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 ARL5B 221079 broad.mit.edu 37 10 18961589 18961595 + Frame_Shift_Del DEL ACTAGCT ACTAGCT - TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:18961589_18961595delACTAGCT ENST00000377275.3 + 4 527_533 c.294_300delACTAGCT c.(292-300)cgactagctfs p.RLA98fs NM_178815.3 NP_848930.1 Q96KC2 ARL5B_HUMAN ADP-ribosylation factor-like 5B 2 ACAGGGAACGACTAGCTATTACAAAAG 0.309000 0 SO:0001589 frameshift_variant ENST00000377275.3 1 1 hg19 CCDS7131.1 TCGA-HZ-A49I-01A-12D-A26I-08 ARL5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047078.1 1 0 0 39 555 0 259 0 3.995909e-02 1 4 0 259 2 0 0 0 0 0 0 1 0.998148 60 568 4 259 20 -7.858647 1 1 0 0 1 0 1 1 2.049442 0 0.350000 1.860000 0.348861 0.370000 0.260000 0.490000 0.380000 0.381637 0.370000 0 0.310000 0.440000 MFHAS1 9258 broad.mit.edu 37 8 8749703 8749703 + Frame_Shift_Del DEL G G - TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr8:8749703delG ENST00000276282.6 - 1 1452 c.866delC c.(865-867)cctfs p.P289fs NM_004225.2 NP_004216.2 Q9Y4C4 MFHA1_HUMAN malignant fibrous histiocytoma amplified sequence 1 21 Hepatocellular(245;0.217) CAGCGCGGCAGGGAACTCCTC 0.627000 Melanoma(103;1201 2045 17515 28966) 0 SO:0001589 frameshift_variant ENST00000276282.6 1 0 hg19 CCDS34844.1 TCGA-HZ-A49I-01A-12D-A26I-08 MFHAS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374724.2 1 0 0 54 282 0 121 0 3.191968e-01 1 6 0 121 2 0 0 0 0 0 0 1 0.999983 64 278 4 122 22 -20.000000 1 1 0 0 1 1 2 3 2.059506 0 0.350000 1.860000 0.352267 0.920000 0.700000 1.000000 1.000000 0.909728 0.920000 1 0.800000 1.000000 OTUD6B 51633 broad.mit.edu 37 8 92097044 92097046 + In_Frame_Del DEL ATT ATT - TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr8:92097044_92097046delATT ENST00000285420.4 + 7 1019_1021 c.920_922delATT c.(919-924)cattat>cat p.Y308del OTUD6B_ENST00000404789.3_In_Frame_Del_p.Y177del NM_016023.3 NP_057107.3 Q8N6M0 OTU6B_HUMAN OTU domain containing 6B 11 BRCA - Breast invasive adenocarcinoma(11;0.0187) TTAGGAGAACATTATAATTCGGT 0.276000 0 SO:0001651 inframe_deletion ENST00000285420.4 0 1 hg19 CCDS6253.2 TCGA-HZ-A49I-01A-12D-A26I-08 OTUD6B-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000319968.1 1 0 0 15 90 0 33 0 2.833040e-01 0 7 0 33 2 0 0 0 0 0 0 1 0.999864 7 92 0 32 2 -10.055960 1 1 0 0 1 0 0 0 2.025635 0 0.350000 1.860000 0.340771 0.800000 0.480000 1.000000 1.000000 0.805918 0.800000 0 0.630000 1.000000 PSD 5662 broad.mit.edu 37 10 104173704 104173704 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:104173704C>T ENST00000020673.5 - 5 1901 c.1375G>A c.(1375-1377)Gcc>Acc p.A459T PSD_ENST00000492902.2_5'Flank|PSD_ENST00000406432.1_Missense_Mutation_p.A459T NM_001270966.1|NM_002779.4 NP_001257895.1|NP_002770.3 A5PKW4 PSD1_HUMAN pleckstrin and Sec7 domain containing 34 GCAAGTGGGGCGGGAGCTGGT 0.657000 0 SO:0001583 missense ENST00000020673.5 1 1 hg19 CCDS31272.1 . . . . . . . . . . C 15.49 2.847795 0.51164 . . ENSG00000059915 ENST00000020673;ENST00000541902;ENST00000406432 T;T 0.49720 0.77;0.77 4.78 4.78 0.61160 . 0.277670 0.29396 N 0.012273 T 0.31544 0.0800 L 0.27053 0.805 0.35766 D 0.820535 P 0.35551 0.509 B 0.20184 0.028 T 0.37314 -0.9711 10 0.19147 T 0.46 . 17.8792 0.88835 0.0:1.0:0.0:0.0 . 459 A5PKW4 PSD1_HUMAN T 459;362;459 ENSP00000020673:A459T;ENSP00000384830:A459T ENSP00000020673:A459T A - 1 0 PSD 104163694 1.000000 0.71417 0.995000 0.50966 0.271000 0.26615 5.034000 0.64152 2.224000 0.72417 0.555000 0.69702 GCC TCGA-HZ-A49I-01A-12D-A26I-08 PSD-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050041.2 1 0 1 75 329 0 193 1 2.364117e-01 3 2 0 193 2 0 0 0 0 0 2 1 1.000000 73 324 0 190 2 -3.267264 1 1 121408 3 32 1 0 1 1 2.049385 0 0.350000 1.860000 0.348861 0.990000 0.850000 1.000000 1.000000 0.981164 0.990000 1 0.940000 1.000000 CUBN 8029 broad.mit.edu 37 10 17026279 17026279 + Splice_Site SNP C C A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:17026279C>A ENST00000377833.4 - 30 4416 c.e30-1 NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CTCCATAGATCTAACATGGGA 0.473000 0 SO:0001630 splice_region_variant ENST00000377833.4 1 1 hg19 CCDS7113.1 . . . . . . . . . . C 18.09 3.547261 0.65311 . . ENSG00000107611 ENST00000377833 . . . 5.96 5.96 0.96718 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.4008 0.98991 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . CUBN 17066285 1.000000 0.71417 0.929000 0.37066 0.742000 0.42306 7.165000 0.77544 2.826000 0.97356 0.655000 0.94253 . TCGA-HZ-A49I-01A-12D-A26I-08 CUBN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047009.1 1 0 1 48 234 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1.000000 48 231 0 99 2 -20.000000 1 1 0 0 1 0 1 1 2.049442 0 0.350000 1.860000 0.348861 0.960000 0.730000 1.000000 1.000000 0.937154 0.960000 1 0.840000 1.000000 ARHGAP12 94134 broad.mit.edu 37 10 32143120 32143120 + Silent SNP T T C TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:32143120T>C ENST00000344936.2 - 5 1197 c.963A>G c.(961-963)gaA>gaG p.E321E ARHGAP12_ENST00000396144.4_Silent_p.E321E|ARHGAP12_ENST00000311380.4_Intron|ARHGAP12_ENST00000375250.5_Silent_p.E321E|ARHGAP12_ENST00000375245.4_Intron NM_001270697.1|NM_018287.6 NP_001257626.1|NP_060757.4 Q8IWW6 RHG12_HUMAN Rho GTPase activating protein 12 31 Prostate(175;0.0199) AGTAGTTTTCTTCCGATGAAA 0.348000 0 SO:0001819 synonymous_variant ENST00000344936.2 1 1 hg19 CCDS7170.1 TCGA-HZ-A49I-01A-12D-A26I-08 ARHGAP12-009 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000047465.1 1 0 0 73 298 0 76 0 9.347391e-01 1 20 0 76 2 0 0 0 0 0 2 1 1.000000 73 296 0 76 2 -20.000000 1 1 0 0 1 0 1 1 2.049442 0 0.350000 1.860000 0.348861 0.990000 0.890000 1.000000 1.000000 0.992313 0.990000 1 0.990000 1.000000 P4HA1 5033 broad.mit.edu 37 10 74806700 74806700 + Missense_Mutation SNP C C G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:74806700C>G ENST00000307116.2 - 8 1176 c.1060G>C c.(1060-1062)Gac>Cac p.D354H P4HA1_ENST00000440381.1_Missense_Mutation_p.D354H|P4HA1_ENST00000373008.2_Missense_Mutation_p.D354H|P4HA1_ENST00000412021.2_Missense_Mutation_p.D354H|P4HA1_ENST00000394890.2_Missense_Mutation_p.D354H|P4HA1_ENST00000263556.3_Missense_Mutation_p.D354H P13674 P4HA1_HUMAN prolyl 4-hydroxylase, alpha polypeptide I 15 Prostate(51;0.0198) Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126) TTTGCTAGGTCTTTGACGATT 0.328000 Colon(147;367 2405 2662 52127) 0 SO:0001583 missense ENST00000307116.2 1 1 hg19 . . . . . . . . . . C 16.17 3.047064 0.55110 . . ENSG00000122884 ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381 T;T;T;T;T;T 0.45668 0.9;0.9;0.9;0.9;0.9;0.89 5.94 5.94 0.96194 Prolyl 4-hydroxylase, alpha subunit (1); 0.204990 0.49916 D 0.000139 T 0.36082 0.0954 L 0.29908 0.895 0.44188 D 0.997006 B;P;P 0.41159 0.002;0.626;0.74 B;B;B 0.36534 0.006;0.227;0.227 T 0.18871 -1.0323 10 0.56958 D 0.05 -16.6435 20.369 0.98888 0.0:1.0:0.0:0.0 . 354;354;354 C9JL12;Q5VSQ6;P13674 .;.;P4HA1_HUMAN H 354 ENSP00000307318:D354H;ENSP00000362099:D354H;ENSP00000411688:D354H;ENSP00000378353:D354H;ENSP00000263556:D354H;ENSP00000414464:D354H ENSP00000263556:D354H D - 1 0 P4HA1 74476706 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.698000 0.61789 2.819000 0.97034 0.650000 0.86243 GAC TCGA-HZ-A49I-01A-12D-A26I-08 P4HA1-001 KNOWN basic protein_coding protein_coding OTTHUMT00000048601.1 0 0 0 17 672 0 187 1 6.968838e-01 2 94 0 187 2 0 0 0 0 0 2 1 0.999962 18 664 0 186 2 -3.263552 1 1 0 0 1 0 0 0 2.040865 0 0.350000 1.860000 0.347717 0.140000 0.080000 0.220000 0.140000 0.147927 0.140000 0 0.100000 0.180000 GRID1 2894 broad.mit.edu 37 10 87628834 87628834 + Missense_Mutation SNP G G A rs143353694 TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:87628834G>A ENST00000327946.7 - 6 969 c.884C>T c.(883-885)aCg>aTg p.T295M NM_017551.2 NP_060021.1 Q9ULK0 GRID1_HUMAN glutamate receptor, ionotropic, delta 1 106 GTTGTTCCTCGTGCATTTCTG 0.572000 Multiple Myeloma(13;0.14) 0 SO:0001583 missense ENST00000327946.7 1 1 hg19 CCDS31236.1 . . . . . . . . . . A 13.04 2.117851 0.37339 0.0 3.49E-4 ENSG00000182771 ENST00000327946 D 0.82526 -1.62 5.71 4.58 0.56647 Extracellular ligand-binding receptor (1); 0.283290 0.48286 N 0.000183 T 0.50769 0.1635 N 0.00436 -1.5 0.80722 D 1 B 0.06786 0.001 B 0.04013 0.001 T 0.44697 -0.9311 10 0.15066 T 0.55 . 8.8037 0.34925 0.8007:0.0:0.1993:0.0 . 295 Q9ULK0 GRID1_HUMAN M 295 ENSP00000330148:T295M ENSP00000330148:T295M T - 2 0 GRID1 87618814 1.000000 0.71417 1.000000 0.80357 0.938000 0.57974 4.464000 0.60134 0.991000 0.38814 -0.254000 0.11334 ACG TCGA-HZ-A49I-01A-12D-A26I-08 GRID1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049148.3 1 0 1 90 370 0 164 0 8.481529e-01 1 15 0 164 2 0 0 0 0 0 2 1 1.000000 90 369 0 162 2 -3.592518 1 1 121412 26 46 1 0 1 1 2.049385 0 0.350000 1.860000 0.348861 0.990000 0.910000 1.000000 1.000000 0.993820 0.990000 1 0.990000 1.000000 TLL2 7093 broad.mit.edu 37 10 98145915 98145915 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr10:98145915G>A ENST00000357947.3 - 15 2135 c.1910C>T c.(1909-1911)cCg>cTg p.P637L NM_012465.3 NP_036597.1 Q9Y6L7 TLL2_HUMAN tolloid-like 2 58 Colorectal(252;0.0846) ATACTCCTTCGGCCACCCAGG 0.532000 0 SO:0001583 missense ENST00000357947.3 1 1 hg19 CCDS7449.1 . . . . . . . . . . G 32 5.175833 0.94807 . . ENSG00000095587 ENST00000357947 T 0.53206 0.63 4.98 4.98 0.66077 CUB (5); 0.000000 0.45361 D 0.000367 T 0.78578 0.4305 H 0.95079 3.62 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.84878 0.0829 10 0.72032 D 0.01 . 17.7792 0.88518 0.0:0.0:1.0:0.0 . 637 Q9Y6L7 TLL2_HUMAN L 637 ENSP00000350630:P637L ENSP00000350630:P637L P - 2 0 TLL2 98135905 1.000000 0.71417 0.988000 0.46212 0.952000 0.60782 9.601000 0.98297 2.761000 0.94854 0.585000 0.79938 CCG TCGA-HZ-A49I-01A-12D-A26I-08 TLL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049608.1 1 0 1 86 518 0 249 0 0 0 0 249 2 0 0 0 0 0 2 1 1.000000 84 515 0 245 2 -2.879520 1 1 0 0 1 0 1 1 2.049385 0 0.350000 1.860000 0.348861 0.800000 0.650000 0.970000 0.810000 0.815906 0.800000 0 0.730000 0.890000 GLB1L2 89944 broad.mit.edu 37 11 134244879 134244879 + Missense_Mutation SNP A A C TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr11:134244879A>C ENST00000535456.2 + 19 2026 c.1838A>C c.