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 ATRNL1 26033 broad.mit.edu 37 10 117221467 117221474 + Frame_Shift_Del DEL TTATCAAT TTATCAAT - TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr10:117221467_117221474delTTATCAAT ENST00000355044.3 + 22 3465_3472 c.3339_3346delTTATCAAT c.(3337-3348)gattatcaatttfs p.YQF1114fs ATRNL1_ENST00000303745.7_Intron|ATRNL1_ENST00000423111.2_Frame_Shift_Del_p.YQF165fs NM_207303.2 NP_997186.1 Q5VV63 ATRN1_HUMAN attractin-like 1 95 all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234) TTTTGATTGATTATCAATTTACCTTCAG 0.322000 0 SO:0001589 frameshift_variant ENST00000355044.3 1 1 hg19 CCDS7592.1 TCGA-3A-A9IZ-01A-12D-A40W-08 ATRNL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050507.3 1 0 0 49 293 0 57 0 0 0 57 0 0 0 0 0 0 1 0.999985 73 324 1 58 22 -20.000000 1 1 0 0 1 1 2 3 2.067555 0 0.560000 1.960000 0.564873 0.510000 3.900000e-01 1.000000 0.510000 0.537446 0.510000 0 0.450000 0.600000 ABCC6 368 broad.mit.edu 37 16 16284067 16284068 + Frame_Shift_Ins INS - - GG TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr16:16284067_16284068insGG ENST00000205557.7 - 12 1617_1618 c.1588_1589insCC c.(1588-1590)ctcfs p.L530fs ABCC6_ENST00000574094.1_5'UTR NM_001171.5 NP_001162 O95255 MRP6_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 6 43 Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570) AGAGAAGAGGAGGCCGGAGGTC 0.594000 0 SO:0001589 frameshift_variant ENST00000205557.7 0 1 hg19 CCDS10568.1 TCGA-3A-A9IZ-01A-12D-A40W-08 ABCC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252232.2 1 0 0 67 430 0 74 0 0 0 1 0 74 2 0 0 0 0 0 0 1 1.000000 68 424 0 66 2 -20.000000 1 1 0 0 1 1 2 3 2.060149 0 0.560000 1.960000 0.564873 0.480000 3.800000e-01 1.000000 0.490000 0.506017 0.480000 0 0.430000 0.550000 SLC6A3 6531 broad.mit.edu 37 5 1432653 1432653 + Frame_Shift_Del DEL A A - TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:1432653delA ENST00000270349.9 - 4 706 c.579delT c.(577-579)catfs p.H193fs SLC6A3_ENST00000453492.2_Frame_Shift_Del_p.H193fs NM_001044.4 NP_001035.1 Q01959 SC6A3_HUMAN solute carrier family 6 (neurotransmitter transporter), member 3 38 OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262) Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285) AGTCACCAGGATGGGCATCCG 0.597000 0 SO:0001589 frameshift_variant ENST00000270349.9 1 1 hg19 CCDS3863.1 TCGA-3A-A9IZ-01A-12D-A40W-08 SLC6A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253650.3 1 0 0 62 428 0 44 0 1.740601e-01 0 6 0 44 2 0 0 0 0 0 0 1 1.000000 61 423 0 41 2 -20.000000 1 1 0 0 1 1 3 4 2.612569 1 0.560000 1.960000 0.666465 0.620000 4.700000e-01 1.000000 0.600000 0.697064 0.620000 0 0.530000 1.000000 SESN1 27244 broad.mit.edu 37 6 109309803 109309828 + Frame_Shift_Del DEL TTCAGGAGTGCAAACAACAGTTTTGA TTCAGGAGTGCAAACAACAGTTTTGA - TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr6:109309803_109309828delTTCAGGAGTGCAAACAACAGTTTTGA ENST00000356644.7 - 9 1404_1429 c.1310_1335delTCAAAACTGTTGTTTGCACTCCTGAA c.(1309-1335)atcaaaactgttgtttgcactcctgaafs p.IKTVVCTPE437fs SESN1_ENST00000436639.2_Frame_Shift_Del_p.IKTVVCTPE496fs|SESN1_ENST00000302071.2_Frame_Shift_Del_p.IKTVVCTPE371fs NM_001199933.1 NP_001186862.1 Q9Y6P5 SESN1_HUMAN sestrin 1 p.E504Q(1) 10 all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637) TGGTAACCTTTTCAGGAGTGCAAACAACAGTTTTGATATAAACTTT 0.341000 1 Substitution - Missense(1) SO:0001589 frameshift_variant ENST00000356644.7 0 1 hg19 CCDS56445.1 TCGA-3A-A9IZ-01A-12D-A40W-08 SESN1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000041738.4 1 0 0 15 69 0 28 0 6.656172e-01 0 12 0 28 2 0 0 0 0 0 0 1 0.959038 48 104 1 30 16 -20.000000 1 1 0 0 1 0 1 1 1.488837 1 0.560000 1.960000 0.391256 0.450000 2.700000e-01 0.680000 0.450000 0.471471 0.450000 0 0.360000 0.570000 C10orf76 79591 broad.mit.edu 37 10 103792843 103792843 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr10:103792843G>C ENST00000370033.4 - 4 365 c.246C>G c.(244-246)ttC>ttG p.F82L C10orf76_ENST00000311122.5_Missense_Mutation_p.F82L NM_024541.2 NP_078817.2 Q5T2E6 CJ076_HUMAN chromosome 10 open reading frame 76 24 Colorectal(252;0.123) TGCAGTGTTGGAATAAGCAAT 0.453000 0 SO:0001583 missense ENST00000370033.4 1 1 hg19 CCDS41563.1 . . . . . . . . . . G 17.24 3.339757 0.60963 . . ENSG00000120029 ENST00000370033;ENST00000311122 T;T 0.61274 0.12;2.32 6.15 2.25 0.28309 . 0.000000 0.85682 D 0.000000 T 0.66386 0.2784 L 0.56124 1.755 0.80722 D 1 P;D 0.71674 0.528;0.998 B;D 0.76071 0.128;0.987 T 0.62765 -0.6785 10 0.45353 T 0.12 -17.9247 8.6237 0.33877 0.5511:0.0:0.4489:0.0 . 82;82 Q5T2E6;Q5T2E7 CJ076_HUMAN;. L 82 ENSP00000359050:F82L;ENSP00000312408:F82L ENSP00000312408:F82L F - 3 2 C10orf76 103782833 1.000000 0.71417 1.000000 0.80357 0.926000 0.56050 1.090000 0.30902 0.455000 0.26910 -0.366000 0.07423 TTC TCGA-3A-A9IZ-01A-12D-A40W-08 C10orf76-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050007.1 0 0 0 10 314 0 88 1 1.144774e-01 2 15 0 88 2 0 0 0 0 0 2 1 0.996751 10 309 0 86 2 -3.159045 1 1 0 0 1 0 1 1 1.493332 1 0.560000 1.960000 0.391256 0.070000 3.000000e-02 0.140000 0.080000 0.086685 0.070000 0 0.050000 0.110000 CUBN 8029 broad.mit.edu 37 10 16882333 16882333 + Missense_Mutation SNP G G A rs150358307 byFrequency TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr10:16882333G>A ENST00000377833.4 - 62 10093 c.10028C>T c.(10027-10029)cCg>cTg p.P3343L NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) TGTTACCTGCGGTGAGTCCTG 0.423000 0 SO:0001583 missense ENST00000377833.4 1 1 hg19 CCDS7113.1 . . . . . . . . . . G 6.344 0.431511 0.12045 0.0 4.65E-4 ENSG00000107611 ENST00000377833;ENST00000545090 T 0.17054 2.3 4.74 0.6 0.17524 CUB (5); 0.659654 0.12465 N 0.466572 T 0.16085 0.0387 M 0.71581 2.175 0.09310 N 0.999999 P 0.46912 0.886 B 0.40410 0.328 T 0.14755 -1.0461 10 0.36615 T 0.2 . 3.4857 0.07618 0.1517:0.1351:0.5736:0.1397 . 3343 O60494 CUBN_HUMAN L 3343;184 ENSP00000367064:P3343L ENSP00000367064:P3343L P - 2 0 CUBN 16922339 0.602000 0.26916 0.058000 0.19502 0.142000 0.21351 1.757000 0.38400 0.061000 0.16311 0.561000 0.74099 CCG TCGA-3A-A9IZ-01A-12D-A40W-08 CUBN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047009.1 1 0 1 58 169 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 56 168 0 50 2 -3.971141 1 1 121412 37 46 1 1 2 3 2.043907 0 0.560000 1.960000 0.562450 0.910000 7.200000e-01 1.000000 1.000000 0.908974 0.910000 1 0.810000 1.000000 ARHGAP19 84986 broad.mit.edu 37 10 99024599 99024599 + Silent SNP A A T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr10:99024599A>T ENST00000358531.4 - 3 415 c.387T>A c.(385-387)atT>atA p.I129I ARHGAP19-SLIT1_ENST00000358308.3_Silent_p.I129I|ARHGAP19_ENST00000371027.1_Silent_p.I120I|ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.I129I|ARHGAP19_ENST00000355366.5_Silent_p.I120I|ARHGAP19-SLIT1_ENST00000316676.8_Silent_p.I129I NM_001204300.1|NM_032900.5 NP_001191229.1|NP_116289.4 Q14CB8 RHG19_HUMAN Rho GTPase activating protein 19 13 Colorectal(252;0.0854) GTAGATACTCAATCAGTTGGT 0.368000 0 SO:0001819 synonymous_variant ENST00000358531.4 1 0 hg19 CCDS7454.2 TCGA-3A-A9IZ-01A-12D-A40W-08 ARHGAP19-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049647.2 1 0 1 68 111 0 64 0 0 1 0 0 64 2 0 0 0 0 0 2 1 1.000000 68 109 0 64 2 -20.000000 1 1 0 0 1 0 1 1 1.493332 1 0.560000 1.960000 0.391256 0.920000 7.700000e-01 1.000000 1.000000 0.924139 0.920000 1 0.850000 0.990000 KCNA4 3739 broad.mit.edu 37 11 30032887 30032887 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:30032887G>A ENST00000328224.6 - 2 2572 c.1339C>T c.