST00000371457.1_Silent_p.Y662Y|PNPLA7_ENST00000406427.1_Silent_p.Y1081Y|PNPLA7_ENST00000492278.1_5'UTR NM_152286.3 NP_689499.3 Q6ZV29 PLPL7_HUMAN patatin-like phospholipase domain containing 7 40 all_cancers(76;0.126) TGGCACGCACGTACCACCACA 0.657000 0 SO:0001819 synonymous_variant ENST00000277531.4 0 1 hg19 CCDS7045.1 TCGA-HZ-8001-01A-11D-2201-08 PNPLA7-007 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000254787.1 0 0 0 3 33 0 9 0 6.486631e-01 0 24 0 9 2 0 0 0 0 0 2 1 0.812676 3 33 0 9 2 0 0 0 0 9 2 -7.971221 1 1 119426 5 30 1 0 0 0 1.946438 0 0.150000 1.920000 0.116883 0.920000 0.300000 1.000000 1.000000 0.824929 0.920000 1 5.600000e-01 1 RECK 8434 broad.mit.edu 37 9 36058869 36058869 + Nonsense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr9:36058869C>T ENST00000377966.3 + 3 771 c.205C>T c.(205-207)Cga>Tga p.R69* RECK_ENST00000479053.1_3'UTR NM_021111.2 NP_066934.1 O95980 RECK_HUMAN reversion-inducing-cysteine-rich protein with kazal motifs 32 LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228) TCTGTTGCAGCGAGCCCCAGA 0.333000 0 SO:0001587 stop_gained ENST00000377966.3 0 1 hg19 CCDS6597.1 . . . . . . . . . . C 41 8.818781 0.98966 . . ENSG00000122707 ENST00000377966 . . . 5.75 2.47 0.30058 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -10.11 13.1884 0.59695 0.5131:0.4869:0.0:0.0 . . . . X 69 . ENSP00000367202:R69X R + 1 2 RECK 36048869 1.000000 0.71417 0.999000 0.59377 0.993000 0.82548 1.024000 0.30077 0.720000 0.32209 0.491000 0.48974 CGA TCGA-HZ-8001-01A-11D-2201-08 RECK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052409.1 1 0 1 35 225 0 52 0 7.467936e-01 0 19 0 52 2 0 0 0 0 0 2 1 1.000000 34 217 0 51 2 0 0 0 0 52 2 -3.223439 1 1 0 0 1 0 2 2 1.956826 1 0.150000 1.920000 0.150000 0.990000 0.990000 1.000000 1.000000 0.999972 0.990000 1 9.900000e-01 1 PTPRD 5789 broad.mit.edu 37 9 8492935 8492935 + Silent SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chr9:8492935G>A ENST00000381196.4 - 24 2937 c.2394C>T c.(2392-2394)ctC>ctT p.L798L PTPRD_ENST00000360074.4_Silent_p.L785L|PTPRD_ENST00000358503.5_Silent_p.L776L|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000356435.5_Silent_p.L798L|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000540109.1_Silent_p.L798L|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000486161.1_Intron NM_002839.3 NP_002830.1 P23468 PTPRD_HUMAN protein tyrosine phosphatase, receptor type, D 168 all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824) CTGTGACGGTGAGGGAGTAGG 0.493000 TSP Lung(15;0.13) 0 SO:0001819 synonymous_variant ENST00000381196.4 1 1 hg19 CCDS43786.1 TCGA-HZ-8001-01A-11D-2201-08 PTPRD-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055395.3 1 0 1 76 633 0 127 0 0 0 0 127 2 0 0 0 0 0 2 1 1.000000 75 623 0 125 2 0 0 0 0 127 2 -19.999850 1 1 0 0 1 0 2 2 1.956826 1 0.150000 1.920000 0.150000 0.990000 0.990000 1.000000 1.000000 0.999965 0.990000 1 9.900000e-01 1 NRK 203447 broad.mit.edu 37 X 105153065 105153065 + Missense_Mutation SNP C C T TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chrX:105153065C>T ENST00000243300.9 + 13 1735 c.1432C>T c.(1432-1434)Ctc>Ttc p.L478F NRK_ENST00000428173.2_Missense_Mutation_p.L479F NM_198465.2 NP_940867.2 Q7Z2Y5 NRK_HUMAN Nik related kinase 76 AGCCAGGGTGCTCATGCCACT 0.547000 HNSCC(51;0.14) 0 SO:0001583 missense ENST00000243300.9 1 1 hg19 . . . . . . . . . . C 9.268 1.045033 0.19748 . . ENSG00000123572 ENST00000243300;ENST00000428173 T;T 0.19105 2.17;2.17 4.49 -1.28 0.09318 . 0.656459 0.13499 N 0.383421 T 0.12518 0.0304 L 0.31065 0.9 0.19575 N 0.999962 B;B 0.09022 0.002;0.001 B;B 0.11329 0.006;0.001 T 0.20739 -1.0266 10 0.54805 T 0.06 . 4.6589 0.12632 0.148:0.3881:0.0:0.4639 . 