(1837-1839)gAg>gCg p.E613A GLB1L2_ENST00000389881.3_Missense_Mutation_p.E613A|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Missense_Mutation_p.E613A NM_138342.3 NP_612351.2 Q8IW92 GLBL2_HUMAN galactosidase, beta 1-like 2 41 all_hematologic(175;0.127) all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844) ATCGTTTTTGAGGAGACGATG 0.627000 0 SO:0001583 missense ENST00000535456.2 1 1 hg19 CCDS31724.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 17.02|17.02 3.280796|3.280796 0.59758|0.59758 .|. .|. ENSG00000149328|ENSG00000149328 ENST00000339772;ENST00000535456;ENST00000389881|ENST00000525089 D;D;D|. 0.95001|. -3.58;-3.58;-3.58|. 5.32|5.32 5.32|5.32 0.75619|0.75619 Galactose-binding domain-like (1);|. 0.000000|. 0.85682|. D|. 0.000000|. D|. 0.86497|. 0.5947|. H|H 0.95539|0.95539 3.685|3.685 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.70016|. 0.967|. D|. 0.90373|. 0.4382|. 10|. 0.87932|. D|. 0|. -36.4735|-36.4735 13.8558|13.8558 0.63527|0.63527 1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0 .|. 613|. Q8IW92|. GLBL2_HUMAN|. A|C 613|551 ENSP00000344659:E613A;ENSP00000444628:E613A;ENSP00000374531:E613A|. ENSP00000344659:E613A|. E|X +|+ 2|3 0|0 GLB1L2|GLB1L2 133750089|133750089 1.000000|1.000000 0.71417|0.71417 0.996000|0.996000 0.52242|0.52242 0.192000|0.192000 0.23643|0.23643 6.939000|6.939000 0.75911|0.75911 2.001000|2.001000 0.58596|0.58596 0.482000|0.482000 0.46254|0.46254 GAG|TGA TCGA-HZ-A49I-01A-12D-A26I-08 GLB1L2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393629.2 1 0 1 21 107 0 55 1 9.646393e-01 15 16 0 55 2 0 0 0 0 0 2 1 0.999998 21 102 0 55 2 -20.000000 1 1 121406 1 29 1 0 0 0 2.036179 0 0.350000 1.860000 0.345418 0.920000 0.600000 1.000000 1.000000 0.896003 0.920000 1 0.750000 1.000000 RSRC2 65117 broad.mit.edu 37 12 122999745 122999745 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr12:122999745C>T ENST00000331738.7 - 6 777 c.632G>A c.(631-633)aGa>aAa p.R211K RSRC2_ENST00000354654.2_Missense_Mutation_p.R163K|RSRC2_ENST00000392442.2_5'Flank NM_023012.5 NP_075388.2 Q7L4I2 RSRC2_HUMAN arginine/serine-rich coiled-coil 2 24 all_neural(191;0.0837)|Medulloblastoma(191;0.163) GCTAAATCTTCTCGGCTTTTC 0.378000 0 SO:0001583 missense ENST00000331738.7 1 1 hg19 CCDS31920.1 . . . . . . . . . . C 19.31 3.802748 0.70682 . . ENSG00000111011 ENST00000331738;ENST00000354654;ENST00000418773;ENST00000344591 T;T;T 0.23950 2.35;1.88;1.88 5.63 5.63 0.86233 . 0.144353 0.64402 D 0.000005 T 0.21590 0.0520 L 0.27053 0.805 0.39090 D 0.961074 P;B;P;B 0.40834 0.73;0.397;0.73;0.397 B;B;B;B 0.38755 0.281;0.173;0.281;0.173 T 0.02909 -1.1095 10 0.20519 T 0.43 . 20.0442 0.97604 0.0:1.0:0.0:0.0 . 211;163;211;152 F5GXM2;Q7L4I2-2;Q7L4I2;E1B6W4 .;.;RSRC2_HUMAN;. K 211;163;211;152 ENSP00000330188:R211K;ENSP00000346678:R163K;ENSP00000343315:R152K ENSP00000330188:R211K R - 2 0 RSRC2 121565698 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.692000 0.54727 2.814000 0.96858 0.655000 0.94253 AGA TCGA-HZ-A49I-01A-12D-A26I-08 RSRC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395096.3 1 0 1 70 334 0 114 1 9.999997e-01 50 55 0 114 2 0 0 0 0 0 2 1 1.000000 69 331 0 114 2 -20.000000 1 1 0 0 1 0 1 1 1.808274 1 0.350000 1.860000 0.228487 0.820000 0.660000 1.000000 0.830000 0.832943 0.820000 0 0.730000 0.920000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HZ-A49I-01A-12D-A26I-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 43 101 0 33 1 8.439835e-01 7 3 0 33 2 1 1 78 185 0 500 2 1 1.000000 42 100 0 33 2 -20.000000 1 1 121404 2 44 1 2 2 4 2.654299 1 0.350000 1.860000 0.505703 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MDM2 4193 broad.mit.edu 37 12 69218184 69218184 + Missense_Mutation SNP C C G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr12:69218184C>G ENST00000350057.5 + 4 307 c.307C>G c.(307-309)Cac>Gac p.H103D MDM2_ENST00000360430.2_Intron|MDM2_ENST00000299252.4_Intron|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000478070.1_Intron|MDM2_ENST00000517852.1_Intron|MDM2_ENST00000428863.2_Intron|MDM2_ENST00000356290.4_Intron|MDM2_ENST00000393410.1_Intron|MDM2_ENST00000393413.3_Intron|MDM2_ENST00000258149.5_Intron|MDM2_ENST00000393412.3_Intron|MDM2_ENST00000462284.1_Missense_Mutation_p.H134D|MDM2_ENST00000540827.1_Intron|MDM2_ENST00000258148.7_Intron|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000348801.2_Intron Q00987 MDM2_HUMAN MDM2 proto-oncogene, E3 ubiquitin protein ligase 19 all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684) all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143) GAACAGGTGTCACCTTGAAGG 0.423000 A sarcoma, glioma, colorectal, other Dom yes 12 12q15 4193 Mdm2 p53 binding protein homolog M, O, E, L 0 SO:0001583 missense ENST00000350057.5 1 1 hg19 . . . . . . . . . . C 0.304 -0.971751 0.02215 . . ENSG00000135679 ENST00000462284;ENST00000544648;ENST00000311440;ENST00000311420;ENST00000539479;ENST00000393415;ENST00000393416;ENST00000350057 T;T;T 0.43688 1.54;0.94;1.54 5.65 3.79 0.43588 . 0.565311 0.20923 N 0.083253 T 0.20455 0.0492 N 0.08118 0 0.26660 N 0.971938 B;B;B;B 0.19331 0.0;0.023;0.035;0.0 B;B;B;B 0.14023 0.001;0.01;0.009;0.001 T 0.17258 -1.0375 9 . . . -9.2634 8.905 0.35519 0.1483:0.7763:0.0:0.0755 . 83;128;128;134 Q00987-9;Q00987;Q8NDW2;Q00987-11 .;MDM2_HUMAN;.;. D 134;83;128;89;128;128;159;103 ENSP00000417281:H134D;ENSP00000444430:H128D;ENSP00000266624:H103D . H + 1 0 MDM2 67504451 0.104000 0.21937 0.032000 0.17829 0.219000 0.24729 1.031000 0.30165 0.833000 0.34828 0.585000 0.79938 CAC TCGA-HZ-A49I-01A-12D-A26I-08 MDM2-033 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000402665.1 1 0 1 44 247 0 46 0 9.652173e-01 0 33 0 46 2 0 0 0 0 0 2 1 1.000000 44 247 0 46 2 -3.326894 1 1 0 0 1 1 2 3 2.249255 1 0.350000 1.860000 0.408957 0.990000 0.720000 1.000000 1.000000 0.942601 0.990000 1 0.840000 1.000000 GPR183 1880 broad.mit.edu 37 13 99947840 99947840 + Missense_Mutation SNP A A G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 A G A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr13:99947840A>G ENST00000376414.4 - 2 643 c.560T>C c.(559-561)tTt>tCt p.F187S UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron NM_004951.4 NP_004942.1 P32249 GP183_HUMAN G protein-coupled receptor 183 23 AGTTTCTTCAAAGTTTGGATA 0.413000 0 SO:0001583 missense ENST00000376414.4 1 1 hg19 CCDS9492.1 . . . . . . . . . . A 21.9 4.213653 0.79352 . . ENSG00000169508 ENST00000376414 T 0.38401 1.14 5.76 5.76 0.90799 GPCR, rhodopsin-like superfamily (1); 0.053527 0.85682 D 0.000000 T 0.54111 0.1838 L 0.51422 1.61 0.58432 D 0.999999 D 0.76494 0.999 D 0.73380 0.98 T 0.50189 -0.8857 9 . . . . 16.0843 0.81031 1.0:0.0:0.0:0.0 . 187 P32249 GP183_HUMAN S 187 ENSP00000365596:F187S . F - 2 0 GPR183 98745841 1.000000 0.71417 1.000000 0.80357 0.964000 0.63967 8.962000 0.93254 2.191000 0.70037 0.533000 0.62120 TTT TCGA-HZ-A49I-01A-12D-A26I-08 GPR183-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045582.2 1 0 1 88 416 0 125 0 9.999917e-01 0 81 0 125 2 0 0 0 0 0 2 1 1.000000 88 413 0 124 2 -20.000000 1 1 0 0 1 1 2 3 2.053284 0 0.350000 1.860000 0.351136 0.990000 0.810000 1.000000 1.000000 0.963024 0.990000 1 0.900000 1.000000 DHRS4 10901 broad.mit.edu 37 14 24429127 24429127 + Missense_Mutation SNP G G T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr14:24429127G>T ENST00000313250.5 + 3 526 c.323G>T c.(322-324)gGa>gTa p.G108V DHRS4_ENST00000397075.3_Missense_Mutation_p.G108V|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000558581.1_Intron|DHRS4_ENST00000382761.3_Missense_Mutation_p.G90V|DHRS4_ENST00000558263.1_Missense_Mutation_p.G108V|DHRS4_ENST00000421831.1_Intron|DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000543741.2_Missense_Mutation_p.G108V|DHRS4_ENST00000308178.8_Intron NM_021004.2 NP_066284.2 Q9BTZ2 DHRS4_HUMAN dehydrogenase/reductase (SDR family) member 4 14 Vitamin A(DB00162) AAGCTTCATGGAGGTATCGAT 0.478000 0 SO:0001583 missense ENST00000313250.5 1 0 hg19 CCDS9605.1 . . . . . . . . . . . 14.94 2.686814 0.48097 . . ENSG00000157326 ENST00000313250;ENST00000382761;ENST00000397075;ENST00000543741 T;T;D;T 0.89617 1.12;1.12;-2.54;1.12 2.87 1.93 0.25924 NAD(P)-binding domain (1); 0.111999 0.64402 D 0.000011 D 0.94892 0.8349 H 0.95260 3.645 0.80722 D 1 D;D;P;D 0.89917 0.983;1.0;0.906;0.995 P;D;P;D 0.79108 0.809;0.992;0.624;0.964 D 0.93034 0.6451 10 0.87932 D 0 . 6.9126 0.24342 0.1546:0.0:0.8454:0.0 . 108;108;108;108 F5GWZ1;Q9BTZ2-2;Q9BTZ2-7;Q9BTZ2 .;.;.;DHRS4_HUMAN V 108;90;108;108 ENSP00000326219:G108V;ENSP00000372209:G90V;ENSP00000380265:G108V;ENSP00000440508:G108V ENSP00000326219:G108V G + 2 0 DHRS4 23498967 1.000000 0.71417 0.375000 0.26029 0.848000 0.48234 6.768000 0.74980 0.494000 0.27859 0.484000 0.47621 GGA TCGA-HZ-A49I-01A-12D-A26I-08 DHRS4-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071857.3 1 0 0 304 1662 1 731 0 7.905803e-01 1 17 1 731 2 0 0 0 0 0 2 1 1.000000 302 1620 1 776 11 -20.000000 1 1 0 0 1 0 0 0 2.036303 0 0.350000 1.860000 0.345418 0.870000 0.780000 0.970000 0.880000 0.878457 0.870000 1 0.820000 0.920000 DHRS4L2 317749 broad.mit.edu 37 14 24464257 24464257 + Missense_Mutation SNP G G T rs148508271 byFrequency TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr14:24464257G>T ENST00000335125.6 + 3 449 c.323G>T c.(322-324)gGa>gTa p.G108V DHRS4L2_ENST00000534993.1_Missense_Mutation_p.G7V|DHRS4L2_ENST00000537912.1_Intron|DHRS4L2_ENST00000558753.1_Intron|DHRS4L2_ENST00000397071.1_Missense_Mutation_p.G108V|DHRS4L2_ENST00000545240.1_Missense_Mutation_p.G108V|DHRS4L2_ENST00000382755.4_Missense_Mutation_p.G106V|DHRS4L2_ENST00000543805.1_Intron NM_198083.3 NP_932349.2 Q6PKH6 DR4L2_HUMAN dehydrogenase/reductase (SDR family) member 4 like 2 10 AAGCTTCATGGAGGTATCGAT 0.493000 0 SO:0001583 missense ENST00000335125.6 1 0 hg19 CCDS9606.2 . . . . . . . . . . - 17.18 3.323563 0.60634 . . ENSG00000187630 ENST00000534993;ENST00000397071;ENST00000335125;ENST00000545240;ENST00000382755 D;T;T;T 0.89617 -2.54;-0.02;1.12;1.12 4.37 3.46 0.39613 NAD(P)-binding domain (1); 0.112267 0.64402 D 0.000011 D 0.95143 0.8426 H 0.94462 3.54 0.39857 D 0.973325 D 0.64830 0.994 D 0.73708 0.981 D 0.94913 0.8066 10 0.87932 D 0 . 9.2784 0.37714 0.1119:0.0:0.8881:0.0 . 