(1339-1341)Cgt>Tgt p.R447C KCNA4_ENST00000526518.1_5'Flank NM_002233.3 NP_002224.1 P22459 KCNA4_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 4 78 Dalfampridine(DB06637) CGGACCAGACGAATGATTCTG 0.587000 0 SO:0001583 missense ENST00000328224.6 1 1 hg19 CCDS41629.1 . . . . . . . . . . G 19.02 3.745893 0.69418 . . ENSG00000182255 ENST00000328224 D 0.99259 -5.64 5.32 5.32 0.75619 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.99799 0.9914 H 0.99897 4.91 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.96415 0.9307 10 0.87932 D 0 . 19.003 0.92841 0.0:0.0:1.0:0.0 . 447 P22459 KCNA4_HUMAN C 447 ENSP00000328511:R447C ENSP00000328511:R447C R - 1 0 KCNA4 29989463 1.000000 0.71417 0.889000 0.34880 0.979000 0.70002 9.869000 0.99810 2.491000 0.84063 0.650000 0.86243 CGT TCGA-3A-A9IZ-01A-12D-A40W-08 KCNA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388074.2 1 0 0 12 230 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 0.999142 12 228 0 71 2 -3.333451 1 1 0 0 1 0 1 1 1.475442 1 0.560000 1.960000 0.388889 0.120000 6.000000e-02 0.210000 0.130000 0.136109 0.120000 0 0.090000 0.170000 OR51A7 119687 broad.mit.edu 37 11 4928955 4928955 + Missense_Mutation SNP C C A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:4928955C>A ENST00000359350.4 + 1 356 c.356C>A c.(355-357)tCt>tAt p.S119Y MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron NM_001004749.1 NP_001004749.1 Q8NH64 O51A7_HUMAN olfactory receptor, family 51, subfamily A, member 7 33 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086) CTAATTATGTCTTTGGACCGC 0.403000 0 SO:0001583 missense ENST00000359350.4 1 1 hg19 CCDS31364.1 . . . . . . . . . . C 17.39 3.377814 0.61735 . . ENSG00000176895 ENST00000359350;ENST00000545959;ENST00000544684 T 0.81415 -1.49 5.02 5.02 0.67125 GPCR, rhodopsin-like superfamily (1); 0.145141 0.32328 N 0.006243 D 0.92463 0.7607 H 0.94808 3.585 0.31719 N 0.6385 D 0.89917 1.0 D 0.76575 0.988 D 0.93516 0.6857 10 0.87932 D 0 . 17.069 0.86568 0.0:1.0:0.0:0.0 . 119 Q8NH64 O51A7_HUMAN Y 119;119;108 ENSP00000352305:S119Y ENSP00000352305:S119Y S + 2 0 OR51A7 4885531 1.000000 0.71417 1.000000 0.80357 0.411000 0.31082 5.325000 0.65869 2.596000 0.87737 0.655000 0.94253 TCT TCGA-3A-A9IZ-01A-12D-A40W-08 OR51A7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142175.1 0 0 1 141 211 0 139 0 0 0 0 139 2 0 0 0 0 0 2 1 1.000000 141 209 0 138 2 -20.000000 1 1 0 0 1 0 1 1 1.475442 1 0.560000 1.960000 0.388889 0.960000 8.600000e-01 1.000000 0.990000 0.958966 0.960000 1 0.910000 0.990000 OR9Q2 219957 broad.mit.edu 37 11 57958767 57958767 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:57958767G>A ENST00000311591.3 + 1 862 c.805G>A c.(805-807)Gag>Aag p.E269K NM_001005283.2 NP_001005283.1 Q8NGE9 OR9Q2_HUMAN olfactory receptor, family 9, subfamily Q, member 2 p.E269K(1) 41 Breast(21;0.0589) CCAGTCCTCCGAGGGAGACCG 0.552000 1 Substitution - Missense(1) SO:0001583 missense ENST00000311591.3 1 1 hg19 CCDS31544.1 . . . . . . . . . . G 9.517 1.107203 0.20714 . . ENSG00000186513 ENST00000311591 T 0.00099 8.73 5.09 2.85 0.33270 GPCR, rhodopsin-like superfamily (1); 0.463064 0.18027 N 0.154059 T 0.00109 0.0003 N 0.25825 0.765 0.09310 N 1 B 0.27932 0.194 B 0.22601 0.04 T 0.21042 -1.0257 10 0.59425 D 0.04 -9.1453 9.2658 0.37641 0.0947:0.1872:0.7181:0.0 . 269 Q8NGE9 OR9Q2_HUMAN K 269 ENSP00000308714:E269K ENSP00000308714:E269K E + 1 0 OR9Q2 57715343 0.006000 0.16342 0.072000 0.20136 0.347000 0.29111 1.109000 0.31135 1.338000 0.45544 0.655000 0.94253 GAG TCGA-3A-A9IZ-01A-12D-A40W-08 OR9Q2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394540.1 1 0 1 80 289 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1.000000 81 286 0 73 2 -3.544887 1 1 0 0 1 1 2 3 2.032037 0 0.560000 1.960000 0.561229 0.770000 6.200000e-01 0.940000 0.780000 0.780191 0.770000 0 0.690000 0.860000 OR1S2 219958 broad.mit.edu 37 11 57970714 57970714 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:57970714G>A ENST00000302592.6 - 1 939 c.940C>T c.(940-942)Ctg>Ttg p.L314L NM_001004459.1 NP_001004459.1 Q8NGQ3 OR1S2_HUMAN olfactory receptor, family 1, subfamily S, member 2 46 Breast(21;0.0589) AGCTTTCTCAGGGCACCTTTC 0.418000 0 SO:0001819 synonymous_variant ENST00000302592.6 0 1 hg19 CCDS31545.1 TCGA-3A-A9IZ-01A-12D-A40W-08 OR1S2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394703.2 0 0 0 7 642 0 144 0 0 0 0 144 2 0 0 0 0 0 2 1 0.975668 7 601 0 147 2 -2.101409 0 1 0 0 1 1 2 3 2.032037 0 0.560000 1.960000 0.561229 0.030000 0 0.080000 0.040000 0.043963 0.030000 0 0.020000 0.060000 ZNF215 7762 broad.mit.edu 37 11 6953847 6953847 + Missense_Mutation SNP A A G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:6953847A>G ENST00000278319.5 + 3 932 c.344A>G c.(343-345)aAc>aGc p.N115S ZNF215_ENST00000414517.2_Missense_Mutation_p.N115S|ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000529903.1_Missense_Mutation_p.N115S NM_013250.2 NP_037382.2 Q9UL58 ZN215_HUMAN zinc finger protein 215 32 CATCCAAACAACAGTAAAGAT 0.378000 0 SO:0001583 missense ENST00000278319.5 1 1 hg19 CCDS7775.1 . . . . . . . . . . A 6.216 0.407981 0.11754 . . ENSG00000149054 ENST00000278319;ENST00000414517;ENST00000529903 T;T;T 0.04015 3.73;3.73;3.73 4.14 0.197 0.15164 Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3); 0.168848 0.28166 N 0.016350 T 0.02342 0.0072 N 0.13352 0.335 0.22903 N 0.998588 B;B;B 0.32409 0.248;0.37;0.181 B;B;B 0.35770 0.112;0.21;0.074 T 0.44682 -0.9312 10 0.05959 T 0.93 -7.9422 6.3872 0.21568 0.6446:0.0:0.3554:0.0 . 115;115;115 B4DYW9;Q96C84;Q9UL58 .;.;ZN215_HUMAN S 115 ENSP00000278319:N115S;ENSP00000393202:N115S;ENSP00000432306:N115S ENSP00000278319:N115S N + 2 0 ZNF215 6910423 0.062000 0.20869 0.987000 0.45799 0.144000 0.21451 -0.089000 0.11180 0.022000 0.15160 0.533000 0.62120 AAC TCGA-3A-A9IZ-01A-12D-A40W-08 ZNF215-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000384550.1 1 0 1 28 141 0 47 0 0 1 0 0 47 2 0 0 0 0 0 2 1 1.000000 28 139 0 45 2 -20.000000 1 1 121412 1 33 1 0 1 1 1.475442 1 0.560000 1.960000 0.388889 0.420000 2.900000e-01 0.570000 0.420000 0.432058 0.420000 0 0.350000 0.500000 PLEKHB1 58473 broad.mit.edu 37 11 73364058 73364058 + Splice_Site SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:73364058C>G ENST00000354190.5 + 5 820 c.389C>G c.