146;478 Q7Z2Y5-2;Q7Z2Y5 .;NRK_HUMAN F 478;479 ENSP00000434830:L478F;ENSP00000438378:L479F ENSP00000434830:L478F L + 1 0 NRK 105039721 0.208000 0.23494 0.026000 0.17262 0.093000 0.18481 -0.620000 0.05565 -0.437000 0.07243 -0.380000 0.06706 CTC TCGA-HZ-8001-01A-11D-2201-08 NRK-001 KNOWN non_canonical_conserved|basic|appris_candidate protein_coding protein_coding OTTHUMT00000106480.6 1 0 1 42 141 0 25 0 0 0 1 0 25 2 0 0 0 0 0 2 1 1.000000 42 141 0 25 2 0 0 0 0 25 2 -20.000000 1 1 120988 3 33 1 0 1 1 0.150000 1.920000 0.150000 0.960000 0.830000 1.000000 0.990000 0.956337 0.960000 1 9.100000e-01 1 MECP2 4204 broad.mit.edu 37 X 153297998 153297998 + Missense_Mutation SNP A A G TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chrX:153297998A>G ENST00000303391.6 - 3 286 c.37T>C c.(37-39)Tca>Cca p.S13P MECP2_ENST00000453960.2_Missense_Mutation_p.S25P|MECP2_ENST00000407218.1_Missense_Mutation_p.S13P|MECP2_ENST00000460227.1_5'UTR NM_004992.3 NP_004983.1 P51608 MECP2_HUMAN methyl CpG binding protein 2 23 all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) TGGTCTTCTGACTTTTCTTCC 0.473000 0 SO:0001583 missense ENST00000303391.6 0 1 hg19 CCDS14741.1 . . . . . . . . . . A 18.80 3.701581 0.68501 . . ENSG00000169057 ENST00000303391;ENST00000545451;ENST00000453960;ENST00000369964;ENST00000407218;ENST00000415944 D;D;D;D 0.98221 -2.86;-2.82;-4.8;-2.33 5.65 5.65 0.86999 . 0.237548 0.35235 N 0.003354 D 0.97414 0.9154 L 0.27053 0.805 0.38439 D 0.946649 D;D 0.69078 0.997;0.995 P;P 0.60949 0.881;0.763 D 0.98968 1.0800 10 0.52906 T 0.07 -7.5146 13.811 0.63264 1.0:0.0:0.0:0.0 . 25;13 P51608-2;P51608 .;MECP2_HUMAN P 13;13;25;13;13;13 ENSP00000301948:S13P;ENSP00000395535:S25P;ENSP00000384865:S13P;ENSP00000416267:S13P ENSP00000301948:S13P S - 1 0 MECP2 152951192 0.998000 0.40836 1.000000 0.80357 0.996000 0.88848 1.596000 0.36718 1.907000 0.55213 0.430000 0.28490 TCA TCGA-HZ-8001-01A-11D-2201-08 MECP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000061144.1 0 0 0 9 370 0 58 0 3.359203e-01 0 45 0 58 2 0 0 0 0 0 2 1 0.993618 8 361 0 57 2 0 0 0 0 58 2 -8.953115 1 1 0 0 1 0 1 1 0.150000 1.920000 0.150000 0.160000 0.070000 0.280000 0.160000 0.172362 0.160000 0 1.100000e-01 2.200000e-01 P2RY8 286530 broad.mit.edu 37 X 1584907 1584907 + Missense_Mutation SNP G G A TCGA-HZ-8001-01A-11D-2201-08 TCGA-HZ-8001-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx a2dfddac-7a27-4b29-b730-d155fac52da4 b31ec204-dc5d-4b68-9139-6b928429f1e7 g.chrX:1584907G>A ENST00000381297.4 - 2 755 c.545C>T c.(544-546)aCg>aTg p.T182M P2RY8_ENST00000460672.1_5'Flank NM_178129.4 NP_835230.1 Q86VZ1 P2RY8_HUMAN purinergic receptor P2Y, G-protein coupled, 8 23 all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122) GGGGAGCATCGTCCACTTGAG 0.632000 T CRLF2 B-ALL, Downs associated ALL Dom yes X,Y Xp22.3; Yp11.3 286530 purinergic receptor P2Y, G-protein coupled, 8 L 0 SO:0001583 missense ENST00000381297.4 1 1 hg19 CCDS14115.1 . . . . . . . . . . g 6.863 0.528508 0.13127 . . ENSG00000182162 ENST00000381297 T 0.37235 1.21 2.41 -0.826 0.10805 GPCR, rhodopsin-like superfamily (1); 0.698644 0.12787 U 0.439216 T 0.29158 0.0725 L 0.43923 1.385 0.09310 N 1 D 0.53885 0.963 P 0.45138 0.471 T 0.16748 -1.0392 10 0.49607 T 0.09 . 6.573 0.22549 0.0:0.2502:0.5237:0.2261 . 182 Q86VZ1 P2RY8_HUMAN M 182 ENSP00000370697:T182M ENSP00000370697:T182M T - 2 0 P2RY8 1544907 0.027000 0.19231 0.944000 0.38274 0.013000 0.08279 0.307000 0.19296 -0.018000 0.14079 0.279000 0.19357 ACG TCGA-HZ-8001-01A-11D-2201-08 P2RY8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055602.1 1 0 0 16 252 0 62 0 2.281943e-02 0 4 0 62 2 0 0 0 0 0 2 1 0.999931 15 248 0 62 2 0 0 0 0 62 2 -3.220975 1 1 0 0 1 0 1 1 0.150000 1.920000 0.150000 0.390000 0.230000 0.600000 0.390000 0.410908 0.390000 0 3.100000e-01 5.000000e-01