106 Q6PKH6 DR4L2_HUMAN V 7;108;108;108;106 ENSP00000380261:G108V;ENSP00000334801:G108V;ENSP00000437883:G108V;ENSP00000372203:G106V ENSP00000334801:G108V G + 2 0 DHRS4L2 23534097 1.000000 0.71417 0.125000 0.21846 0.175000 0.22909 6.775000 0.75018 0.796000 0.33947 0.398000 0.26397 GGA TCGA-HZ-A49I-01A-12D-A26I-08 DHRS4L2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000071858.4 1 0 0 159 4069 0 1714 0 5.278142e-02 0 10 0 1714 2 0 0 0 0 0 2 1 1.000000 145 3915 0 1764 2 -4.564867 1 1 0 0 1 0 0 0 2.036303 0 0.350000 1.860000 0.345418 0.200000 0.170000 0.250000 0.210000 0.214540 0.200000 0 0.190000 0.230000 SERPINA6 866 broad.mit.edu 37 14 94780770 94780770 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr14:94780770C>T ENST00000341584.3 - 2 362 c.216G>A c.(214-216)atG>atA p.M72I NM_001756.3 NP_001747 P08185 CBG_HUMAN serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6 26 all_cancers(154;0.0482)|all_epithelial(191;0.166) Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620) TAGCTAAGGCCATGGAGATGC 0.547000 0 SO:0001583 missense ENST00000341584.3 1 1 hg19 CCDS9924.1 . . . . . . . . . . C 8.748 0.920648 0.17982 . . ENSG00000170099 ENST00000341584;ENST00000557225 D;D 0.87103 -2.21;-1.55 5.07 -2.48 0.06423 Serpin domain (3); 0.436617 0.21388 N 0.075360 T 0.72961 0.3526 L 0.38649 1.16 0.27668 N 0.946854 B 0.10296 0.003 B 0.14023 0.01 T 0.57551 -0.7792 10 0.09590 T 0.72 . 5.0497 0.14501 0.4235:0.254:0.0:0.3226 . 72 P08185 CBG_HUMAN I 72 ENSP00000342850:M72I;ENSP00000452018:M72I ENSP00000342850:M72I M - 3 0 SERPINA6 93850523 0.158000 0.22850 0.484000 0.27391 0.982000 0.71751 -0.421000 0.07053 -0.761000 0.04670 0.563000 0.77884 ATG TCGA-HZ-A49I-01A-12D-A26I-08 SERPINA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413065.1 1 0 1 61 257 0 112 0 2.506738e-01 0 5 0 112 2 0 0 0 0 0 2 1 1.000000 61 256 0 111 2 -20.000000 1 1 0 0 1 0 0 0 2.036303 0 0.350000 1.860000 0.345418 0.990000 0.850000 1.000000 1.000000 0.984377 0.990000 1 0.960000 1.000000 NLRC3 197358 broad.mit.edu 37 16 3607671 3607671 + RNA SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr16:3607671C>T ENST00000301749.7 - 0 2427 NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000603507.1_RNA NM_178844.2 NP_849172.2 Q7RTR2 NLRC3_HUMAN NLR family, CARD domain containing 3 34 TCTGGTTCTCCGCCAAGCTGC 0.527000 0 ENST00000301749.7 1 0 hg19 TCGA-HZ-A49I-01A-12D-A26I-08 NLRC3-201 KNOWN basic|appris_principal protein_coding polymorphic_pseudogene 1 0 1 20 110 0 71 0 2.631579e-02 0 2 0 71 2 0 0 0 0 0 2 1 0.999997 20 109 0 70 2 -2.968520 1 1 120956 3 32 1 0 0 0 2.036081 0 0.350000 1.860000 0.345418 0.870000 0.560000 1.000000 1.000000 0.859079 0.870000 1 0.700000 1.000000 CASKIN2 57513 broad.mit.edu 37 17 73497867 73497867 + Silent SNP G G T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr17:73497867G>T ENST00000321617.3 - 18 3874 c.3288C>A c.(3286-3288)ccC>ccA p.P1096P CASKIN2_ENST00000433559.2_Silent_p.P1014P NM_020753.3 NP_065804.2 Q8WXE0 CSKI2_HUMAN CASK interacting protein 2 18 all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246) all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154) TACCTGCTCCGGGCACCTTGA 0.637000 0 SO:0001819 synonymous_variant ENST00000321617.3 1 1 hg19 CCDS11723.1 TCGA-HZ-A49I-01A-12D-A26I-08 CASKIN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447609.1 0 0 0 15 707 0 295 1 4.586077e-01 2 69 0 295 2 0 0 0 0 0 2 1 0.999855 15 696 0 293 2 -2.368556 0 1 0 0 1 0 1 1 2.045126 0 0.350000 1.860000 0.348861 0.110000 0.060000 0.190000 0.120000 0.125736 0.110000 0 0.080000 0.160000 TP53 7157 broad.mit.edu 37 17 7577544 7577544 + Missense_Mutation SNP A A C TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 A C A A Valid Somatic Phase_I WXS targeted Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr17:7577544A>C ENST00000269305.4 - 7 926 c.737T>G c.(736-738)aTg>aGg p.M246R TP53_ENST00000445888.2_Missense_Mutation_p.M246R|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.M246R|TP53_ENST00000420246.2_Missense_Mutation_p.M246R|TP53_ENST00000359597.4_Missense_Mutation_p.M246R|TP53_ENST00000413465.2_Missense_Mutation_p.M246R 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.M246R(10)|p.M246T(9)|p.0?(8)|p.M246K(7)|p.?(5)|p.M246_P250delMNRRP(2)|p.G244fs*17(1)|p.M153T(1)|p.C242fs*98(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*14(1)|p.G245fs*16(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CCTCCGGTTCATGCCGCCCAT 0.572000 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 47 Substitution - Missense(27)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(4)|Deletion - In frame(3) 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 . . . . . . . . . . A 21.6 4.177746 0.78564 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99800 -6.8;-6.8;-6.8;-6.8;-6.8;-6.8;-6.8;-6.8 4.62 4.62 0.57501 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 0.99736 0.9896 M 0.87971 2.92 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;0.998;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;0.997;0.96;1.0;1.0;0.998 D 0.97237 0.9888 10 0.87932 D 0 -28.5667 12.3101 0.54924 1.0:0.0:0.0:0.0 . 246;246;153;246;246;246 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. R 246;246;246;246;246;246;235;153;114;153 ENSP00000410739:M246R;ENSP00000352610:M246R;ENSP00000269305:M246R;ENSP00000398846:M246R;ENSP00000391127:M246R;ENSP00000391478:M246R;ENSP00000425104:M114R;ENSP00000423862:M153R ENSP00000269305:M246R M - 2 0 TP53 7518269 1.000000 0.71417 1.000000 0.80357 0.963000 0.63663 9.087000 0.94110 2.074000 0.62210 0.379000 0.24179 ATG TCGA-HZ-A49I-01A-12D-A26I-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 38 217 0 148 1 9.999051e-01 44 39 0 148 2 1 1 52 347 0 1075 2 1 1.000000 38 214 0 148 2 -20.000000 1 1 0 0 1 0 1 1 1.699086 1 0.350000 1.860000 0.212121 0.690000 0.500000 0.900000 0.690000 0.703616 0.690000 0 0.590000 0.800000 TCF4 6925 broad.mit.edu 37 18 52924608 52924608 + Missense_Mutation SNP A A G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr18:52924608A>G ENST00000356073.4 - 14 1695 c.1084T>C c.(1084-1086)Tgg>Cgg p.W362R TCF4_ENST00000398339.1_Missense_Mutation_p.W464R|TCF4_ENST00000564999.1_Missense_Mutation_p.W362R|TCF4_ENST00000564403.2_Missense_Mutation_p.W368R|TCF4_ENST00000567880.1_Missense_Mutation_p.W302R|TCF4_ENST00000568740.1_Missense_Mutation_p.W337R|TCF4_ENST00000561831.3_Missense_Mutation_p.W202R|TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000566286.1_Missense_Mutation_p.W359R|TCF4_ENST00000561992.1_Missense_Mutation_p.W232R|TCF4_ENST00000537578.1_Missense_Mutation_p.W338R|TCF4_ENST00000570287.2_Missense_Mutation_p.W202R|TCF4_ENST00000565018.2_Missense_Mutation_p.W362R|TCF4_ENST00000540999.1_Missense_Mutation_p.W338R|TCF4_ENST00000570177.2_Missense_Mutation_p.W232R|TCF4_ENST00000457482.3_Missense_Mutation_p.W202R|TCF4_ENST00000543082.1_Missense_Mutation_p.W320R|TCF4_ENST00000537856.3_Missense_Mutation_p.W232R|TCF4_ENST00000568673.1_Missense_Mutation_p.W338R|TCF4_ENST00000544241.2_Missense_Mutation_p.W291R|TCF4_ENST00000564228.1_Missense_Mutation_p.W291R|TCF4_ENST00000566279.1_Missense_Mutation_p.W302R|TCF4_ENST00000354452.3_Missense_Mutation_p.W362R NM_003199.2 NP_003190.1 P15884 ITF2_HUMAN transcription factor 4 41 TTTCTAGACCAAACAGCTGTG 0.408000 0 SO:0001583 missense ENST00000356073.4 1 1 hg19 CCDS11960.1 . . . . . . . . . . A 23.7 4.446962 0.84101 . . ENSG00000196628 ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339 T;T;T;T;T;T;T;T;T 0.62498 0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02 5.89 5.89 0.94794 . 0.000000 0.85682 D 0.000000 T 0.81837 0.4907 M 0.87971 2.92 0.80722 D 1 D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D 0.97110 0.999;1.0;1.0;0.999;0.999;0.999;0.999;1.0;0.999 D 0.84986 0.0891 10 0.72032 D 0.01 -8.4202 15.2952 0.73898 1.0:0.0:0.0:0.0 . 338;362;202;464;362;320;291;202;359 B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5 .;.;.;.;ITF2_HUMAN;.;.;.;. R 362;202;362;320;338;338;291;232;464 ENSP00000346440:W362R;ENSP00000409447:W202R;ENSP00000348374:W362R;ENSP00000439656:W320R;ENSP00000445202:W338R;ENSP00000440731:W338R;ENSP00000441562:W291R;ENSP00000439827:W232R;ENSP00000381382:W464R ENSP00000346440:W362R W - 1 0 TCF4 51075606 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.685000 0.91246 2.246000 0.74042 0.533000 0.62120 TGG TCGA-HZ-A49I-01A-12D-A26I-08 TCF4-002 KNOWN upstream_uORF|basic|CCDS protein_coding protein_coding OTTHUMT00000256014.1 0 0 0 16 611 0 228 0 2.960845e-02 0 10 0 228 2 0 0 0 0 0 2 1 0.999927 16 604 0 228 2 -13.437080 1 1 0 0 1 0 1 1 1.695842 1 0.350000 1.860000 0.213789 0.110000 0.060000 0.190000 0.120000 0.126932 0.110000 0 0.090000 0.160000 ZNF532 55205 broad.mit.edu 37 18 56585592 56585592 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr18:56585592G>A ENST00000336078.4 + 4 849 c.73G>A c.(73-75)Gat>Aat p.D25N ZNF532_ENST00000591230.1_Missense_Mutation_p.D25N|ZNF532_ENST00000591808.1_Missense_Mutation_p.D25N|ZNF532_ENST00000591083.1_Missense_Mutation_p.D25N|ZNF532_ENST00000589288.1_Missense_Mutation_p.D25N NM_018181.4 NP_060651.2 Q9HCE3 ZN532_HUMAN zinc finger protein 532 52 AGATATGGTCGATCCTAAAGC 0.468000 0 SO:0001583 missense ENST00000336078.4 1 1 hg19 CCDS11969.1 . . . . . . . . . . G 35 5.584685 0.96578 . . ENSG00000074657 ENST00000336078 T 0.07688 3.17 5.47 5.47 0.80525 . 0.000000 0.85682 D 0.000000 T 0.33818 0.0876 M 0.80422 2.495 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.07424 -1.0773 10 0.87932 D 0 -18.7627 18.9367 0.92589 0.0:0.0:1.0:0.0 . 25 Q9HCE3 ZN532_HUMAN N 25 ENSP00000338217:D25N ENSP00000338217:D25N D + 1 0 ZNF532 54736572 1.000000 0.71417 0.986000 0.45419 0.908000 0.53690 9.403000 0.97302 2.560000 0.86352 0.555000 0.69702 GAT TCGA-HZ-A49I-01A-12D-A26I-08 ZNF532-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256130.1 1 0 1 70 283 0 148 0 7.204050e-01 1 11 0 148 2 0 0 0 0 0 2 1 1.000000 71 282 0 148 2 -20.000000 1 1 0 0 1 0 1 1 1.695842 1 0.350000 1.860000 0.213789 0.900000 0.730000 1.000000 1.000000 0.897426 0.900000 1 0.810000 0.970000 FAM129C 199786 broad.mit.edu 37 19 17660273 17660273 + Missense_Mutation SNP G G T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr19:17660273G>T ENST00000335393.4 + 15 1918 c.1780G>T c.