(388-390)cCg>cGg p.P130R PLEKHB1_ENST00000398494.4_Splice_Site_p.P111R|PLEKHB1_ENST00000227214.6_Splice_Site_p.P111R|PLEKHB1_ENST00000535129.1_Splice_Site_p.P111R|PLEKHB1_ENST00000398492.4_Splice_Site_p.P130R|PLEKHB1_ENST00000543085.1_Splice_Site_p.P60R NM_021200.2 NP_067023.1 Q9UF11 PKHB1_HUMAN pleckstrin homology domain containing, family B (evectins) member 1 7 AACTCCACCCCGGTGAGTCTC 0.582000 0 SO:0001630 splice_region_variant ENST00000354190.5 0 1 hg19 CCDS44672.1 . . . . . . . . . . C 11.54 1.668309 0.29604 . . ENSG00000021300 ENST00000354190;ENST00000398492;ENST00000227214;ENST00000398494;ENST00000543085;ENST00000539157;ENST00000546251;ENST00000535582;ENST00000538227;ENST00000539549;ENST00000542185;ENST00000543524;ENST00000541597;ENST00000535129;ENST00000542389;ENST00000540431 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.29142 1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58 4.53 3.62 0.41486 Pleckstrin homology-type (1);Pleckstrin homology domain (1); 0.176334 0.50627 D 0.000115 T 0.41236 0.1150 L 0.38175 1.15 0.39250 D 0.964026 D;D;D;P 0.89917 0.975;1.0;1.0;0.954 D;D;D;P 0.91635 0.943;0.999;0.999;0.819 T 0.35325 -0.9793 10 0.54805 T 0.06 -18.4952 8.962 0.35854 0.0:0.901:0.0:0.099 . 111;134;130;130 F5GXN2;Q59EU5;Q9UF11-2;Q9UF11 .;.;.;PKHB1_HUMAN R 130;130;111;111;60;118;111;111;111;111;111;111;111;111;111;118 ENSP00000346127:P130R;ENSP00000381505:P130R;ENSP00000227214:P111R;ENSP00000381507:P111R;ENSP00000441224:P60R;ENSP00000445990:P118R;ENSP00000439714:P111R;ENSP00000438809:P111R;ENSP00000445807:P111R;ENSP00000444453:P111R;ENSP00000442136:P111R;ENSP00000442616:P111R;ENSP00000440102:P111R;ENSP00000441558:P118R ENSP00000227214:P111R P + 2 0 PLEKHB1 73041706 1.000000 0.71417 1.000000 0.80357 0.016000 0.09150 1.837000 0.39201 1.517000 0.48917 -0.133000 0.14855 CCG TCGA-3A-A9IZ-01A-12D-A40W-08 PLEKHB1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000397593.1 0 0 0 10 146 0 21 1 4.913512e-01 3 21 0 21 2 0 0 0 0 0 2 1 0.996554 10 140 0 21 2 -3.021303 1 1 0 0 1 1 2 3 2.567761 1 0.560000 1.960000 0.654739 0.300000 1.500000e-01 0.540000 0.300000 0.322510 0.300000 0 0.220000 0.410000 PANX1 24145 broad.mit.edu 37 11 93911725 93911725 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr11:93911725C>T ENST00000227638.3 + 3 897 c.512C>T c.(511-513)tCa>tTa p.S171L PANX1_ENST00000436171.2_Missense_Mutation_p.S171L NM_015368.3 NP_056183.2 Q96RD7 PANX1_HUMAN pannexin 1 20 Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824) Probenecid(DB01032) GGAGCCTGCTCAGTTCCAGGT 0.483000 0 SO:0001583 missense ENST00000227638.3 1 1 hg19 CCDS8296.1 . . . . . . . . . . C 11.94 1.789449 0.31685 . . ENSG00000110218 ENST00000227638;ENST00000436171 T;T 0.26957 1.7;1.7 5.05 5.05 0.67936 . 0.838115 0.11120 N 0.597512 T 0.21427 0.0516 N 0.25647 0.755 0.09310 N 1 B;B 0.20164 0.042;0.034 B;B 0.25506 0.061;0.036 T 0.14035 -1.0487 10 0.25106 T 0.35 -1.3263 13.7438 0.62863 0.0:0.9231:0.0:0.0769 . 171;171 Q96RD7;Q96RD7-2 PANX1_HUMAN;. L 171 ENSP00000227638:S171L;ENSP00000411461:S171L ENSP00000227638:S171L S + 2 0 PANX1 93551373 0.002000 0.14202 0.154000 0.22540 0.125000 0.20455 1.502000 0.35704 2.342000 0.79632 0.563000 0.77884 TCA TCGA-3A-A9IZ-01A-12D-A40W-08 PANX1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396121.1 1 0 1 87 292 0 62 1 9.998076e-01 5 40 0 62 2 0 0 0 0 0 2 1 1.000000 85 288 0 62 2 -4.285428 1 1 121412 12 42 1 1 2 3 2.567761 1 0.560000 1.960000 0.654739 0.990000 8.500000e-01 1.000000 1.000000 0.981167 0.990000 1 0.940000 1.000000 WSB2 55884 broad.mit.edu 37 12 118481162 118481162 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr12:118481162G>C ENST00000315436.3 - 3 344 c.203C>G c.(202-204)gCc>gGc p.A68G WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000441406.2_Missense_Mutation_p.A85G|WSB2_ENST00000535496.1_Missense_Mutation_p.A70G|WSB2_ENST00000542304.1_5'UTR|WSB2_ENST00000544233.1_Intron NM_001278557.1|NM_018639.3 NP_001265486.1|NP_061109.1 Q9NYS7 WSB2_HUMAN WD repeat and SOCS box containing 2 17 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TCGGCTTTTGGCTTCAAACCC 0.493000 0 SO:0001583 missense ENST00000315436.3 1 1 hg19 CCDS9186.1 . . . . . . . . . . G 12.02 1.813241 0.32053 . . ENSG00000176871 ENST00000315436;ENST00000441406;ENST00000535496;ENST00000537945 T;T;T;T 0.61510 0.33;0.35;0.37;0.1 5.24 5.24 0.73138 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.647108 0.14669 N 0.305457 T 0.39145 0.1067 N 0.19112 0.55 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.16247 -1.0409 10 0.02654 T 1 -15.2412 14.0586 0.64786 0.0:0.152:0.848:0.0 . 68 Q9NYS7 WSB2_HUMAN G 68;85;70;70 ENSP00000319474:A68G;ENSP00000409131:A85G;ENSP00000439450:A70G;ENSP00000440386:A70G ENSP00000319474:A68G A - 2 0 WSB2 116965545 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.925000 0.56484 2.731000 0.93534 0.650000 0.86243 GCC TCGA-3A-A9IZ-01A-12D-A40W-08 WSB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401515.1 0 0 0 18 562 0 108 1 8.188137e-01 5 95 0 108 2 0 0 0 0 0 2 1 0.999980 18 555 0 104 2 -3.257625 1 1 0 0 1 0 1 1 2.002778 1 0.560000 1.960000 0.388889 0.070000 4.000000e-02 0.120000 0.080000 0.083712 0.070000 0 0.050000 0.100000 EPS8 2059 broad.mit.edu 37 12 15807213 15807213 + Silent SNP T T G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr12:15807213T>G ENST00000281172.5 - 13 1552 c.1116A>C c.(1114-1116)acA>acC p.T372T EPS8_ENST00000543612.1_Silent_p.T372T|EPS8_ENST00000540613.1_Silent_p.T112T|EPS8_ENST00000542903.1_Silent_p.T112T|EPS8_ENST00000543523.1_Silent_p.T372T NM_004447.5 NP_004438.3 Q12929 EPS8_HUMAN epidermal growth factor receptor pathway substrate 8 33 all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244) CAGGACCTCCTGTTGCCTGCA 0.373000 0 SO:0001819 synonymous_variant ENST00000281172.5 1 1 hg19 CCDS31753.1 TCGA-3A-A9IZ-01A-12D-A40W-08 EPS8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401093.1 1 0 0 19 306 0 79 1 9.825060e-01 7 101 0 79 2 0 0 0 0 0 2 1 0.999991 19 302 0 77 2 -19.994040 1 1 0 0 1 0 0 0 2.023893 0 0.560000 1.960000 0.560000 0.200000 1.200000e-01 0.310000 0.210000 0.217894 0.200000 0 0.160000 0.260000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 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-3A-A9IZ-01A-12D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 56 151 0 59 1 9.980812e-01 19 10 0 59 2 1 1 74 273 0 274 2 1 1.000000 54 150 0 57 2 -20.000000 1 1 121404 2 44 1 0 0 0 2.023893 0 0.560000 1.960000 0.560000 0.960000 7.500000e-01 1.000000 1.000000 0.939583 0.960000 1 0.850000 1.000000 PRMT8 56341 broad.mit.edu 37 12 3649855 3649855 + Silent SNP C C A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr12:3649855C>A ENST00000382622.3 + 2 549 c.159C>A c.(157-159)ccC>ccA p.P53P PRMT8_ENST00000452611.2_Silent_p.P44P|PRMT8_ENST00000261252.4_3'UTR NM_019854.4 NP_062828.3 Q9NR22 ANM8_HUMAN protein arginine methyltransferase 8 37 OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264) CCACTCAACCCAGCTGCCCAG 0.602000 0 SO:0001819 synonymous_variant ENST00000382622.3 1 1 hg19 CCDS8521.2 TCGA-3A-A9IZ-01A-12D-A40W-08 PRMT8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250297.2 1 0 1 251 651 0 157 0 0 0 0 157 2 0 0 0 0 0 2 1 1.000000 249 638 0 152 2 -11.201150 1 1 0 0 1 1 2 3 2.122144 0 0.560000 1.960000 0.570815 0.990000 9.000000e-01 1.000000 1.000000 0.987565 0.990000 1 0.960000 1.000000 CCDC41 0 broad.mit.edu 37 12 94761622 94761622 + Missense_Mutation SNP G G A rs111647062 TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr12:94761622G>A ENST00000397809.5 - 11 1840 c.1291C>T c.