(1780-1782)Gcc>Tcc p.A594S FAM129C_ENST00000595684.1_Missense_Mutation_p.A594S|FAM129C_ENST00000332386.5_Missense_Mutation_p.A594S|FAM129C_ENST00000599164.1_Missense_Mutation_p.A563S|FAM129C_ENST00000601861.1_Missense_Mutation_p.A563S|FAM129C_ENST00000600871.1_Intron|FAM129C_ENST00000352727.3_Missense_Mutation_p.A558S|FAM129C_ENST00000599124.1_Missense_Mutation_p.A527S|FAM129C_ENST00000449408.2_Missense_Mutation_p.A320S NM_173544.4 NP_775815 Q86XR2 NIBL2_HUMAN family with sequence similarity 129, member C 33 GACCCTTGGTGCCAATGATGT 0.527000 0 SO:0001583 missense ENST00000335393.4 1 1 hg19 CCDS12362.1 . . . . . . . . . . G 11.71 1.719856 0.30503 . . ENSG00000167483 ENST00000335393;ENST00000332386;ENST00000352727;ENST00000449408 T;T;T;T 0.46819 1.8;1.82;0.86;1.43 2.87 0.639 0.17747 . 0.762112 0.11046 N 0.605581 T 0.38904 0.1058 M 0.63428 1.95 0.09310 N 1 P;P;P;P 0.36909 0.573;0.573;0.573;0.573 B;B;B;B 0.38378 0.272;0.272;0.272;0.272 T 0.25187 -1.0139 10 0.11182 T 0.66 -4.5539 5.3444 0.16000 0.2787:0.0:0.7213:0.0 . 594;594;558;594 Q86XR2;Q86XR2-3;Q86XR2-4;Q86XR2-2 NIBL2_HUMAN;.;.;. S 594;594;558;320 ENSP00000335040:A594S;ENSP00000333447:A594S;ENSP00000341067:A558S;ENSP00000394929:A320S ENSP00000333447:A594S A + 1 0 FAM129C 17521273 0.005000 0.15991 0.002000 0.10522 0.082000 0.17680 0.151000 0.16283 0.270000 0.21984 0.557000 0.71058 GCC TCGA-HZ-A49I-01A-12D-A26I-08 FAM129C-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000464206.1 1 0 1 106 721 0 295 0 1.675438e-02 0 2 0 295 2 0 0 0 0 0 2 1 1.000000 105 719 0 294 2 -20.000000 1 0 0 0 1 1 2 3 2.052791 0 0.350000 1.860000 0.351136 0.730000 0.600000 0.870000 0.740000 0.737190 0.730000 0 0.660000 0.800000 NLRP2 55655 broad.mit.edu 37 19 55501388 55501388 + Splice_Site SNP A A G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr19:55501388A>G ENST00000543010.1 + 9 2509 c.e9-1 NLRP2_ENST00000448584.2_Splice_Site|NLRP2_ENST00000263437.6_Splice_Site|NLRP2_ENST00000339757.7_Splice_Site|NLRP2_ENST00000537859.1_Splice_Site|NLRP2_ENST00000538819.1_Splice_Site|NLRP2_ENST00000427260.2_Splice_Site|NLRP2_ENST00000391721.4_Splice_Site NM_001174081.1 NP_001167552.1 Q9NX02 NALP2_HUMAN NLR family, pyrin domain containing 2 11 BRCA - Breast invasive adenocarcinoma(297;0.163) TTTCTCCCACAGGTTGGTGTC 0.517000 0 SO:0001630 splice_region_variant ENST00000543010.1 1 1 hg19 CCDS12913.1 2 9.157509157509158E-4 0 0.0 0 0.0 0 0.0 2 0.002638522427440633 a 8.379 0.836995 0.16891 . . ENSG00000022556 ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437 . . . 2.51 2.51 0.30379 . . . . . . . . . . . 0.37549 D 0.918615 . . . . . . . . . . . . . . 6.9916 0.24758 1.0:0.0:0.0:0.0 . . . . . -1 . . . + . . NLRP2 60193200 0.776000 0.28616 0.108000 0.21378 0.127000 0.20565 3.149000 0.50655 1.407000 0.46875 0.529000 0.55759 . TCGA-HZ-A49I-01A-12D-A26I-08 NLRP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396152.1 0 0 1 55 295 1 166 0 0 0 1 166 2 0 0 0 0 0 2 1 1.000000 51 284 1 162 9 -20.000000 1 1 121412 4 36 1 0 1 1 1.727474 1 0.350000 1.860000 0.220390 0.740000 0.570000 0.920000 0.740000 0.749823 0.740000 0 0.650000 0.840000 CLEC4G 339390 broad.mit.edu 37 19 7796974 7796974 + Silent SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr19:7796974C>T ENST00000328853.5 - 1 83 c.15G>A c.(13-15)agG>agA p.R5R CLEC4G_ENST00000598081.1_Splice_Site NM_001244856.1|NM_198492.3 NP_001231785.1|NP_940894.1 Q6UXB4 CLC4G_HUMAN C-type lectin domain family 4, member G 6 ACTTGCTGTACCTGGTGGTGT 0.612000 Esophageal Squamous(146;540 1807 3349 19438 30853) 0 SO:0001819 synonymous_variant ENST00000328853.5 1 0 hg19 CCDS12185.1 TCGA-HZ-A49I-01A-12D-A26I-08 CLEC4G-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461989.1 1 0 1 49 256 0 140 0 0 0 1 0 140 2 0 0 0 0 0 2 1 1.000000 49 256 0 140 2 -20.000000 1 1 121412 5 34 1 1 2 3 2.052791 0 0.350000 1.860000 0.351136 0.910000 0.690000 1.000000 1.000000 0.906038 0.910000 1 0.800000 1.000000 ADORA3 140 broad.mit.edu 37 1 112046027 112046027 + Translation_Start_Site SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:112046027G>A ENST00000241356.4 - 0 355 ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_De_novo_Start_OutOfFrame|ADORA3_ENST00000369717.4_Intron NM_000677.3 NP_000668.1 P33765 AA3R_HUMAN adenosine A3 receptor 12 all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156) Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824) AGCAAGATCCGTCTGTAGGGC 0.542000 0 ENST00000241356.4 0 1 hg19 CCDS839.1 TCGA-HZ-A49I-01A-12D-A26I-08 ADORA3-010 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033065.1 0 0 0 11 50 0 19 0 3.859287e-01 0 7 0 19 2 0 0 0 0 0 2 1 0.998737 11 50 0 19 2 -3.620766 1 1 120666 6 34 1 1 2 3 2.052343 0 0.350000 1.860000 0.351136 0.990000 0.570000 1.000000 1.000000 0.919731 0.990000 1 0.780000 1.000000 SEMA4A 64218 broad.mit.edu 37 1 156128241 156128241 + Silent SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:156128241C>T ENST00000368285.3 + 5 693 c.426C>T c.(424-426)tgC>tgT p.C142C SEMA4A_ENST00000368284.1_Intron|SEMA4A_ENST00000487358.1_3'UTR|SEMA4A_ENST00000368286.2_Intron|SEMA4A_ENST00000355014.2_Silent_p.C142C|SEMA4A_ENST00000368282.1_Silent_p.C142C NM_001193300.1|NM_022367.3 NP_001180229.1|NP_071762.2 Q9H3S1 SEM4A_HUMAN sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A 5 Hepatocellular(266;0.158) TCTACACCTGCGGCACCTTCG 0.537000 0 SO:0001819 synonymous_variant ENST00000368285.3 1 1 hg19 CCDS1132.1 TCGA-HZ-A49I-01A-12D-A26I-08 SEMA4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039484.2 1 0 0 149 788 0 267 0 4.328970e-01 0 9 0 267 2 0 0 0 0 0 2 1 1.000000 146 775 0 266 2 -20.000000 1 1 121412 4 44 1 0 0 0 2.034416 0 0.350000 1.860000 0.345418 0.890000 0.760000 1.000000 1.000000 0.901840 0.890000 1 0.830000 0.970000 HSPA6 3310 broad.mit.edu 37 1 161495096 161495096 + Silent SNP T T G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:161495096T>G ENST00000309758.4 + 1 1061 c.648T>G c.(646-648)gcT>gcG p.A216A RP11-25K21.6_ENST00000537821.2_RNA NM_002155.3 NP_002146.2 P17066 HSP76_HUMAN heat shock 70kDa protein 6 (HSP70B') p.A216A(1) 21 all_cancers(52;4.89e-16)|all_hematologic(112;0.0207) BRCA - Breast invasive adenocarcinoma(70;0.00376) CCATTGACGCTGGTGTCTTTG 0.597000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000309758.4 1 1 hg19 CCDS1231.1 TCGA-HZ-A49I-01A-12D-A26I-08 HSPA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083308.1 1 0 1 31 227 0 116 0 3.060620e-01 0 9 0 116 2 0 0 0 0 0 2 1 1.000000 29 227 0 115 2 -3.142893 1 1 0 0 1 0 0 0 2.034416 0 0.350000 1.860000 0.345418 0.680000 0.470000 0.910000 0.680000 0.692930 0.680000 0 0.570000 0.800000 ZBTB17 7709 broad.mit.edu 37 1 16269204 16269204 + Missense_Mutation SNP C C A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:16269204C>A ENST00000375743.4 - 14 2090 c.1858G>T c.(1858-1860)Ggg>Tgg p.G620W ZBTB17_ENST00000537142.1_Missense_Mutation_p.G538W|ZBTB17_ENST00000375733.2_Missense_Mutation_p.G620W NM_003443.2 NP_003434.2 Q13105 ZBT17_HUMAN zinc finger and BTB domain containing 17 15 Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) AAGCCACGCCCACACTTATCA 0.612000 0 SO:0001583 missense ENST00000375743.4 1 1 hg19 CCDS165.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 21.9|21.9 4.210920|4.210920 0.79240|0.79240 .|. .|. ENSG00000116809|ENSG00000116809 ENST00000375743;ENST00000375733;ENST00000444654;ENST00000537142;ENST00000375729|ENST00000440560 T;T;T|. 0.02525|. 4.26;4.26;4.26|. 5.52|5.52 5.52|5.52 0.82312|0.82312 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.85775|0.85775 0.5775|0.5775 M|M 0.93462|0.93462 3.42|3.42 0.80722|0.80722 D|D 1|1 D;D;D|. 0.89917|. 1.0;1.0;1.0|. D;D;D|. 0.91635|. 0.997;0.997;0.999|. D|D 0.89151|0.89151 0.3523|0.3523 10|5 0.87932|. D|. 0|. .|. 14.9728|14.9728 0.71246|0.71246 0.0:0.8577:0.1423:0.0|0.0:0.8577:0.1423:0.0 .|. 620;538;620|. Q13105-2;F5H411;Q13105|. .;.;ZBT17_HUMAN|. W|L 620;620;539;538;176|19 ENSP00000364895:G620W;ENSP00000364885:G620W;ENSP00000438529:G538W|. ENSP00000364881:G176W|. G|W -|- 1|2 0|0 ZBTB17|ZBTB17 16141791|16141791 0.999000|0.999000 0.42202|0.42202 0.890000|0.890000 0.34922|0.34922 0.996000|0.996000 0.88848|0.88848 4.586000|4.586000 0.60984|0.60984 2.579000|2.579000 0.87056|0.87056 0.563000|0.563000 0.77884|0.77884 GGG|TGG TCGA-HZ-A49I-01A-12D-A26I-08 ZBTB17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025998.1 1 0 1 25 214 0 91 1 9.604565e-01 8 40 0 91 2 0 0 0 0 0 2 1 1.000000 25 212 0 91 2 -2.841694 1 1 0 0 1 1 2 3 2.058303 0 0.350000 1.860000 0.351136 0.600000 0.400000 0.850000 0.600000 0.612745 0.600000 0 0.490000 0.730000 CEP350 9857 broad.mit.edu 37 1 180063129 180063129 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:180063129G>A ENST00000367607.3 + 34 8307 c.7889G>A c.(7888-7890)aGt>aAt p.S2630N CEP350_ENST00000490141.1_3'UTR NM_014810.4 NP_055625.4 Q5VT06 CE350_HUMAN centrosomal protein 350kDa p.S2630I(2) 66 GTTAATAGAAGTAGAAGCCTT 0.388000 2 Substitution - Missense(2) SO:0001583 missense ENST00000367607.3 1 1 hg19 CCDS1336.1 . . . . . . . . . . G 0.016 -1.521005 0.00967 . . ENSG00000135837 ENST00000367607;ENST00000417046 T 0.59083 0.29 2.15 0.983 0.19767 . . . . . T 0.41282 0.1152 L 0.36672 1.1 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.23084 -1.0198 8 . . . . 5.4385 0.16494 0.6897:0.0:0.3103:0.0 . 2630;2630 E7EU22;Q5VT06 .;CE350_HUMAN N 2630;94 ENSP00000356579:S2630N . S + 2 0 CEP350 178329752 0.000000 0.05858 0.551000 0.28230 0.817000 0.46193 0.141000 0.16076 0.258000 0.21686 -0.383000 0.06682 AGT TCGA-HZ-A49I-01A-12D-A26I-08 CEP350-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085315.2 0 0 0 8 215 0 79 0 5.089151e-02 0 9 0 79 2 0 0 0 0 0 2 1 0.989749 8 215 0 79 2 -9.941549 1 1 0 0 1 0 0 0 2.041305 0 0.350000 1.860000 0.347717 0.210000 0.090000 0.380000 0.200000 0.225865 0.210000 0 0.140000 0.300000 CR2 1380 broad.mit.edu 37 1 207647654 207647654 + Missense_Mutation SNP T T A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:207647654T>A ENST00000367058.3 + 12 2321 c.2132T>A c.(2131-2133)aTt>aAt p.I711N CR2_ENST00000458541.2_Missense_Mutation_p.I684N|CR2_ENST00000367057.3_Missense_Mutation_p.I770N|CR2_ENST00000367059.3_Missense_Mutation_p.I711N NM_001877.4 NP_001868.2 P20023 CR2_HUMAN complement component (3d/Epstein Barr virus) receptor 2 69 TTCAAAAAGATTCCACTTTGT 0.388000 0 SO:0001583 missense ENST00000367058.3 1 1 hg19 CCDS1478.1 . . . . . . . . . . T 11.38 1.622221 0.28889 . . ENSG00000117322 ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541 T;T;T;T 0.62788 0.0;0.0;0.0;0.0 5.66 0.325 0.15903 Complement control module (2);Sushi/SCR/CCP (3); . . . . T 0.62392 0.2424 M 0.69823 2.125 0.09310 N 0.999998 P;P;P 0.48294 0.87;0.908;0.565 P;P;P 0.53006 0.632;0.715;0.568 T 0.51236 -0.8731 9 0.17832 T 0.49 . 2.5985 0.04860 0.1401:0.0791:0.2912:0.4896 . 711;711;770 Q5SR47;P20023;P20023-3 .;CR2_HUMAN;. N 711;770;711;684 ENSP00000356025:I711N;ENSP00000356024:I770N;ENSP00000356026:I711N;ENSP00000404222:I684N ENSP00000356024:I770N I + 2 0 CR2 205714277 0.840000 0.29493 0.001000 0.08648 0.112000 0.19704 -0.039000 0.12124 -0.193000 0.10415 -0.336000 0.08194 ATT TCGA-HZ-A49I-01A-12D-A26I-08 CR2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000088274.1 0 0 0 18 520 0 158 0 3.895860e-02 0 9 0 158 2 0 0 0 0 0 2 1 0.999982 19 519 0 158 2 -16.544230 1 1 0 0 1 0 0 0 2.041305 0 0.350000 1.860000 0.347717 0.190000 0.110000 0.290000 0.190000 0.199659 0.190000 0 0.140000 0.240000 CR1L 1379 broad.mit.edu 37 1 207867914 207867914 + Missense_Mutation SNP C C G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:207867914C>G ENST00000508064.2 + 5 740 c.680C>G c.(679-681)cCt>cGt p.P227R CR1L_ENST00000530905.1_Intron NM_175710.1 NP_783641.1 Q2VPA4 CR1L_HUMAN complement component (3b/4b) receptor 1-like 22 TGCATTATACCTAACAAATGC 0.448000 0 SO:0001583 missense ENST00000508064.2 1 1 hg19 CCDS44310.1 . . . . . . . . . . C 7.803 0.714144 0.15306 . . ENSG00000197721 ENST00000444269;ENST00000508064 T 0.35605 1.3 2.38 -0.917 0.10485 . . . . . T 0.24890 0.0604 L 0.35644 1.08 0.09310 N 1 P 0.38800 0.648 B 0.39419 0.299 T 0.15780 -1.0425 9 0.35671 T 0.21 . 4.9771 0.14146 0.0:0.4127:0.0:0.5873 . 227 Q2VPA4 CR1L_HUMAN R 227 ENSP00000421736:P227R ENSP00000434864:P171R P + 2 0 CR1L 205934537 0.001000 0.12720 0.032000 0.17829 0.207000 0.24258 0.336000 0.19823 -0.069000 0.12931 0.298000 0.19748 CCT TCGA-HZ-A49I-01A-12D-A26I-08 CR1L-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390247.1 1 0 1 265 1154 0 506 0 0 0 0 506 2 0 0 0 0 0 2 1 1.000000 246 1092 0 538 2 -2.794973 1 1 0 0 1 0 0 0 2.037921 0 0.350000 1.860000 0.345418 0.990000 0.940000 1.000000 1.000000 0.995541 0.990000 1 0.990000 1.000000 EPHA8 2046 broad.mit.edu 37 1 22928191 22928191 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:22928191G>A ENST00000166244.3 + 17 3047 c.2975G>A c.(2974-2976)cGg>cAg p.R992Q NM_020526.3 NP_065387.1 P29322 EPHA8_HUMAN EPH receptor A8 61 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) CAGACCATGCGGGCCCAGCTG 0.682000 0 SO:0001583 missense ENST00000166244.3 1 1 hg19 CCDS225.1 . . . . . . . . . . G 28.5 4.928399 0.92389 0.0 2.34E-4 ENSG00000070886 ENST00000166244 T 0.52983 0.64 5.23 5.23 0.72850 Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1); 0.000000 0.64402 D 0.000001 T 0.64182 0.2575 L 0.54965 1.715 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.61422 -0.7066 10 0.42905 T 0.14 . 16.319 0.82939 0.0:0.0:1.0:0.0 . 992 P29322 EPHA8_HUMAN Q 992 ENSP00000166244:R992Q ENSP00000166244:R992Q R + 2 0 EPHA8 22800778 1.000000 0.71417 1.000000 0.80357 0.957000 0.61999 6.524000 0.73791 2.722000 0.93159 0.491000 0.48974 CGG TCGA-HZ-A49I-01A-12D-A26I-08 EPHA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008085.1 1 0 1 6 38 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 0.968676 6 38 0 22 2 -12.665530 1 1 119470 13 42 1 0 0 0 2.043636 0 0.350000 1.860000 0.347717 0.790000 0.340000 1.000000 1.000000 0.777507 0.790000 0 0.540000 1.000000 OR2M7 391196 broad.mit.edu 37 1 248487356 248487356 + Missense_Mutation SNP C C T rs145948434 TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:248487356C>T ENST00000317965.2 - 1 543 c.515G>A c.(514-516)cGg>cAg p.R172Q NM_001004691.1 NP_001004691.1 Q8NG81 OR2M7_HUMAN olfactory receptor, family 2, subfamily M, member 7 p.R172L(1)|p.R172Q(1) 42 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) GGCTATTTCCCGAGACCCACA 0.433000 2 Substitution - Missense(2) SO:0001583 missense ENST00000317965.2 1 1 hg19 CCDS31111.1 . . . . . . . . . . C 9.874 1.199628 0.22121 . . ENSG00000177186 ENST00000317965 T 0.00044 8.83 1.54 0.552 0.17230 GPCR, rhodopsin-like superfamily (1); 0.295108 0.18339 U 0.144258 T 0.00109 0.0003 L 0.43701 1.375 0.09310 N 1 B 0.31519 0.327 B 0.32583 0.148 T 0.21965 -1.0230 10 0.52906 T 0.07 . 3.5068 0.07693 0.0:0.4143:0.0:0.5857 . 172 Q8NG81 OR2M7_HUMAN Q 172 ENSP00000324557:R172Q ENSP00000324557:R172Q R - 2 0 OR2M7 246553979 0.002000 0.14202 0.390000 0.26220 0.131000 0.20780 0.708000 0.25719 0.845000 0.35118 0.184000 0.17185 CGG TCGA-HZ-A49I-01A-12D-A26I-08 OR2M7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097357.1 1 0 1 314 1493 0 518 0 0 0 0 518 2 0 0 0 0 0 2 1 1.000000 312 1449 0 533 2 -2.136597 0 1 121412 4 42 1 0 0 0 2.037921 0 0.350000 1.860000 0.345418 0.980000 0.880000 1.000000 1.000000 0.972423 0.980000 1 0.930000 1.000000 ZC3H12A 80149 broad.mit.edu 37 1 37947235 37947235 + Missense_Mutation SNP A A T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:37947235A>T ENST00000373087.6 + 4 733 c.617A>T c.(616-618)aAg>aTg p.K206M NM_025079.2 NP_079355.2 zinc finger CCCH-type containing 12A p.K206R(1) 21 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) GAGAAGAAGAAGATCCTGGTG 0.607000 1 Substitution - Missense(1) SO:0001583 missense ENST00000373087.6 1 1 hg19 CCDS417.1 . . . . . . . . . . A 28.9 4.957246 0.92726 0.0 1.16E-4 ENSG00000163874 ENST00000373087;ENST00000373082 T 0.45668 0.89 5.42 5.42 0.78866 Ribonuclease Zc3h12a-like (1); 0.000000 0.85682 D 0.000000 T 0.62097 0.2400 M 0.62723 1.935 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 T 0.64871 -0.6305 10 0.62326 D 0.03 -37.7323 15.4665 0.75406 1.0:0.0:0.0:0.0 . 206 Q5D1E8 ZC12A_HUMAN M 206 ENSP00000362179:K206M ENSP00000362174:K206M K + 2 0 ZC3H12A 37719822 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 5.267000 0.65530 2.054000 0.61138 0.459000 0.35465 AAG TCGA-HZ-A49I-01A-12D-A26I-08 ZC3H12A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012154.2 1 0 1 72 398 0 222 1 9.999026e-01 22 54 0 222 2 0 0 0 0 0 2 1 1.000000 67 404 0 224 2 -20.000000 1 0 121412 9 46 1 1 2 3 2.052343 0 0.350000 1.860000 0.351136 0.870000 0.690000 1.000000 1.000000 0.876360 0.870000 1 0.780000 0.980000 MACF1 23499 broad.mit.edu 37 1 39950371 39950371 + Silent SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:39950371G>A ENST00000372915.3 + 96 21966 c.21879G>A c.(21877-21879)ccG>ccA p.P7293P MACF1_ENST00000564288.1_Silent_p.P7460P|MACF1_ENST00000289893.4_Silent_p.P5843P|MACF1_ENST00000361689.2_Silent_p.P5335P|MACF1_ENST00000539005.1_Silent_p.P5205P|MACF1_ENST00000567887.1_Silent_p.P7497P|MACF1_ENST00000317713.7_Silent_p.P5335P|MACF1_ENST00000545844.1_Silent_p.P5335P Q9UPN3 MACF1_HUMAN microtubule-actin crosslinking factor 1 203 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) GTTCTTCCCCGGCCTCCACAG 0.488000 0 SO:0001819 synonymous_variant ENST00000372915.3 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 10.37|10.37 1.331374|1.331374 0.24167|0.24167 .|. .|. ENSG00000127603|ENSG00000127603 ENST00000372925;ENST00000446276|ENST00000360115;ENST00000442046 .|. .|. .|. 6.03|6.03 -2.55|-2.55 0.06288|0.06288 .|. .|. .|. .|. .|. T|T 0.39655|0.39655 0.1086|0.1086 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. T|T 0.30357|0.30357 -0.9981|-0.9981 4|4 .|. .|. .|. .|. 2.3493|2.3493 0.04280|0.04280 0.2315:0.3717:0.2762:0.1206|0.2315:0.3717:0.2762:0.1206 .|. .|. .|. .|. S|Q 4339;360|448;273 .|. .|. G|R +|+ 1|2 0|0 MACF1|MACF1 39722958|39722958 0.005000|0.005000 0.15991|0.15991 0.992000|0.992000 0.48379|0.48379 0.996000|0.996000 0.88848|0.88848 -1.287000|-1.287000 0.02785|0.02785 -0.376000|-0.376000 0.07943|0.07943 -0.290000|-0.290000 0.09829|0.09829 GGC|CGG TCGA-HZ-A49I-01A-12D-A26I-08 MACF1-028 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding protein_coding OTTHUMT00000392096.1 1 0 1 106 565 0 288 1 1 93 264 0 288 2 1 1 45 274 1 714 4 1 1.000000 108 561 0 287 2 -2.922118 1 1 121412 3 37 1 1 2 3 2.052343 0 0.350000 1.860000 0.351136 0.900000 0.740000 1.000000 1.000000 0.902089 0.900000 1 0.820000 0.990000 COL24A1 255631 broad.mit.edu 37 1 86372901 86372901 + Silent SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr1:86372901C>T ENST00000370571.2 - 28 3120 c.2754G>A c.(2752-2754)ggG>ggA p.G918G COL24A1_ENST00000436319.1_Silent_p.G918G NM_152890.5 NP_690850.2 Q17RW2 COOA1_HUMAN collagen, type XXIV, alpha 1 101 GACCTTGACTCCCAGGTGGTC 0.348000 0 SO:0001819 synonymous_variant ENST00000370571.2 1 1 hg19 CCDS41353.1 TCGA-HZ-A49I-01A-12D-A26I-08 COL24A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029335.4 1 0 1 71 452 0 115 0 0 0 1 0 115 2 0 0 0 0 0 2 1 1.000000 69 448 0 114 2 -3.318825 1 1 0 0 1 1 2 3 2.052343 0 0.350000 1.860000 0.351136 0.770000 0.610000 0.960000 0.780000 0.782004 0.770000 0 0.690000 0.870000 KIAA1755 85449 broad.mit.edu 37 20 36855620 36855620 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr20:36855620C>T ENST00000279024.4 - 7 2259 c.1988G>A c.(1987-1989)cGg>cAg p.R663Q NM_001029864.1 NP_001025035.1 Q5JYT7 K1755_HUMAN KIAA1755 54 Myeloproliferative disorder(115;0.00874) GAGAATAGCCCGGATAGAGGC 0.572000 0 SO:0001583 missense ENST00000279024.4 1 1 hg19 CCDS33467.1 . . . . . . . . . . C 10.88 1.474685 0.26511 . . ENSG00000149633 ENST00000279024;ENST00000373398;ENST00000435901 T;T 0.61158 0.13;1.2 4.53 0.919 0.19392 . 0.986535 0.08237 N 0.976570 T 0.36552 0.0971 N 0.17082 0.46 0.09310 N 1 B 0.14438 0.01 B 0.08055 0.003 T 0.21211 -1.0252 10 0.19590 T 0.45 . 6.2707 0.20953 0.0:0.4404:0.0:0.5596 . 663 Q5JYT7 K1755_HUMAN Q 663;210;1 ENSP00000279024:R663Q;ENSP00000393503:R1Q ENSP00000279024:R663Q R - 2 0 KIAA1755 36289034 0.204000 0.23447 0.000000 0.03702 0.000000 0.00434 1.432000 0.34936 0.215000 0.20761 -0.808000 0.03180 CGG TCGA-HZ-A49I-01A-12D-A26I-08 KIAA1755-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079144.3 1 0 1 21 139 0 87 0 7.590005e-01 0 20 0 87 2 0 0 0 0 0 2 1 0.999998 21 137 0 86 2 -3.081980 1 1 121412 4 31 1 0 0 0 2.017515 0 0.350000 1.860000 0.338422 0.730000 0.480000 1.000000 1.000000 0.748828 0.730000 0 0.590000 0.900000 KIAA1755 85449 broad.mit.edu 37 20 36859706 36859706 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr20:36859706C>T ENST00000279024.4 - 5 2040 c.1769G>A c.