(1291-1293)Cgg>Tgg p.R431W CCDC41_ENST00000549352.1_5'Flank|CCDC41_ENST00000397807.2_Missense_Mutation_p.R398W|CCDC41_ENST00000339839.5_Missense_Mutation_p.R431W NM_016122.2 NP_057206.2 Q9Y592 CEP83_HUMAN 27 TGTGAAGCCCGCAATTTCTCT 0.373000 0 SO:0001583 missense ENST00000397809.5 0 1 hg19 CCDS41820.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 14.11 2.438221 0.43326 2.7E-4 2.43E-4 ENSG00000173588 ENST00000339839;ENST00000397809;ENST00000397807 T;T;T 0.53857 1.94;1.94;0.6 5.83 4.94 0.65067 . . . . . T 0.56761 0.2007 L 0.56769 1.78 0.36865 D 0.888618 D;D 0.76494 0.999;0.993 P;P 0.50896 0.653;0.534 T 0.67515 -0.5651 9 0.87932 D 0 -8.5225 10.5268 0.44954 0.0683:0.0:0.7969:0.1348 . 398;423 Q9Y592-2;Q9Y592 .;CCD41_HUMAN W 431;431;398 ENSP00000344655:R431W;ENSP00000380911:R431W;ENSP00000380909:R398W ENSP00000344655:R431W R - 1 2 CCDC41 93285753 1.000000 0.71417 1.000000 0.80357 0.006000 0.05464 6.105000 0.71505 1.461000 0.47929 -0.181000 0.13052 CGG TCGA-3A-A9IZ-01A-12D-A40W-08 CCDC41-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408147.3 0 0 0 6 653 0 157 0 7.719552e-03 0 12 0 157 2 0 0 0 0 0 2 1 0.963397 4 645 0 152 2 -1.808643 0 1 120824 50 52 1 0 1 1 2.002778 1 0.560000 1.960000 0.388889 0.020000 0 0.050000 0.020000 0.027161 0.020000 0 0.010000 0.040000 SLC15A1 6564 broad.mit.edu 37 13 99339977 99339977 + Splice_Site SNP T T C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr13:99339977T>C ENST00000376503.5 - 21 1740 c.1685A>G c.(1684-1686)aAt>aGt p.N562S NM_005073.3 NP_005064.1 P46059 S15A1_HUMAN solute carrier family 15 (oligopeptide transporter), member 1 30 all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610) GCAGCTGTCATTCTGCAGCAG 0.408000 0 SO:0001630 splice_region_variant ENST00000376503.5 1 0 hg19 CCDS9489.1 . . . . . . . . . . T 0.258 -1.001780 0.02128 . . ENSG00000088386 ENST00000376503 T 0.01998 4.51 5.45 -5.68 0.02436 Major facilitator superfamily domain, general substrate transporter (1); 1.941670 0.01609 N 0.022434 T 0.00936 0.0031 N 0.02120 -0.675 0.09310 N 1 B 0.06786 0.001 B 0.04013 0.001 T 0.45205 -0.9277 10 0.02654 T 1 -29.6666 8.1832 0.31324 0.0:0.3927:0.3876:0.2197 . 562 P46059 S15A1_HUMAN S 562 ENSP00000365686:N562S ENSP00000365686:N562S N - 2 0 SLC15A1 98137978 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.980000 0.03770 -1.882000 0.01122 -0.460000 0.05396 AAT TCGA-3A-A9IZ-01A-12D-A40W-08 SLC15A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045560.3 1 0 1 85 142 0 79 1 7.207349e-01 5 1 0 79 2 0 0 0 0 0 2 1 1.000000 84 139 0 78 2 -20.000000 1 1 0 0 1 0 1 1 1.506971 1 0.560000 1.960000 0.391256 0.920000 7.900000e-01 1.000000 1.000000 0.925466 0.920000 1 0.860000 0.990000 RCOR1 23186 broad.mit.edu 37 14 103180896 103180896 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr14:103180896C>T ENST00000570597.1 + 8 986 c.986C>T c.(985-987)aCt>aTt p.T329I RCOR1_ENST00000262241.6_Missense_Mutation_p.T332I Q9UKL0 RCOR1_HUMAN REST corepressor 1 12 GCCAATGCCACTGCTGCTACC 0.413000 0 SO:0001583 missense ENST00000570597.1 0 1 hg19 . . . . . . . . . . C 17.53 3.412066 0.62511 . . ENSG00000089902 ENST00000262241 . . . 6.07 5.16 0.70880 . 0.206697 0.50627 D 0.000108 T 0.35998 0.0951 N 0.22421 0.69 0.51233 D 0.999914 P 0.40032 0.699 B 0.33620 0.167 T 0.26155 -1.0111 9 0.46703 T 0.11 -16.8936 12.052 0.53511 0.1363:0.7327:0.131:0.0 . 329 Q9UKL0 RCOR1_HUMAN I 329 . ENSP00000262241:T329I T + 2 0 RCOR1 102250649 0.999000 0.42202 0.981000 0.43875 0.985000 0.73830 4.443000 0.59994 1.516000 0.48900 0.655000 0.94253 ACT TCGA-3A-A9IZ-01A-12D-A40W-08 RCOR1-201 KNOWN basic|appris_candidate protein_coding protein_coding 0 0 0 6 314 0 63 0 1.797436e-01 0 35 0 63 2 0 0 0 0 0 2 1 0.963978 5 311 0 61 2 -6.541969 1 0 0 0 1 1 2 3 2.030033 0 0.560000 1.960000 0.561229 0.060000 2.000000e-02 0.150000 0.070000 0.077685 0.060000 0 0.040000 0.110000 PSMB11 122706 broad.mit.edu 37 14 23511502 23511502 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr14:23511502G>C ENST00000408907.2 + 1 127 c.68G>C c.(67-69)cGg>cCg p.R23P NM_001099780.1 NP_001093250.1 A5LHX3 PSB11_HUMAN proteasome (prosome, macropain) subunit, beta type, 11 7 all_cancers(95;3.3e-05) CACCTGCCTCGGGCTGGCGGC 0.637000 0 SO:0001583 missense ENST00000408907.2 0 1 hg19 CCDS41923.1 . . . . . . . . . . G 1.987 -0.432710 0.04669 . . ENSG00000222028 ENST00000408907 T 0.27890 1.64 5.53 -11.1 0.00147 . 1.913640 0.03285 N 0.186696 T 0.12774 0.0310 N 0.12961 0.28 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.08617 -1.0713 10 0.27082 T 0.32 -1.412 4.21 0.10507 0.2548:0.2667:0.3906:0.088 . 23 A5LHX3 PSB11_HUMAN P 23 ENSP00000386212:R23P ENSP00000386212:R23P R + 2 0 PSMB11 22581342 0.000000 0.05858 0.000000 0.03702 0.230000 0.25150 -2.830000 0.00744 -2.417000 0.00567 -1.044000 0.02363 CGG TCGA-3A-A9IZ-01A-12D-A40W-08 PSMB11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408294.1 0 0 0 9 505 0 91 0 0 0 0 91 2 0 0 0 0 0 2 1 0.993532 9 491 0 88 2 -2.268914 0 1 0 0 1 1 2 3 2.030033 0 0.560000 1.960000 0.561229 0.060000 2.000000e-02 0.120000 0.060000 0.069305 0.060000 0 0.040000 0.090000 FBN1 2200 broad.mit.edu 37 15 48766481 48766481 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 C G C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr15:48766481C>G ENST00000316623.5 - 34 4636 c.4181G>C c.(4180-4182)gGa>gCa p.G1394A NM_000138.4 NP_000129 P35555 FBN1_HUMAN fibrillin 1 139 all_lung(180;0.00279) ACCTGTGTATCCTTCCTTGCA 0.473000 0 SO:0001583 missense ENST00000316623.5 1 1 hg19 CCDS32232.1 . . . . . . . . . . C 16.18 3.049649 0.55218 . . ENSG00000166147 ENST00000316623;ENST00000544030 D 0.92595 -3.07 5.29 5.29 0.74685 EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.097281 0.64402 D 0.000001 D 0.97636 0.9225 H 0.96604 3.85 0.80722 D 1 D 0.76494 0.999 D 0.91635 0.999 D 0.98621 1.0667 10 0.87932 D 0 . 18.7133 0.91666 0.0:1.0:0.0:0.0 . 1394 P35555 FBN1_HUMAN A 1394;284 ENSP00000325527:G1394A ENSP00000325527:G1394A G - 2 0 FBN1 46553773 1.000000 0.71417 0.972000 0.41901 0.983000 0.72400 7.597000 0.82733 2.753000 0.94483 0.650000 0.86243 GGA TCGA-3A-A9IZ-01A-12D-A40W-08 FBN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417355.1 1 0 1 73 148 0 60 0 9.999978e-01 0 44 0 60 2 0 0 0 0 0 2 1 1.000000 73 147 0 58 2 -20.000000 1 1 0 0 1 0 1 1 2.015215 0 0.560000 1.960000 0.558765 0.990000 9.500000e-01 1.000000 1.000000 0.997664 0.990000 1 0.990000 1.000000 CYP1A1 1543 broad.mit.edu 37 15 75014944 75014944 + Missense_Mutation SNP C C A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr15:75014944C>A ENST00000379727.3 - 2 693 c.495G>T c.(493-495)aaG>aaT p.K165N CYP1A1_ENST00000395048.2_Missense_Mutation_p.K165N|CYP1A1_ENST00000564596.1_Intron|CYP1A1_ENST00000567032.1_Missense_Mutation_p.K165N|CYP1A1_ENST00000395049.4_Missense_Mutation_p.K165N P04798 CP1A1_HUMAN cytochrome P450, family 1, subfamily A, polypeptide 1 34 Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682) CCTCAGCCTCCTTGCTCACAT 0.572000 Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia 0 SO:0001583 missense Familial Cancer Database ;AIMAH, Cushing disease, Adrenal, Familial ENST00000379727.3 1 1 hg19 CCDS10268.1 . . . . . . . . . . C 11.24 1.580074 0.28180 . . ENSG00000140465 ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062 T;T;T 0.69561 -0.41;-0.41;-0.41 4.91 -1.8 0.07907 . 