(1768-1770)cGg>cAg p.R590Q NM_001029864.1 NP_001025035.1 Q5JYT7 K1755_HUMAN KIAA1755 54 Myeloproliferative disorder(115;0.00874) AAGCAGGGGCCGCCCGGCCCT 0.637000 0 SO:0001583 missense ENST00000279024.4 1 1 hg19 CCDS33467.1 . . . . . . . . . . C 27.2 4.812690 0.90707 . . ENSG00000149633 ENST00000279024;ENST00000373398 T 0.68903 -0.36 4.97 4.02 0.46733 . 0.163457 0.27473 N 0.019219 T 0.79718 0.4494 M 0.90019 3.08 0.43579 D 0.995916 D 0.69078 0.997 P 0.54629 0.757 T 0.83267 -0.0045 10 0.54805 T 0.06 . 12.3865 0.55335 0.0:0.9191:0.0:0.0809 . 590 Q5JYT7 K1755_HUMAN Q 590;137 ENSP00000279024:R590Q ENSP00000279024:R590Q R - 2 0 KIAA1755 36293120 0.995000 0.38212 0.993000 0.49108 0.985000 0.73830 2.737000 0.47393 1.307000 0.44944 0.655000 0.94253 CGG TCGA-HZ-A49I-01A-12D-A26I-08 KIAA1755-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079144.3 1 0 1 23 86 0 41 0 9.724847e-01 0 25 0 41 2 0 0 0 0 0 2 1 1.000000 22 85 0 40 2 -20.000000 1 1 0 0 1 0 0 0 2.017515 0 0.350000 1.860000 0.338422 0.990000 0.790000 1.000000 1.000000 0.980805 0.990000 1 0.970000 1.000000 SON 6651 broad.mit.edu 37 21 34925124 34925124 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr21:34925124C>T ENST00000356577.4 + 3 4062 c.3587C>T c.(3586-3588)cCt>cTt p.P1196L SON_ENST00000290239.6_Missense_Mutation_p.P1196L|SON_ENST00000381679.4_Missense_Mutation_p.P1196L|SON_ENST00000300278.4_Missense_Mutation_p.P1196L|SON_ENST00000381692.2_Intron NM_138927.1 NP_620305 P18583 SON_HUMAN SON DNA binding protein 72 AATACTTGGCCTACAGAGGTG 0.527000 0 SO:0001583 missense ENST00000356577.4 1 1 hg19 CCDS13629.1 . . . . . . . . . . C 15.46 2.840064 0.51057 . . ENSG00000159140 ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679 T;T;T;T 0.12672 2.85;2.84;2.83;2.66 5.42 5.42 0.78866 . 0.627323 0.14275 N 0.329894 T 0.15522 0.0374 L 0.40543 1.245 0.19775 N 0.999954 P;P;B;P;P 0.49253 0.804;0.872;0.015;0.804;0.921 B;B;B;B;B 0.40864 0.288;0.139;0.014;0.288;0.342 T 0.10989 -1.0606 10 0.72032 D 0.01 . 16.7237 0.85416 0.0:1.0:0.0:0.0 . 1196;1196;877;1196;1196 P18583-10;P18583;P18583-2;P18583-3;P18583-6 .;SON_HUMAN;.;.;. L 1196 ENSP00000348984:P1196L;ENSP00000290239:P1196L;ENSP00000300278:P1196L;ENSP00000371095:P1196L ENSP00000290239:P1196L P + 2 0 SON 33846994 0.862000 0.29867 0.893000 0.35052 0.752000 0.42762 3.035000 0.49759 2.549000 0.85964 0.563000 0.77884 CCT TCGA-HZ-A49I-01A-12D-A26I-08 SON-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000140978.2 1 0 1 158 776 0 310 1 9.976298e-01 10 36 0 310 2 0 0 0 0 0 2 1 1.000000 158 774 0 307 2 -20.000000 1 1 0 0 1 0 1 1 2.047266 0 0.350000 1.860000 0.348861 0.950000 0.820000 1.000000 1.000000 0.952273 0.950000 1 0.890000 1.000000 BRWD1 54014 broad.mit.edu 37 21 40650700 40650700 + Silent SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr21:40650700G>A ENST00000333229.2 - 10 1299 c.972C>T c.(970-972)ggC>ggT p.G324G BRWD1_ENST00000342449.3_Silent_p.G324G|BRWD1_ENST00000380800.3_Silent_p.G324G NM_018963.4 NP_061836.2 Q9NSI6 BRWD1_HUMAN bromodomain and WD repeat domain containing 1 58 Prostate(19;8.44e-08)|all_epithelial(19;0.223) GCATTTGAACGCCTGGCCTAG 0.333000 Melanoma(170;988 1986 4794 16843 39731) 0 SO:0001819 synonymous_variant ENST00000333229.2 1 1 hg19 CCDS13662.1 . . . . . . . . . . G 10.30 1.312047 0.23821 . . ENSG00000185658 ENST00000455867 . . . 5.1 -9.33 0.00639 . . . . . T 0.32436 0.0829 . . . 0.80722 D 1 . . . . . . T 0.40478 -0.9561 4 . . . . 1.5457 0.02564 0.4764:0.1997:0.1196:0.2044 . . . . C 36 . . R - 1 0 BRWD1 39572570 0.000000 0.05858 0.822000 0.32727 0.997000 0.91878 -2.790000 0.00767 -1.651000 0.01504 0.591000 0.81541 CGT TCGA-HZ-A49I-01A-12D-A26I-08 BRWD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141398.3 1 0 1 124 555 0 256 0 0 0 0 256 2 0 0 0 0 0 2 1 1.000000 121 548 0 256 2 -20.000000 1 1 121412 1 33 1 0 1 1 2.047266 0 0.350000 1.860000 0.348861 0.990000 0.870000 1.000000 1.000000 0.984150 0.990000 1 0.950000 1.000000 PARVB 29780 broad.mit.edu 37 22 44559738 44559738 + Splice_Site SNP G G T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr22:44559738G>T ENST00000338758.7 + 12 1009 c.946G>T c.(946-948)Gtc>Ttc p.V316F PARVB_ENST00000404989.1_Splice_Site_p.V279F|PARVB_ENST00000406477.3_Splice_Site_p.V349F NM_013327.4 NP_037459.2 Q9HBI1 PARVB_HUMAN parvin, beta 25 Ovarian(80;0.0246)|all_neural(38;0.0423) TCCTTGGCAGGTCCACAATGT 0.622000 0 SO:0001630 splice_region_variant ENST00000338758.7 0 1 hg19 CCDS14056.1 . . . . . . . . . . G 19.01 3.744371 0.69418 . . ENSG00000188677 ENST00000406477;ENST00000338758;ENST00000404989 D;D;D 0.95307 -3.67;-3.67;-3.67 5.42 3.34 0.38264 Calponin homology domain (5); 0.000000 0.85682 D 0.000000 D 0.97065 0.9041 M 0.88842 2.985 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.85130 0.997;0.997;0.995;0.992 D 0.96302 0.9222 9 . . . -1.022 9.6282 0.39763 0.1707:0.0:0.8293:0.0 . 316;279;316;349 A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2 .;.;PARVB_HUMAN;. F 349;316;279 ENSP00000384515:V349F;ENSP00000342492:V316F;ENSP00000384353:V279F . V + 1 0 PARVB 42891071 1.000000 0.71417 0.993000 0.49108 0.614000 0.37383 7.331000 0.79192 0.662000 0.31006 0.491000 0.48974 GTC TCGA-HZ-A49I-01A-12D-A26I-08 PARVB-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319518.2 0 0 0 8 338 0 157 0 5.076672e-01 0 68 0 157 2 0 0 0 0 0 2 1 0.989575 8 338 0 156 2 -8.130326 1 1 0 0 1 0 1 1 2.047147 0 0.350000 1.860000 0.348861 0.130000 0.060000 0.250000 0.130000 0.146730 0.130000 0 0.090000 0.190000 LRP1B 53353 broad.mit.edu 37 2 141200116 141200116 + Silent SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr2:141200116G>A ENST00000389484.3 - 66 11342 c.10371C>T c.(10369-10371)gaC>gaT p.D3457D NM_018557.2 NP_061027.2 Q9NZR2 LRP1B_HUMAN low density lipoprotein receptor-related protein 1B 606 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) CTGGATCCTCGTCACAAACCC 0.463000 TSP Lung(27;0.18) Colon(99;50 2074 2507 20106) 0 SO:0001819 synonymous_variant ENST00000389484.3 1 1 hg19 CCDS2182.1 TCGA-HZ-A49I-01A-12D-A26I-08 LRP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254736.2 1 0 1 81 431 0 162 0 0 0 0 162 2 0 0 0 0 0 2 1 1.000000 82 429 0 162 2 -20.000000 1 1 0 0 1 0 0 0 2.026445 0 0.350000 1.860000 0.340771 0.880000 0.710000 1.000000 1.000000 0.889275 0.880000 1 0.790000 0.980000 TTN 7273 broad.mit.edu 37 2 179583694 179583694 + Missense_Mutation SNP G G T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr2:179583694G>T ENST00000591111.1 - 82 23506 c.23282C>A c.(23281-23283)cCa>cAa p.P7761Q TTN_ENST00000342992.6_Missense_Mutation_p.P6834Q|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.P8078Q|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) TTCAAAAGATGGTGGTTCTAG 0.443000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . G 13.44 2.237650 0.39598 . . ENSG00000155657 ENST00000342992 T 0.81078 -1.45 5.71 5.71 0.89125 Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . D 0.94241 0.8151 H 0.97896 4.1 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.95629 0.8688 9 0.87932 D 0 . 20.2245 0.98337 0.0:0.0:1.0:0.0 . 7761 Q8WZ42 TITIN_HUMAN Q 6834 ENSP00000343764:P6834Q ENSP00000343764:P6834Q P - 2 0 TTN 179291939 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 9.434000 0.97515 2.861000 0.98227 0.650000 0.86243 CCA TCGA-HZ-A49I-01A-12D-A26I-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 9 82 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.994740 9 81 0 34 2 -15.347340 1 1 0 0 1 0 0 0 2.026445 0 0.350000 1.860000 0.340771 0.570000 0.280000 0.950000 0.550000 0.591315 0.570000 0 0.410000 0.760000 FANCD2 2177 broad.mit.edu 37 3 10106107 10106107 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr3:10106107C>T ENST00000419585.1 + 22 2176 c.2015C>T c.(2014-2016)cCg>cTg p.P672L FANCD2_ENST00000287647.3_Missense_Mutation_p.P672L|FANCD2_ENST00000383806.1_Missense_Mutation_p.P672L|FANCD2_ENST00000383807.1_Missense_Mutation_p.P672L Q9BXW9 FACD2_HUMAN Fanconi anemia, complementation group D2 51 TGTGTTGTTCCGGAAGGGTAG 0.458000 D, Mis, N, F AML, leukemia Involved in tolerance or repair of DNA crosslinks Fanconi Anemia yes Rec Fanconi anaemia D2 3 3p26 2177 Fanconi anemia, complementation group D2 L 0 SO:0001583 missense Familial Cancer Database Pancytopenia Dysmelia, FA (several complementation groups) ENST00000419585.1 1 1 hg19 CCDS33696.1 . . . . . . . . . . C 11.49 1.654704 0.29425 . . ENSG00000144554 ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585 T;T;T;T 0.44482 0.92;0.92;0.92;0.92 5.58 4.65 0.58169 . 0.272563 0.42172 D 0.000754 T 0.31606 0.0802 L 0.46741 1.465 0.38805 D 0.955286 B;B 0.18610 0.016;0.029 B;B 0.11329 0.006;0.006 T 0.15954 -1.0419 10 0.27785 T 0.31 . 6.7806 0.23643 0.1764:0.7359:0.0:0.0877 . 672;672 Q9BXW9-2;Q9BXW9 .;FACD2_HUMAN L 672 ENSP00000287647:P672L;ENSP00000373318:P672L;ENSP00000373317:P672L;ENSP00000398754:P672L ENSP00000287647:P672L P + 2 0 FANCD2 10081107 0.601000 0.26907 0.984000 0.44739 0.786000 0.44442 2.069000 0.41481 2.808000 0.96608 0.585000 0.79938 CCG TCGA-HZ-A49I-01A-12D-A26I-08 FANCD2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000339873.1 0 0 0 39 730 0 287 0 1.090857e-01 0 11 0 287 2 0 0 0 0 0 2 1 1.000000 38 709 0 359 2 -3.136632 1 1 121412 3 37 1 0 0 0 2.037599 0 0.350000 1.860000 0.345418 0.280000 0.200000 0.380000 0.290000 0.293660 0.280000 0 0.240000 0.340000 NEK10 152110 broad.mit.edu 37 3 27346443 27346443 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr3:27346443G>A ENST00000429845.2 - 13 1185 c.823C>T c.(823-825)Cgc>Tgc p.R275C NEK10_ENST00000341435.5_Missense_Mutation_p.R275C Q6ZWH5 NEK10_HUMAN NIMA-related kinase 10 41 CAAAGTAGGCGCAGCAACTCC 0.502000 0 SO:0001583 missense ENST00000429845.2 0 1 hg19 . . . . . . . . . . G 14.46 2.541047 0.45280 . . ENSG00000163491 ENST00000341435;ENST00000396636 T 0.51071 0.72 5.38 5.38 0.77491 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.65647 0.2711 M 0.61703 1.905 0.80722 D 1 D 0.89917 1.0 D 0.79108 0.992 T 0.67608 -0.5627 10 0.87932 D 0 . 