0.245514 0.46758 D 0.000263 T 0.63486 0.2515 M 0.77712 2.385 0.42656 D 0.993469 B;B 0.30664 0.289;0.171 B;B 0.40477 0.33;0.22 T 0.55023 -0.8205 10 0.52906 T 0.07 . 2.396 0.04390 0.1025:0.3183:0.1675:0.4117 . 165;165 E7EMT5;P04798 .;CP1A1_HUMAN N 165 ENSP00000369050:K165N;ENSP00000378488:K165N;ENSP00000378489:K165N ENSP00000268062:K165N K - 3 2 CYP1A1 72801997 0.191000 0.23288 0.983000 0.44433 0.772000 0.43724 -0.386000 0.07370 -0.412000 0.07519 -0.379000 0.06801 AAG TCGA-3A-A9IZ-01A-12D-A40W-08 CYP1A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286396.1 1 0 1 125 391 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 1.000000 122 384 0 60 2 -4.871128 1 1 0 0 1 0 5 5 2.437396 1 0.560000 1.960000 0.633822 0.990000 8.800000e-01 1.000000 1.000000 0.987405 0.990000 1 0.960000 1.000000 PRM1 5619 broad.mit.edu 37 16 11374992 11374992 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr16:11374992C>G ENST00000312511.3 - 1 215 c.104G>C c.(103-105)aGa>aCa p.R35T RMI2_ENST00000572173.1_Intron NM_002761.2 NP_002752.1 P04553 HSP1_HUMAN protamine 1 p.0?(1) 4 ACTCATGGCTCTCCTCCGTGT 0.617000 1 Whole gene deletion(1) SO:0001583 missense ENST00000312511.3 0 1 hg19 CCDS10547.1 . . . . . . . . . . C 5.402 0.259367 0.10239 . . ENSG00000175646 ENST00000312511 . . . 3.2 2.23 0.28157 . 0.610754 0.13387 N 0.391708 T 0.30198 0.0757 . . . 0.09310 N 1 P 0.44139 0.827 B 0.42087 0.375 T 0.14420 -1.0473 8 0.87932 D 0 1.6873 6.2261 0.20708 0.0:0.8559:0.0:0.1441 . 35 P04553 HSP1_HUMAN T 35 . ENSP00000310515:R35T R - 2 0 PRM1 11282493 0.006000 0.16342 0.004000 0.12327 0.055000 0.15305 0.194000 0.17135 0.560000 0.29169 0.430000 0.28490 AGA TCGA-3A-A9IZ-01A-12D-A40W-08 PRM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207010.1 0 0 0 7 485 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 0.978659 6 472 0 106 2 -2.974678 1 1 0 0 1 1 2 3 2.060149 0 0.560000 1.960000 0.564873 0.050000 1.000000e-02 1.000000 0.060000 0.085558 0.050000 0 0.030000 0.080000 C16orf45 89927 broad.mit.edu 37 16 15677014 15677014 + Splice_Site SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr16:15677014G>C ENST00000300006.4 + 5 780 c.421G>C c.(421-423)Gag>Cag p.E141Q C16orf45_ENST00000561692.1_Splice_Site_p.E93Q|C16orf45_ENST00000452191.2_Splice_Site_p.E124Q|C16orf45_ENST00000566490.1_Intron|C16orf45_ENST00000565913.1_3'UTR NM_033201.2 NP_149978.1 Q96MC5 CP045_HUMAN chromosome 16 open reading frame 45 11 CTTTCACAGGGAGCAAGAAGA 0.378000 0 SO:0001630 splice_region_variant ENST00000300006.4 1 0 hg19 CCDS10561.1 . . . . . . . . . . G 28.5 4.921388 0.92249 . . ENSG00000166780 ENST00000300006;ENST00000452191 T;T 0.59224 0.28;0.28 5.27 5.27 0.74061 Domain of unknown function DUF3585 (1); 0.000000 0.85682 D 0.000000 T 0.79082 0.4386 M 0.84082 2.675 0.58432 D 0.999999 D;D 0.76494 0.997;0.999 D;D 0.83275 0.995;0.996 T 0.82452 -0.0450 10 0.87932 D 0 -19.9858 18.4883 0.90838 0.0:0.0:1.0:0.0 . 85;141 B4DE25;Q96MC5 .;CP045_HUMAN Q 141;124 ENSP00000300006:E141Q;ENSP00000408976:E124Q ENSP00000300006:E141Q E + 1 0 C16orf45 15584515 1.000000 0.71417 1.000000 0.80357 0.942000 0.58702 8.318000 0.89990 2.434000 0.82447 0.650000 0.86243 GAG TCGA-3A-A9IZ-01A-12D-A40W-08 C16orf45-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252130.2 1 0 0 51 503 0 120 1 9.383021e-01 2 46 0 120 2 0 0 0 0 0 2 1 1.000000 50 497 0 120 2 -14.256170 1 1 0 0 1 1 2 3 2.060149 0 0.560000 1.960000 0.564873 0.330000 2.400000e-01 1.000000 0.330000 0.356368 0.330000 0 0.280000 0.390000 HAGH 3029 broad.mit.edu 37 16 1869148 1869148 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr16:1869148G>A ENST00000397356.3 - 5 915 c.509C>T c.(508-510)cCc>cTc p.P170L HAGH_ENST00000455446.2_Intron|HAGH_ENST00000566709.1_Missense_Mutation_p.P122L|HAGH_ENST00000397353.2_Missense_Mutation_p.P122L NM_005326.4 NP_005317.2 Q16775 GLO2_HUMAN hydroxyacylglutathione hydrolase 5 Hepatocellular(780;0.00335) Glutathione(DB00143) CGAGCCTCCGGGCTTGCTCAC 0.627000 Pancreas(55;1048 1176 25227 40124 41333) 0 SO:0001583 missense ENST00000397356.3 1 1 hg19 CCDS10447.2 . . . . . . . . . . G 12.68 2.010153 0.35415 . . ENSG00000063854 ENST00000397356;ENST00000397353 D;D 0.95622 -3.76;-3.76 4.92 4.92 0.64577 Beta-lactamase-like (2); 0.232302 0.44285 D 0.000476 D 0.90587 0.7049 N 0.25201 0.72 0.80722 D 1 P;B;P 0.39717 0.536;0.099;0.684 B;B;B 0.34824 0.067;0.023;0.19 D 0.90163 0.4229 10 0.30078 T 0.28 -11.5709 17.4781 0.87666 0.0:0.0:1.0:0.0 . 167;122;170 B4DT01;Q16775-2;Q16775 .;.;GLO2_HUMAN L 170;122 ENSP00000380514:P170L;ENSP00000380511:P122L ENSP00000380511:P122L P - 2 0 HAGH 1809149 1.000000 0.71417 0.945000 0.38365 0.042000 0.13812 6.522000 0.73783 2.435000 0.82474 0.555000 0.69702 CCC TCGA-3A-A9IZ-01A-12D-A40W-08 HAGH-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250548.2 1 0 1 36 83 0 22 1 9.999974e-01 3 50 0 22 2 0 0 0 0 0 2 1 1.000000 36 81 0 22 2 -20.000000 1 1 0 0 1 1 2 3 2.060149 0 0.560000 1.960000 0.564873 0.990000 8.100000e-01 1.000000 1.000000 0.978133 0.990000 1 0.940000 1.000000 CDR2 1039 broad.mit.edu 37 16 22385600 22385600 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr16:22385600C>G ENST00000268383.2 - 1 338 c.31G>C c.(31-33)Gag>Cag p.E11Q RP11-21M24.2_ENST00000567158.1_RNA|RP11-21M24.2_ENST00000568827.1_RNA|CDR2_ENST00000569045.1_Intron NM_001802.1 NP_001793.1 Q01850 CDR2_HUMAN cerebellar degeneration-related protein 2, 62kDa 11 TCCTTCATCTCAAACTCCTCT 0.736000 0 SO:0001583 missense ENST00000268383.2 1 1 hg19 CCDS32404.1 . . . . . . . . . . C 17.18 3.323911 0.60634 . . ENSG00000140743 ENST00000268383 T 0.30981 1.51 4.23 4.23 0.50019 . 0.055975 0.64402 U 0.000001 T 0.45538 0.1347 L 0.52364 1.645 0.50171 D 0.999852 D 0.71674 0.998 D 0.66351 0.943 T 0.28396 -1.0045 10 0.14656 T 0.56 -17.8946 16.6203 0.84928 0.0:1.0:0.0:0.0 . 11 Q01850 CDR2_HUMAN Q 11 ENSP00000268383:E11Q ENSP00000268383:E11Q E - 1 0 CDR2 22293101 1.000000 0.71417 0.998000 0.56505 0.952000 0.60782 4.673000 0.61604 1.899000 0.54978 0.462000 0.41574 GAG TCGA-3A-A9IZ-01A-12D-A40W-08 CDR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000430081.1 1 0 0 105 324 0 72 1 9.976890e-01 13 18 0 72 2 0 0 0 0 0 2 1 1.000000 104 319 0 70 2 -20.000000 1 1 0 0 1 1 2 3 2.060149 0 0.560000 1.960000 0.564873 0.880000 7.300000e-01 1.000000 1.000000 0.887525 0.880000 1 0.800000 0.970000 PKD1L2 114780 broad.mit.edu 37 16 81232548 81232548 + RNA SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr16:81232548C>G ENST00000525539.1 - 0 1261 PKD1L2_ENST00000337114.4_RNA NM_052892.3 NP_443124.3 Q7Z442 PK1L2_HUMAN polycystic kidney disease 1-like 2 44 GCGGTGCCTCCCAGGGCCCAT 0.567000 0 ENST00000525539.1 1 0 hg19 . . . . . . . . . . C 13.41 2.229880 0.39399 . . ENSG00000166473 ENST00000337114 T 0.11495 2.77 5.25 4.31 0.51392 . 0.000000 0.85682 D 0.000000 T 0.33059 0.0850 . . . 0.29345 N 0.865728 P;D 0.89917 0.906;1.0 P;D 0.75020 0.81;0.985 T 0.25328 -1.0135 9 0.87932 D 0 -25.724 15.4173 0.74980 0.1403:0.8597:0.0:0.0 . 