14.7031 0.69168 0.0717:0.0:0.9283:0.0 . 275 Q6ZWH5 NEK10_HUMAN C 275 ENSP00000343847:R275C ENSP00000343847:R275C R - 1 0 NEK10 27321447 1.000000 0.71417 1.000000 0.80357 0.111000 0.19643 4.640000 0.61368 2.695000 0.91970 0.650000 0.86243 CGC TCGA-HZ-A49I-01A-12D-A26I-08 NEK10-016 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000438156.1 0 0 0 6 136 0 44 0 1.480307e-02 0 4 0 44 2 0 0 0 0 0 2 1 0.965248 6 135 0 44 2 -8.857866 1 1 120400 6 32 1 0 0 0 2.037599 0 0.350000 1.860000 0.345418 0.250000 0.100000 0.480000 0.230000 0.272178 0.250000 0 0.160000 0.370000 SLC6A20 54716 broad.mit.edu 37 3 45817325 45817325 + Silent SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr3:45817325C>T ENST00000358525.4 - 4 625 c.510G>A c.(508-510)ccG>ccA p.P170P SLC6A20_ENST00000456124.2_Silent_p.P170P|SLC6A20_ENST00000353278.4_Silent_p.P170P NM_020208.3 NP_064593.1 Q9NP91 S6A20_HUMAN solute carrier family 6 (proline IMINO transporter), member 20 13 GGCACAGCGCCGGCTCCCACT 0.622000 0 SO:0001819 synonymous_variant ENST00000358525.4 1 1 hg19 CCDS43077.1 TCGA-HZ-A49I-01A-12D-A26I-08 SLC6A20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257318.3 1 0 1 107 453 0 223 1 9.637646e-01 3 22 0 223 2 0 0 0 0 0 2 1 1.000000 107 442 0 222 2 -3.180656 1 1 121412 3 38 1 0 0 0 2.037599 0 0.350000 1.860000 0.345418 0.990000 0.900000 1.000000 1.000000 0.991416 0.990000 1 0.980000 1.000000 ENPP6 133121 broad.mit.edu 37 4 185033945 185033945 + Silent SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr4:185033945G>A ENST00000296741.2 - 6 1014 c.873C>T c.(871-873)agC>agT p.S291S NM_153343.3 NP_699174.1 Q6UWR7 ENPP6_HUMAN ectonucleotide pyrophosphatase/phosphodiesterase 6 15 all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749) GTTCCACTGTGCTCAGTTTGT 0.398000 0 SO:0001819 synonymous_variant ENST00000296741.2 1 1 hg19 CCDS3834.1 TCGA-HZ-A49I-01A-12D-A26I-08 ENPP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000361428.1 1 0 0 107 445 0 191 0 0 0 0 191 2 0 0 0 0 0 2 1 1.000000 108 440 1 191 12 -20.000000 1 1 0 0 1 0 0 0 1.706032 1 0.350000 1.860000 0.212121 0.890000 0.750000 0.990000 0.910000 0.893266 0.890000 1 0.820000 0.960000 NUDT9 53343 broad.mit.edu 37 4 88370318 88370318 + Missense_Mutation SNP T T A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr4:88370318T>A ENST00000302174.4 + 5 879 c.555T>A c.(553-555)aaT>aaA p.N185K NUDT9_ENST00000473942.1_Missense_Mutation_p.N135K|NUDT9_ENST00000515371.1_3'UTR NM_024047.4 NP_076952.1 Q9BW91 NUDT9_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 9 11 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242) GCAGTGGAAATAAAATCATGC 0.338000 0 SO:0001583 missense ENST00000302174.4 1 1 hg19 CCDS3620.1 . . . . . . . . . . T 7.271 0.607206 0.14002 . . ENSG00000170502 ENST00000302174;ENST00000512216;ENST00000473942;ENST00000440591 T;T;T;T 0.14022 2.54;2.54;2.54;2.54 5.18 3.95 0.45737 NUDIX hydrolase domain (1);NUDIX hydrolase domain-like (1); 0.390200 0.31697 N 0.007215 T 0.08626 0.0214 L 0.34521 1.04 0.38231 D 0.941037 B;B 0.34200 0.144;0.441 B;B 0.30401 0.019;0.115 T 0.19289 -1.0310 10 0.09590 T 0.72 -20.4549 9.3747 0.38275 0.0:0.0829:0.0:0.9171 . 185;185 Q96KB3;Q9BW91 .;NUDT9_HUMAN K 185;135;135;153 ENSP00000303575:N185K;ENSP00000424702:N135K;ENSP00000421811:N135K;ENSP00000410270:N153K ENSP00000303575:N185K N + 3 2 NUDT9 88589342 1.000000 0.71417 1.000000 0.80357 0.671000 0.39405 1.139000 0.31504 0.878000 0.35920 0.460000 0.39030 AAT TCGA-HZ-A49I-01A-12D-A26I-08 NUDT9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253035.2 1 0 1 77 198 0 118 1 9.999950e-01 34 16 0 118 2 0 0 0 0 0 2 1 1.000000 76 196 1 117 10 -20.000000 1 1 0 0 1 0 0 0 1.720113 1 0.350000 1.860000 0.208764 0.950000 0.860000 1.000000 0.970000 0.953341 0.950000 1 0.910000 0.980000 ITK 3702 broad.mit.edu 37 5 156675985 156675985 + Missense_Mutation SNP G G A rs56005928 byFrequency TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr5:156675985G>A ENST00000422843.3 + 16 1911 c.1759G>A c.(1759-1761)Gtc>Atc p.V587I ITK_ENST00000519749.1_3'UTR NM_005546.3 NP_005537.3 Q08881 ITK_HUMAN IL2-inducible T-cell kinase 70 Renal(175;0.00212) Medulloblastoma(196;0.0354)|all_neural(177;0.1) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) Pazopanib(DB06589) CTCCACACACGTCTACCAGAT 0.507000 T SYK peripheral T-cell lymphoma Esophageal Squamous(70;1378 1469 8785 19883) Dom yes 5 5q31-q32 3702 IL2-inducible T-cell kinase L 0 SO:0001583 missense ENST00000422843.3 1 0 hg19 CCDS4336.1 7 0.003205128205128205 0 0.0 0 0.0 1 0.0017482517482517483 6 0.0079155672823219 G 2.773 -0.255181 0.05829 4.54E-4 0.002674 ENSG00000113263 ENST00000422843 D 0.82433 -1.61 5.41 0.282 0.15692 Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.405452 0.29987 N 0.010696 T 0.55497 0.1924 N 0.14661 0.345 0.26058 N 0.981382 B 0.02656 0.0 B 0.04013 0.001 T 0.41875 -0.9484 10 0.11794 T 0.64 . 9.2885 0.37771 0.6236:0.0:0.3764:0.0 rs56005928 587 Q08881 ITK_HUMAN I 587 ENSP00000398655:V587I ENSP00000398655:V587I V + 1 0 ITK 156608563 0.001000 0.12720 0.084000 0.20598 0.536000 0.34869 0.012000 0.13287 -0.100000 0.12241 -0.806000 0.03193 GTC TCGA-HZ-A49I-01A-12D-A26I-08 ITK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252569.2 0 0 1 49 263 1 116 0 0 0 1 1 116 2 0 0 0 0 0 2 1 1.000000 49 258 1 114 11 -3.620247 1 1 121412 415 58 1 0 1 1 2.049467 0 0.350000 1.860000 0.348861 0.890000 0.670000 1.000000 1.000000 0.888646 0.890000 1 0.780000 1.000000 MTMR12 54545 broad.mit.edu 37 5 32235181 32235181 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr5:32235181G>A ENST00000382142.3 - 14 1569 c.1399C>T c.(1399-1401)Ccc>Tcc p.P467S MTMR12_ENST00000510216.1_5'Flank|MTMR12_ENST00000264934.5_Intron|MTMR12_ENST00000280285.5_Missense_Mutation_p.P467S|RNU6-1079P_ENST00000362861.1_RNA NM_001040446.1 NP_001035536.1 Q9C0I1 MTMRC_HUMAN myotubularin related protein 12 34 AATGCCGGGGGATGCTGGTGC 0.453000 0 SO:0001583 missense ENST00000382142.3 1 1 hg19 CCDS34138.1 . . . . . . . . . . G 16.35 3.097433 0.56075 . . ENSG00000150712 ENST00000280285;ENST00000382142 D;D 0.96619 -4.07;-4.07 5.12 3.3 0.37823 Myotubularin phosphatase domain (1); 0.281329 0.35903 N 0.002906 D 0.94430 0.8208 M 0.73753 2.245 0.80722 D 1 B;P 0.48503 0.116;0.911 B;B 0.39840 0.051;0.311 D 0.91776 0.5431 10 0.54805 T 0.06 . 9.7409 0.40418 0.0733:0.0:0.7865:0.1402 . 467;467 Q9C0I1-2;Q9C0I1 .;MTMRC_HUMAN S 467 ENSP00000280285:P467S;ENSP00000371577:P467S ENSP00000280285:P467S P - 1 0 MTMR12 32270938 1.000000 0.71417 0.998000 0.56505 0.982000 0.71751 5.051000 0.64257 0.529000 0.28599 0.462000 0.41574 CCC TCGA-HZ-A49I-01A-12D-A26I-08 MTMR12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366579.1 0 0 0 8 268 0 93 0 1.077405e-01 1 16 0 93 2 0 0 0 0 0 2 1 0.989655 8 268 0 91 2 -9.460262 1 1 121412 1 32 1 1 2 3 2.050384 0 0.350000 1.860000 0.351136 0.170000 0.070000 0.320000 0.160000 0.184082 0.170000 0 0.110000 0.240000 ITGA1 3672 broad.mit.edu 37 5 52235424 52235424 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr5:52235424C>T ENST00000282588.6 + 25 3541 c.3083C>T c.(3082-3084)gCa>gTa p.A1028V CTD-2175A23.1_ENST00000503559.1_RNA|CTD-2175A23.1_ENST00000505701.1_RNA NM_181501.1 NP_852478.1 P56199 ITA1_HUMAN integrin, alpha 1 51 Lung NSC(810;5.05e-05)|Breast(144;0.0851) TTCTAGAATGCAAACTGCAGA 0.383000 0 SO:0001583 missense ENST00000282588.6 1 1 hg19 CCDS3955.1 . . . . . . . . . . C 8.986 0.976553 0.18736 . . ENSG00000213949 ENST00000282588 T 0.43688 0.94 6.05 0.357 0.16079 Integrin alpha-2 (1); 0.925991 0.09267 N 0.825684 T 0.12347 0.0300 N 0.00583 -1.355 0.20489 N 0.999896 B 0.02656 0.0 B 0.04013 0.001 T 0.31194 -0.9952 10 0.13108 T 0.6 . 8.9331 0.35684 0.0:0.5162:0.0:0.4838 . 1028 P56199 ITA1_HUMAN V 1028 ENSP00000282588:A1028V ENSP00000282588:A1028V A + 2 0 ITGA1 52271181 0.062000 0.20869 0.366000 0.25914 0.548000 0.35241 0.078000 0.14761 0.099000 0.17552 0.650000 0.86243 GCA TCGA-HZ-A49I-01A-12D-A26I-08 ITGA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253855.3 1 0 1 36 238 0 89 1 9.999090e-01 14 82 0 89 2 0 0 0 0 0 2 1 1.000000 36 238 0 89 2 -16.529710 1 1 0 0 1 1 2 3 2.050384 0 0.350000 1.860000 0.351136 0.750000 0.540000 1.000000 0.750000 0.760813 0.750000 0 0.640000 0.880000 PRL 5617 broad.mit.edu 37 6 22292852 22292852 + Missense_Mutation SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr6:22292852C>T ENST00000306482.1 - 3 745 c.227G>A c.(226-228)cGg>cAg p.R76Q RP3-404K8.2_ENST00000561912.1_RNA NM_000948.5|NM_001163558.2 NP_000939.1|NP_001157030.1 P01236 PRL_HUMAN prolactin 16 Ovarian(93;0.163) AATGAACCCCCGGCCATGGGT 0.458000 0 SO:0001583 missense ENST00000306482.1 1 1 hg19 CCDS4548.1 . . . . . . . . . . C 13.24 2.178944 0.38511 . . ENSG00000172179 ENST00000306482;ENST00000438606 D 0.88431 -2.38 6.07 3.33 0.38152 Four-helical cytokine-like, core (1);Four-helical cytokine, core (1); 0.249538 0.42294 N 0.000740 T 0.71290 0.3322 L 0.54863 1.705 0.09310 N 0.999997 B;P 0.43826 0.024;0.818 B;B 0.33799 0.023;0.17 T 0.61662 -0.7017 10 0.33940 T 0.23 2.0715 9.4164 0.38523 0.0:0.7519:0.1196:0.1286 . 76;77 P01236;Q5I0G2 PRL_HUMAN;. Q 76;45 ENSP00000302150:R76Q ENSP00000302150:R76Q R - 2 0 PRL 22400831 0.014000 0.17966 0.001000 0.08648 0.607000 0.37147 0.491000 0.22419 0.443000 0.26582 0.655000 0.94253 CGG TCGA-HZ-A49I-01A-12D-A26I-08 PRL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043327.1 1 0 1 51 184 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 1.000000 51 183 0 95 2 -3.286340 1 1 121412 6 39 1 0 1 1 1.668703 1 0.350000 1.860000 0.212121 0.920000 0.740000 1.000000 0.990000 0.912589 0.920000 1 0.830000 0.980000 BACH2 60468 broad.mit.edu 37 6 90661558 90661558 + Silent SNP C C T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr6:90661558C>T ENST00000257749.4 - 7 974 c.267G>A c.(265-267)ccG>ccA p.P89P RP3-512E2.2_ENST00000413986.1_RNA|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Silent_p.P89P|BACH2_ENST00000343122.3_Silent_p.P89P NM_021813.2 NP_068585.1 Q9BYV9 BACH2_HUMAN BTB and CNC homology 1, basic leucine zipper transcription factor 2 45 all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063) ACTGTAACAGCGGCCCAAAGC 0.527000 0 SO:0001819 synonymous_variant ENST00000257749.4 1 1 hg19 CCDS5026.1 TCGA-HZ-A49I-01A-12D-A26I-08 BACH2-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041522.2 0 0 0 8 280 0 132 0 0 0 1 0 132 2 0 0 0 0 0 2 1 0.989337 8 278 0 132 2 -8.664479 1 1 121370 1 29 1 0 0 0 2.030089 0 0.350000 1.860000 0.345418 0.160000 0.070000 0.290000 0.160000 0.174945 0.160000 0 0.110000 0.230000 MGAM 8972 broad.mit.edu 37 7 141752741 141752741 + Missense_Mutation SNP G G C rs139662456 by1000genomes TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr7:141752741G>C ENST00000549489.2 + 26 3211 c.3116G>C c.(3115-3117)cGc>cCc p.R1039P MGAM_ENST00000475668.2_Missense_Mutation_p.R1039P NM_004668.2 NP_004659.2 O43451 MGA_HUMAN maltase-glucoamylase (alpha-glucosidase) 13 Melanoma(164;0.0272) Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878) AACCCCCTTCGCCTGGATGTC 0.453000 0 SO:0001583 missense ENST00000549489.2 1 0 hg19 CCDS47727.1 . . . . . . . . . . G 13.79 2.343095 0.41498 . . ENSG00000257335 ENST00000549489;ENST00000475668;ENST00000548812 T 0.13538 2.58 4.39 0.436 0.16549 Glycoside hydrolase-type carbohydrate-binding (1); 0.871763 0.09557 N 0.786123 T 0.29945 0.0749 M 0.92122 3.275 0.09310 N 1 P 0.49253 0.921 P 0.47118 0.538 T 0.18493 -1.0335 10 0.62326 D 0.03 . 7.83 0.29336 0.4799:0.0:0.5201:0.0 . 1039 O43451 MGA_HUMAN P 1039;1039;916 ENSP00000447378:R1039P ENSP00000316431:R916P R + 2 0 MGAM 141399210 0.005000 0.15991 0.006000 0.13384 0.017000 0.09413 1.298000 0.33412 -0.287000 0.09064 -0.717000 0.03617 CGC TCGA-HZ-A49I-01A-12D-A26I-08 MGAM-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000351244.3 1 0 1 53 346 0 120 0 0 0 0 120 2 0 0 0 0 0 2 1 1.000000 53 344 0 117 2 -5.553828 1 1 0 0 1 0 0 0 2.043567 0 0.350000 1.860000 0.347717 0.750000 0.570000 0.950000 0.750000 0.762801 0.750000 0 0.660000 0.860000 SKAP2 8935 broad.mit.edu 37 7 26883668 26883668 + Silent SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr7:26883668G>A ENST00000345317.2 - 4 601 c.288C>T c.(286-288)gaC>gaT p.D96D SKAP2_ENST00000539623.1_De_novo_Start_OutOfFrame NM_003930.3 NP_003921.2 O75563 SKAP2_HUMAN src kinase associated phosphoprotein 2 17 GGGCTTCATCGTCTTTATCAT 0.408000 0 SO:0001819 synonymous_variant ENST00000345317.2 1 0 hg19 CCDS5400.1 TCGA-HZ-A49I-01A-12D-A26I-08 SKAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214128.1 1 0 1 144 814 0 357 1 9.510221e-01 8 22 0 357 2 0 0 0 0 0 2 1 1.000000 143 807 0 356 2 -20.000000 1 1 121412 1 39 1 0 1 1 2.046091 0 0.350000 1.860000 0.348861 0.850000 0.720000 0.980000 0.860000 0.859373 0.850000 1 0.780000 0.920000 PLEKHA8 84725 broad.mit.edu 37 7 30094411 30094411 + Missense_Mutation SNP T T G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr7:30094411T>G ENST00000449726.1 + 8 1233 c.883T>G c.(883-885)Tgc>Ggc p.C295G PLEKHA8_ENST00000258679.7_Missense_Mutation_p.C295G|PLEKHA8_ENST00000396257.2_Missense_Mutation_p.C295G|PLEKHA8_ENST00000396259.1_Missense_Mutation_p.C295G NM_001197027.1 NP_001183956.1 Q96JA3 PKHA8_HUMAN pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 17 AGACTCAAGTTGCTCTCCGGA 0.403000 0 SO:0001583 missense ENST00000449726.1 1 1 hg19 CCDS56473.1 . . . . . . . . . . T 6.983 0.551408 0.13374 . . ENSG00000106086 ENST00000258679;ENST00000449726;ENST00000396257;ENST00000396259;ENST00000440706 . . . 5.63 1.47 0.22746 . 1.546830 0.03461 N 0.212180 T 0.19127 0.0459 N 0.14661 0.345 0.09310 N 1 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.06405 0.0;0.0;0.002;0.0 T 0.16541 -1.0399 9 0.20046 T 0.44 -5.9383 0.163 0.00105 0.2309:0.1762:0.2132:0.3797 . 295;295;295;295 Q96JA3-2;Q96JA3;Q96JA3-3;B4DH00 .;PKHA8_HUMAN;.;. G 295;295;295;295;321 . ENSP00000258679:C295G C + 1 0 PLEKHA8 30060936 0.141000 0.22595 0.004000 0.12327 0.048000 0.14542 1.196000 0.32198 0.445000 0.26639 0.533000 0.62120 TGC TCGA-HZ-A49I-01A-12D-A26I-08 PLEKHA8-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 102 549 0 206 0 2.421924e-01 0 6 0 206 2 0 0 0 0 0 2 1 1.000000 102 545 0 205 2 -20.000000 1 1 0 0 1 0 1 1 2.046091 0 0.350000 1.860000 0.348861 0.880000 0.730000 1.000000 1.000000 0.892742 0.880000 1 0.810000 0.980000 VPS13B 157680 broad.mit.edu 37 8 100861089 100861089 + Missense_Mutation SNP G G T TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr8:100861089G>T ENST00000358544.2 + 55 10214 c.10103G>T c.(10102-10104)gGa>gTa p.G3368V VPS13B_ENST00000357162.2_Missense_Mutation_p.G3343V|VPS13B_ENST00000395996.1_3'UTR NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) GCCCCAGAAGGAAAAGCAGGA 0.398000 Colon(161;2205 2542 7338 31318) 0 SO:0001583 missense ENST00000358544.2 1 1 hg19 CCDS6280.1 . . . . . . . . . . G 18.83 3.707973 0.68615 . . ENSG00000132549 ENST00000357162;ENST00000358544 T;T 0.73469 -0.75;-0.75 5.83 4.04 0.47022 . 0.181715 0.47852 D 0.000206 T 0.73458 0.3589 L 0.40543 1.245 0.80722 D 1 P;P 0.47191 0.836;0.891 P;P 0.52343 0.696;0.617 T 0.68762 -0.5323 10 0.27785 T 0.31 . 12.4675 0.55768 0.1326:0.0:0.8674:0.0 . 3343;3368 Q7Z7G8-2;Q7Z7G8 .;VP13B_HUMAN V 3343;3368 ENSP00000349685:G3343V;ENSP00000351346:G3368V ENSP00000349685:G3343V G + 2 0 VPS13B 100930265 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 5.888000 0.69758 0.817000 0.34445 0.650000 0.86243 GGA TCGA-HZ-A49I-01A-12D-A26I-08 VPS13B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000277138.1 0 0 0 16 620 0 177 0 1.427359e-02 0 7 0 177 2 0 0 0 0 0 2 1 0.999928 16 614 0 176 2 -3.218429 1 1 0 0 1 0 1 1 1.655022 1 0.350000 1.860000 0.212121 0.110000 0.060000 0.180000 0.120000 0.124876 0.110000 0 0.080000 0.150000 RP1L1 94137 broad.mit.edu 37 8 10470187 10470187 + Missense_Mutation SNP C C G TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr8:10470187C>G ENST00000382483.3 - 4 1644 c.1421G>C c.(1420-1422)aGg>aCg p.R474T NM_178857.5 NP_849188.4 Q8IWN7 RP1L1_HUMAN retinitis pigmentosa 1-like 1 148 CTCCGGGGTCCTGGGGCAGCA 0.701000 0 SO:0001583 missense ENST00000382483.3 1 1 hg19 CCDS43708.1 . . . . . . . . . . C 11.91 1.778440 0.31502 . . ENSG00000183638 ENST00000382483 T 0.04917 3.53 4.99 4.99 0.66335 . 0.443402 0.16804 U 0.198863 T 0.05914 0.0154 N 0.24115 0.695 0.09310 N 1 P 0.48764 0.915 P 0.45232 0.474 T 0.38394 -0.9663 10 0.30854 T 0.27 -7.7844 8.8491 0.35188 0.0:0.8913:0.0:0.1087 . 474 A6NKC6 . T 474 ENSP00000371923:R474T ENSP00000371923:R474T R - 2 0 RP1L1 10507597 0.041000 0.20044 0.010000 0.14722 0.065000 0.16274 1.394000 0.34509 2.302000 0.77476 0.561000 0.74099 AGG TCGA-HZ-A49I-01A-12D-A26I-08 RP1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375673.1 1 0 1 67 328 0 174 0 0 0 1 0 174 2 0 0 0 0 0 2 1 1.000000 67 325 0 173 2 -3.173588 1 1 120526 1 28 1 1 2 3 2.091493 0 0.350000 1.860000 0.357866 0.980000 0.770000 1.000000 1.000000 0.952008 0.980000 1 0.870000 1.000000 PLEC 5339 broad.mit.edu 37 8 144992083 144992083 + Missense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr8:144992083G>A ENST00000322810.4 - 32 12486 c.12317C>T c.(12316-12318)gCg>gTg p.A4106V PLEC_ENST00000436759.2_Missense_Mutation_p.A3996V|PLEC_ENST00000354589.3_Missense_Mutation_p.A3969V|PLEC_ENST00000527096.1_Missense_Mutation_p.A3992V|PLEC_ENST00000357649.2_Missense_Mutation_p.A3973V|PLEC_ENST00000354958.2_Missense_Mutation_p.A3947V|PLEC_ENST00000345136.3_Missense_Mutation_p.A3969V|PLEC_ENST00000356346.3_Missense_Mutation_p.A3955V|PLEC_ENST00000398774.2_Missense_Mutation_p.A3937V NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 137 GGCCGCCTGCGCCTCCAGGAG 0.632000 0 SO:0001583 missense ENST00000322810.4 1 1 hg19 CCDS43772.1 . . . . . . . . . . G 6.744 0.506057 0.12883 . . ENSG00000178209 ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096 T;T;T;T;T;T;T;T;T 0.77620 -1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11 5.08 4.21 0.49690 . 0.000000 0.64402 U 0.000008 D 0.89410 0.6707 M 0.93854 3.465 0.54753 D 0.999989 D;D;D;D;D;D;D;D 0.89917 0.999;0.999;0.999;1.0;0.999;0.999;0.999;0.999 P;P;P;P;P;P;P;P 0.61940 0.833;0.833;0.833;0.896;0.833;0.833;0.833;0.833 D 0.91813 0.5461 10 0.66056 D 0.02 . 13.6323 0.62202 0.0753:0.0:0.9247:0.0 . 3996;3955;3947;4106;3937;3969;3973;3969 Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4 .;.;.;PLEC_HUMAN;.;.;.;. V 3969;3973;3969;3937;4106;3947;3955;3996;3992 ENSP00000344848:A3969V;ENSP00000350277:A3973V;ENSP00000346602:A3969V;ENSP00000381756:A3937V;ENSP00000323856:A4106V;ENSP00000347044:A3947V;ENSP00000348702:A3955V;ENSP00000388180:A3996V;ENSP00000434583:A3992V ENSP00000323856:A4106V A - 2 0 PLEC 145064071 1.000000 0.71417 0.926000 0.36857 0.002000 0.02628 6.524000 0.73791 1.397000 0.46682 -0.237000 0.12165 GCG TCGA-HZ-A49I-01A-12D-A26I-08 PLEC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383281.1 1 0 1 27 165 0 76 1 1 375 501 0 76 2 0 0 0 0 0 2 1 1.000000 27 161 0 76 2 -20.000000 1 1 121066 2 29 1 1 2 3 2.052290 0 0.350000 1.860000 0.351136 0.800000 0.550000 1.000000 1.000000 0.809929 0.800000 0 0.670000 0.960000 NR6A1 2649 broad.mit.edu 37 9 127316820 127316820 + Nonsense_Mutation SNP G G A TCGA-HZ-A49I-01A-12D-A26I-08 TCGA-HZ-A49I-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx b0121cca-1fde-4733-8fe1-0a949d789d93 b2e6fcfc-a9e5-4afc-8f3f-ca0056488a32 g.chr9:127316820G>A ENST00000487099.2 - 3 329 c.172C>T c.(172-174)Cga>Tga p.R58* NR6A1_ENST00000344523.4_Nonsense_Mutation_p.R58*|NR6A1_ENST00000416460.2_Nonsense_Mutation_p.R54*|NR6A1_ENST00000373584.3_Nonsense_Mutation_p.R54* NM_001278546.1 NP_001265475.1 Q15406 NR6A1_HUMAN nuclear receptor subfamily 6, group A, member 1 17 AGACAGGTTCGTTGTTCAGCC 0.463000 Esophageal Squamous(192;272 2884 6208 20560) 0 SO:0001587 stop_gained ENST00000487099.2 0 1 hg19 CCDS35137.1 . . . . . . . . . . G 32 5.168299 0.94768 . . ENSG00000148200 ENST00000487099;ENST00000373584;ENST00000416460;ENST00000344523;ENST00000475178 . . . 5.46 4.54 0.55810 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.07644 T 0.81 . 12.3582 0.55188 0.0:0.0:0.6932:0.3068 . . . . X 58;54;54;58;16 . ENSP00000341135:R58X R - 1 2 NR6A1 126356641 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 4.424000 0.59868 1.256000 0.44068 0.563000 0.77884 CGA TCGA-HZ-A49I-01A-12D-A26I-08 NR6A1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000054043.4 1 0 1 82 357 0 139 0 0 0 0 139 2 0 0 0 0 0 2 1 1.000000 83 356 0 139 2 -20.000000 1 1 0 0 1 0 0 0 2.038036 0 0.350000 1.860000 0.345418 0.990000 0.850000 1.000000 1.000000 0.982852 0.990000 1 0.950000 1.000000