421;421 Q7Z442-3;Q7Z442 .;PK1L2_HUMAN A 421 ENSP00000337397:G421A ENSP00000337397:G421A G - 2 0 PKD1L2 79790049 0.983000 0.35010 0.253000 0.24343 0.069000 0.16628 3.157000 0.50716 1.237000 0.43756 -0.235000 0.12190 GGG TCGA-3A-A9IZ-01A-12D-A40W-08 PKD1L2-001 KNOWN non_canonical_polymorphism|basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000387972.2 1 0 1 126 423 0 119 0 0 0 0 119 2 0 0 0 0 0 2 1 1.000000 120 414 0 118 2 -20.000000 1 1 0 0 1 0 0 0 2.008269 0 0.560000 1.960000 0.557522 0.810000 6.800000e-01 0.940000 0.810000 0.817323 0.810000 0 0.740000 0.880000 SLC4A1 6521 broad.mit.edu 37 17 42336630 42336630 + Silent SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr17:42336630C>T ENST00000262418.6 - 9 932 c.777G>A c.(775-777)ccG>ccA p.P259P AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'Flank NM_000342.3 NP_000333.1 P02730 B3AT_HUMAN solute carrier family 4 (anion exchanger), member 1 (Diego blood group) p.P259P(1) 40 Breast(137;0.014)|Prostate(33;0.0181) GTATAGGCACCGGCAGCTCCA 0.652000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000262418.6 1 1 hg19 CCDS11481.1 TCGA-3A-A9IZ-01A-12D-A40W-08 SLC4A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346194.1 1 0 1 69 157 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 1.000000 68 153 0 48 2 -7.160123 1 1 121410 3 35 1 1 2 3 2.052408 0 0.560000 1.960000 0.562450 0.990000 8.800000e-01 1.000000 1.000000 0.989696 0.990000 1 0.980000 1.000000 SDK2 54549 broad.mit.edu 37 17 71381998 71381998 + Silent SNP T T A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr17:71381998T>A ENST00000392650.3 - 32 4557 c.4557A>T c.(4555-4557)ctA>ctT p.L1519L SDK2_ENST00000388726.3_Silent_p.L1519L NM_001144952.1 NP_001138424.1 Q58EX2 SDK2_HUMAN sidekick cell adhesion molecule 2 86 GCCATCGGATTAGCACGGAGG 0.647000 0 SO:0001819 synonymous_variant ENST00000392650.3 1 1 hg19 CCDS45769.1 TCGA-3A-A9IZ-01A-12D-A40W-08 SDK2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000327598.2 1 0 1 23 61 0 16 0 0 0 0 16 2 0 3.131725e-01 0 4 0 2 2 1 1.000000 21 58 0 15 2 -20.000000 1 1 0 0 1 1 2 3 2.119855 0 0.560000 1.960000 0.570815 0.990000 6.800000e-01 1.000000 1.000000 0.941241 0.990000 1 0.840000 1.000000 TP53 7157 broad.mit.edu 37 17 7577559 7577559 + Missense_Mutation SNP G G T rs28934573 TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr17:7577559G>T ENST00000269305.4 - 7 911 c.722C>A c.(721-723)tCc>tAc p.S241Y TP53_ENST00000445888.2_Missense_Mutation_p.S241Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.S241Y|TP53_ENST00000420246.2_Missense_Mutation_p.S241Y|TP53_ENST00000359597.4_Missense_Mutation_p.S241Y|TP53_ENST00000413465.2_Missense_Mutation_p.S241Y 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.S241F(85)|p.S241C(26)|p.0?(8)|p.S241Y(8)|p.C242fs*5(6)|p.?(5)|p.S241del(5)|p.S148F(4)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.S148C(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCCCATGCAGGAACTGTTACA 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 160 Substitution - Missense(124)|Deletion - In frame(13)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(5)|Complex - deletion inframe(1) GRCh37 CM920673 TP53 M rs28934573 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 17.25 3.341685 0.61073 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99857 -7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22 4.62 3.64 0.41730 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.120078 0.56097 D 0.000022 D 0.99871 0.9939 M 0.92784 3.345 0.52501 D 0.999952 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0 D 0.96551 0.9408 10 0.87932 D 0 -35.4617 12.8645 0.57932 0.0:0.1651:0.8349:0.0 . 241;241;148;241;241;241 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. Y 241;241;241;241;241;241;230;148;109;148 ENSP00000410739:S241Y;ENSP00000352610:S241Y;ENSP00000269305:S241Y;ENSP00000398846:S241Y;ENSP00000391127:S241Y;ENSP00000391478:S241Y;ENSP00000425104:S109Y;ENSP00000423862:S148Y ENSP00000269305:S241Y S - 2 0 TP53 7518284 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 2.346000 0.44027 1.295000 0.44724 0.462000 0.41574 TCC TCGA-3A-A9IZ-01A-12D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 74 117 0 45 1 9.999669e-01 17 12 0 45 2 1 1 198 386 0 615 2 1 1.000000 69 114 0 45 2 -20.000000 1 1 0 0 1 0 1 1 1.519349 1 0.560000 1.960000 0.391256 0.940000 7.900000e-01 1.000000 1.000000 0.934798 0.940000 1 0.870000 0.990000 PFAS 5198 broad.mit.edu 37 17 8170106 8170106 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr17:8170106G>A ENST00000314666.6 + 23 2990 c.2857G>A c.(2857-2859)Gtg>Atg p.V953M PFAS_ENST00000545834.1_Missense_Mutation_p.V529M NM_012393.2 NP_036525.1 O15067 PUR4_HUMAN phosphoribosylformylglycinamidine synthase 35 L-Glutamine(DB00130) GCCAGGCCTCGTGCTGGAGGT 0.662000 0 SO:0001583 missense ENST00000314666.6 1 1 hg19 CCDS11136.1 . . . . . . . . . . G 27.1 4.799131 0.90538 . . ENSG00000178921 ENST00000545834;ENST00000314666;ENST00000546020 T;T 0.39997 1.05;1.05 5.24 5.24 0.73138 AIR synthase-related protein, C-terminal (2); 0.000000 0.85682 D 0.000000 T 0.73521 0.3597 H 0.94542 3.55 0.80722 D 1 D;D 0.71674 0.998;0.998 D;D 0.69479 0.964;0.964 T 0.81758 -0.0786 10 0.87932 D 0 -17.4026 16.6687 0.85260 0.0:0.0:1.0:0.0 . 953;953 A8K8N7;O15067 .;PUR4_HUMAN M 529;953;362 ENSP00000441706:V529M;ENSP00000313490:V953M ENSP00000313490:V953M V + 1 0 PFAS 8110831 1.000000 0.71417 1.000000 0.80357 0.833000 0.47200 6.109000 0.71528 2.605000 0.88082 0.561000 0.74099 GTG TCGA-3A-A9IZ-01A-12D-A40W-08 PFAS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000226994.2 1 0 1 69 109 0 47 0 1.508712e-01 1 1 0 47 2 0 0 0 0 0 2 1 1.000000 67 108 0 44 2 -20.000000 1 1 121412 2 32 1 0 1 1 1.519349 1 0.560000 1.960000 0.391256 0.930000 7.900000e-01 1.000000 1.000000 0.932439 0.930000 1 0.860000 0.990000 DSG2 1829 broad.mit.edu 37 18 29116237 29116237 + Missense_Mutation SNP T T G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr18:29116237T>G ENST00000261590.8 + 11 1705 c.1496T>G c.(1495-1497)cTg>cGg p.L499R NM_001943.3 NP_001934.2 Q14126 DSG2_HUMAN desmoglein 2 49 OV - Ovarian serous cystadenocarcinoma(10;0.0068) TGTCCCACACTGATAGAGCCT 0.428000 0 SO:0001583 missense ENST00000261590.8 1 1 hg19 CCDS42423.1 . . . . . . . . . . T 15.21 2.764658 0.49574 . . ENSG00000046604 ENST00000261590 T 0.63913 -0.07 5.89 5.89 0.94794 Cadherin (2);Cadherin-like (1); 0.143841 0.32218 N 0.006411 D 0.82513 0.5053 M 0.88181 2.935 0.80722 D 1 D 0.89917 1.0 D 0.76575 0.988 D 0.85990 0.1488 10 0.87932 D 0 . 16.3127 0.82898 0.0:0.0:0.0:1.0 . 499 Q14126 DSG2_HUMAN R 499 ENSP00000261590:L499R ENSP00000261590:L499R L + 2 0 DSG2 27370235 1.000000 0.71417 0.757000 0.31301 0.015000 0.08874 6.161000 0.71868 2.246000 0.74042 0.533000 0.62120 CTG TCGA-3A-A9IZ-01A-12D-A40W-08 DSG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447506.1 0 0 0 13 360 0 76 1 9.647442e-01 12 146 0 76 2 0 0 0 0 0 2 1 0.999503 13 354 0 74 2 -13.243290 1 1 0 0 1 1 2 3 2.065193 0 0.560000 1.960000 0.564873 0.120000 6.000000e-02 1.000000 0.120000 0.159462 0.120000 0 0.090000 0.170000 FCGBP 8857 broad.mit.edu 37 19 40424379 40424379 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr19:40424379G>A ENST00000221347.6 - 4 1831 c.1824C>T c.(1822-1824)tgC>tgT p.C608C NM_003890.2 NP_003881.2 Q9Y6R7 FCGBP_HUMAN Fc fragment of IgG binding protein 165 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) CACACAGCCCGCACACCTGGT 0.617000 0 SO:0001819 synonymous_variant ENST00000221347.6 0 1 hg19 CCDS12546.1 TCGA-3A-A9IZ-01A-12D-A40W-08 FCGBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462507.1 0 0 0 6 379 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 0.963830 6 374 0 52 2 -2.334176 0 1 121412 20 47 1 1 2 3 2.072647 0 0.560000 1.960000 0.566075 0.050000 1.000000e-02 1.000000 0.060000 0.100887 0.050000 0 0.030000 0.100000 IZUMO1 284359 broad.mit.edu 37 19 49245529 49245529 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr19:49245529G>C ENST00000332955.2 - 7 1084 c.537C>G c.(535-537)atC>atG p.I179M RASIP1_ENST00000222145.4_5'Flank NM_182575.2 NP_872381.2 Q8IYV9 IZUM1_HUMAN izumo sperm-egg fusion 1 17 all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113) CACAGTCCAGGATCATGTCTT 0.478000 0 SO:0001583 missense ENST00000332955.2 0 1 hg19 CCDS12732.1 . . . . . . . . . . G 13.99 2.401774 0.42613 . . ENSG00000182264 ENST00000332955 D 0.84070 -1.8 4.67 2.5 0.30297 Immunoglobulin subtype (1);Immunoglobulin-like fold (1); 0.764345 0.11908 N 0.517951 T 0.77718 0.4172 N 0.24115 0.695 0.23519 N 0.997503 P 0.40794 0.729 P 0.48400 0.576 T 0.66586 -0.5886 10 0.54805 T 0.06 -19.8514 7.5894 0.28012 0.1976:0.0:0.8024:0.0 . 179 Q8IYV9 IZUM1_HUMAN M 179 ENSP00000327786:I179M ENSP00000327786:I179M I - 3 3 IZUMO1 53937341 0.907000 0.30839 0.774000 0.31636 0.682000 0.39822 0.508000 0.22692 0.697000 0.31718 0.561000 0.74099 ATC TCGA-3A-A9IZ-01A-12D-A40W-08 IZUMO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466189.1 0 0 0 5 492 0 105 0 0 0 0 105 2 0 0 0 0 0 2 1 0.936161 6 486 0 102 2 -2.872003 1 1 0 0 1 1 2 3 2.072647 0 0.560000 1.960000 0.566075 0.030000 0 1.000000 0.040000 0.079458 0.030000 0 0.010000 0.070000 SHANK1 50944 broad.mit.edu 37 19 51200361 51200361 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr19:51200361G>A ENST00000293441.1 - 14 1974 c.1956C>T c.(1954-1956)ggC>ggT p.G652G SHANK1_ENST00000391814.1_Silent_p.G652G|SHANK1_ENST00000359082.3_Intron NM_016148.2 NP_057232.2 Q9Y566 SHAN1_HUMAN SH3 and multiple ankyrin repeat domains 1 64 all_neural(266;0.057) ACCTCCCTGGGCCAATCCCAT 0.647000 0 SO:0001819 synonymous_variant ENST00000293441.1 0 1 hg19 CCDS12799.1 TCGA-3A-A9IZ-01A-12D-A40W-08 SHANK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268071.1 0 0 0 6 368 1 62 0 0 0 1 62 2 0 0 0 0 0 2 0 0.004675 6 352 1 60 19 -2.313953 0 1 0 0 1 1 2 3 2.072647 0 0.560000 1.960000 0.566075 0.060000 1.000000e-02 1.000000 0.060000 0.102722 0.060000 0 0.030000 0.100000 VAV1 7409 broad.mit.edu 37 19 6829851 6829851 + Silent SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr19:6829851C>G ENST00000602142.1 + 14 1402 c.1320C>G c.(1318-1320)tcC>tcG p.S440S VAV1_ENST00000599806.1_Silent_p.S385S|VAV1_ENST00000539284.1_Silent_p.S343S|VAV1_ENST00000304076.2_Silent_p.S440S|VAV1_ENST00000596764.1_Silent_p.S408S NM_005428.3 NP_005419.2 P15498 VAV_HUMAN vav 1 guanine nucleotide exchange factor 62 GGGGAGACTCCTATGACCTCA 0.527000 0 SO:0001819 synonymous_variant ENST00000602142.1 1 1 hg19 CCDS12174.1 TCGA-3A-A9IZ-01A-12D-A40W-08 VAV1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458475.1 1 0 0 21 268 0 79 0 5.954903e-03 0 2 0 79 2 0 0 0 0 0 2 1 0.999998 21 266 0 77 2 -3.017728 1 1 0 0 1 0 1 1 1.533322 1 0.560000 1.960000 0.393605 0.180000 1.100000e-01 0.270000 0.190000 0.194873 0.180000 0 0.140000 0.230000 DENND2D 79961 broad.mit.edu 37 1 111730759 111730759 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:111730759G>C ENST00000357640.4 - 11 1562 c.1333C>G c.(1333-1335)Cct>Gct p.P445A DENND2D_ENST00000369752.5_Missense_Mutation_p.P442A NM_024901.3 NP_079177.2 Q9H6A0 DEN2D_HUMAN DENN/MADD domain containing 2D 25 all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499) GTACCTGCAGGAGGATTCTTG 0.468000 0 SO:0001583 missense ENST00000357640.4 1 1 hg19 CCDS831.1 . . . . . . . . . . G 3.119 -0.180963 0.06380 . . ENSG00000162777 ENST00000357640;ENST00000369752 T;T 0.12569 2.67;2.67 5.76 5.76 0.90799 . 0.169277 0.52532 D 0.000071 T 0.02380 0.0073 N 0.14661 0.345 0.27874 N 0.939913 B;B 0.34015 0.43;0.435 B;B 0.30179 0.112;0.057 T 0.32214 -0.9915 10 0.02654 T 1 -14.1137 15.8146 0.78589 0.0:0.0:1.0:0.0 . 442;445 Q9H6A0-2;Q9H6A0 .;DEN2D_HUMAN A 445;442 ENSP00000350266:P445A;ENSP00000358767:P442A ENSP00000350266:P445A P - 1 0 DENND2D 111532282 1.000000 0.71417 1.000000 0.80357 0.882000 0.50991 4.599000 0.61076 2.882000 0.98803 0.655000 0.94253 CCT TCGA-3A-A9IZ-01A-12D-A40W-08 DENND2D-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000034456.1 0 0 0 9 303 0 63 1 5.661327e-01 4 58 0 63 2 0 0 0 0 0 2 1 0.994228 8 302 0 63 2 -3.289091 1 1 0 0 1 1 2 3 2.063257 0 0.560000 1.960000 0.564873 0.100000 4.000000e-02 1.000000 0.100000 0.140212 0.100000 0 0.070000 0.160000 NGF 4803 broad.mit.edu 37 1 115828736 115828736 + Silent SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:115828736C>T ENST00000369512.2 - 3 849 c.681G>A c.(679-681)acG>acA p.T227T RP4-663N10.1_ENST00000425449.1_RNA NM_002506.2 NP_002497.2 P01138 NGF_HUMAN nerve growth factor (beta polypeptide) 13 Lung SC(450;0.211) all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05) Clenbuterol(DB01407) ACACACAGGCCGTATCTATCC 0.587000 0 SO:0001819 synonymous_variant ENST00000369512.2 1 1 hg19 CCDS882.1 TCGA-3A-A9IZ-01A-12D-A40W-08 NGF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032832.1 0 0 0 14 342 1 63 0 0 0 1 1 63 2 0 0 0 0 0 2 0 0.263347 14 332 1 62 18 -2.778537 1 1 121410 7 40 1 1 2 3 2.063257 0 0.560000 1.960000 0.564873 0.140000 7.000000e-02 1.000000 0.140000 0.175429 0.140000 0 0.100000 0.190000 PDE4DIP 9659 broad.mit.edu 37 1 144994654 144994654 + Missense_Mutation SNP G G C rs147804991 byFrequency TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:144994654G>C ENST00000369354.3 - 1 267 c.78C>G c.(76-78)atC>atG p.I26M PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I163M|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I163M|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.I26M|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.I163M|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.I26M|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I26M|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I92M|PDE4DIP_ENST00000369347.4_Missense_Mutation_p.I26M Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein 176 CCAGGAAGTAGATGCGCAGCT 0.582000 T PDGFRB MPD Dom yes 1 1q12 9659 phosphodiesterase 4D interacting protein (myomegalin) L 0 SO:0001583 missense ENST00000369354.3 1 0 hg19 CCDS30824.1 . . . . . . . . . . G 26.5 4.743780 0.89663 . . ENSG00000178104 ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000530078;ENST00000534536;ENST00000369347;ENST00000369348;ENST00000531369 T;T;T;T;T;T;T;T;T;T;T 0.34667 1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35 5.78 4.86 0.63082 Spindle associated (1); . . . . T 0.57770 0.2076 M 0.88979 2.995 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.999;0.999;0.999;1.0;1.0;0.999;0.999 T 0.64271 -0.6447 9 0.87932 D 0 . 11.8519 0.52415 0.0836:0.0:0.9164:0.0 . 26;92;26;163;92;29;26 Q5VU43-7;Q5VU43-3;Q5VU43;E9PJ64;E9PQH9;E9PS60;Q5VU43-10 .;.;MYOME_HUMAN;.;.;.;. M 92;26;26;163;163;26;26;92;29;26;163;93 ENSP00000327209:I92M;ENSP00000358360:I26M;ENSP00000358363:I26M;ENSP00000435654:I163M;ENSP00000358366:I163M;ENSP00000358357:I26M;ENSP00000358355:I26M;ENSP00000435920:I29M;ENSP00000358353:I26M;ENSP00000358354:I163M;ENSP00000435616:I93M ENSP00000327209:I92M I - 3 3 PDE4DIP 143706011 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 4.787000 0.62432 2.731000 0.93534 0.650000 0.86243 ATC TCGA-3A-A9IZ-01A-12D-A40W-08 PDE4DIP-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000038858.2 1 0 0 43 505 0 115 0 7.796182e-02 0 6 0 115 2 0 0 0 0 0 2 1 1.000000 42 501 0 113 2 -1.263798 0 1 0 0 1 0 1 1 1.975425 0 0.560000 1.960000 0.424686 0.210000 1.500000e-01 0.280000 0.210000 0.217975 0.210000 0 0.180000 0.250000 FLG 2312 broad.mit.edu 37 1 152275642 152275642 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:152275642C>T ENST00000368799.1 - 3 11755 c.11720G>A c.(11719-11721)cGc>cAc p.R3907H FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GGCTGTATCGCGGTGAGAGGA 0.502000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . C 3.195 -0.164938 0.06502 . . ENSG00000143631 ENST00000368799 T 0.01705 4.68 2.27 -4.54 0.03452 . . . . . T 0.00210 0.0006 N 0.02011 -0.69 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.42120 -0.9470 9 0.39692 T 0.17 . 4.5721 0.12216 0.1364:0.5422:0.1378:0.1835 . 3907 P20930 FILA_HUMAN H 3907 ENSP00000357789:R3907H ENSP00000357789:R3907H R - 2 0 FLG 150542266 0.001000 0.12720 0.000000 0.03702 0.000000 0.00434 -0.243000 0.08915 -3.346000 0.00182 -3.949000 0.00015 CGC TCGA-3A-A9IZ-01A-12D-A40W-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 1 0 0 20 289 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 0.999995 20 282 0 77 2 -5.705387 1 1 121412 8 42 1 0 0 0 2.018049 0 0.560000 1.960000 0.560000 0.230000 1.400000e-01 0.340000 0.230000 0.240531 0.230000 0 0.180000 0.290000 FLG 2312 broad.mit.edu 37 1 152282178 152282178 + Missense_Mutation SNP C C A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:152282178C>A ENST00000368799.1 - 3 5219 c.5184G>T c.(5182-5184)gaG>gaT p.E1728D FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GTGTGTCTGACTCTTCTGAGT 0.597000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . G 0.079 -1.187332 0.01620 . . ENSG00000143631 ENST00000368799 T 0.00832 5.64 3.81 -4.15 0.03881 . . . . . T 0.00073 0.0002 N 0.00690 -1.25 0.09310 N 1 B 0.06786 0.001 B 0.01281 0.0 T 0.27606 -1.0069 9 0.12103 T 0.63 . 1.4188 0.02307 0.3032:0.163:0.4043:0.1295 . 1728 P20930 FILA_HUMAN D 1728 ENSP00000357789:E1728D ENSP00000357789:E1728D E - 3 2 FLG 150548802 0.000000 0.05858 0.000000 0.03702 0.007000 0.05969 -3.340000 0.00506 -1.071000 0.03145 -1.906000 0.00525 GAG TCGA-3A-A9IZ-01A-12D-A40W-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 1 0 0 348 897 0 274 0 0 0 0 274 2 0 0 0 0 0 2 1 1.000000 342 880 0 269 2 -20.000000 1 1 0 0 1 0 0 0 2.018049 0 0.560000 1.960000 0.560000 0.990000 9.000000e-01 1.000000 1.000000 0.981097 0.990000 1 0.940000 1.000000 TBX19 9095 broad.mit.edu 37 1 168262442 168262442 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:168262442G>C ENST00000367821.3 + 3 580 c.529G>C c.(529-531)Gcc>Ccc p.A177P NM_005149.2 NP_005140.1 O60806 TBX19_HUMAN T-box 19 34 all_hematologic(923;0.215) TGTTGGAAGTGCCCATCGAAT 0.463000 0 SO:0001583 missense ENST00000367821.3 0 1 hg19 CCDS1272.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 2.307|2.307 -0.358921|-0.358921 0.05138|0.05138 .|. .|. ENSG00000143178|ENSG00000143178 ENST00000367821;ENST00000367828|ENST00000431969 D|. 0.88124|. -2.34|. 5.02|5.02 0.2|0.2 0.15181|0.15181 p53-like transcription factor, DNA-binding (1);|. 0.552786|. 0.18396|. N|. 0.142516|. T|T 0.02230|0.02230 0.0069|0.0069 N|N 0.02420|0.02420 -0.555|-0.555 .|. .|. .|. B;B|. 0.10296|. 0.001;0.003|. B;B|. 0.08055|. 0.002;0.003|. T|T 0.40683|0.40683 -0.9550|-0.9550 9|4 0.27785|. T|. 0.31|. .|. 0.0479|0.0479 0.00011|0.00011 0.2718:0.1897:0.2341:0.3044|0.2718:0.1897:0.2341:0.3044 .|. 177;108|. O60806;B3KRD9|. TBX19_HUMAN;.|. P|S 177;117|109 ENSP00000356795:A177P|. ENSP00000356795:A177P|. A|C +|+ 1|2 0|0 TBX19|TBX19 166529066|166529066 0.000000|0.000000 0.05858|0.05858 0.588000|0.588000 0.28705|0.28705 0.461000|0.461000 0.32589|0.32589 0.244000|0.244000 0.18124|0.18124 0.447000|0.447000 0.26695|0.26695 0.563000|0.563000 0.77884|0.77884 GCC|TGC TCGA-3A-A9IZ-01A-12D-A40W-08 TBX19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083825.1 0 0 0 9 363 0 47 0 4.508221e-03 0 4 0 47 2 0 0 0 0 0 2 1 0.993919 9 357 0 45 2 -3.484213 1 1 0 0 1 1 2 3 2.595994 1 0.560000 1.960000 0.656250 0.110000 4.000000e-02 0.200000 0.120000 0.122046 0.110000 0 0.070000 0.160000 XCL2 6846 broad.mit.edu 37 1 168510202 168510202 + Silent SNP G G A rs149372418 byFrequency TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:168510202G>A ENST00000367819.2 - 3 365 c.333C>T c.(331-333)acC>acT p.T111T NM_003175.3 NP_003166.1 Q9UBD3 XCL2_HUMAN chemokine (C motif) ligand 2 p.T111T(1) 8 all_hematologic(923;0.215) AGCCAGTCAGGGTCACAGCTG 0.498000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000367819.2 0 1 hg19 CCDS1273.1 TCGA-3A-A9IZ-01A-12D-A40W-08 XCL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083613.1 0 0 0 8 267 1 36 0 0 0 1 36 2 0 0 0 0 0 2 0 0.006145 8 265 1 36 22 -2.050794 0 1 121390 46 36 1 1 2 3 2.595994 1 0.560000 1.960000 0.656250 0.130000 5.000000e-02 0.250000 0.130000 0.148240 0.130000 0 0.090000 0.200000 ZSCAN20 7579 broad.mit.edu 37 1 33957115 33957115 + Silent SNP T T C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:33957115T>C ENST00000361328.3 + 6 1410 c.1257T>C c.(1255-1257)gaT>gaC p.D419D ZSCAN20_ENST00000373413.2_Silent_p.D365D NM_145238.3 NP_660281 P17040 ZSC20_HUMAN zinc finger and SCAN domain containing 20 31 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211) GAGCCACAGATGGCCCAGGAG 0.607000 0 SO:0001819 synonymous_variant ENST00000361328.3 1 1 hg19 CCDS41300.1 TCGA-3A-A9IZ-01A-12D-A40W-08 ZSCAN20-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277003.2 1 0 1 55 163 0 42 0 1.626513e-01 1 2 0 42 2 0 0 0 0 0 2 1 1.000000 54 157 0 42 2 -20.000000 1 1 0 0 1 1 2 3 2.063257 0 0.560000 1.960000 0.564873 0.910000 7.100000e-01 1.000000 1.000000 0.905407 0.910000 1 0.800000 1.000000 CSMD2 114784 broad.mit.edu 37 1 34383705 34383705 + Missense_Mutation SNP A A T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:34383705A>T ENST00000373381.4 - 5 1086 c.910T>A c.(910-912)Tcc>Acc p.S304T NM_001281956.1|NM_052896.3 NP_001268885.1|NP_443128.2 Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) CAGAGGGAGGAGCCTTCTGTC 0.537000 0 SO:0001583 missense ENST00000373381.4 1 1 hg19 . . . . . . . . . . A 10.17 1.276798 0.23307 . . ENSG00000121904 ENST00000373381 D 0.87650 -2.28 5.48 4.36 0.52297 CUB (5); 0.072866 0.56097 D 0.000029 T 0.80237 0.4586 N 0.20483 0.58 0.80722 D 1 P;B 0.36183 0.542;0.354 P;B 0.44921 0.464;0.183 T 0.74668 -0.3588 10 0.14656 T 0.56 . 10.0631 0.42286 0.9216:0.0:0.0784:0.0 . 264;304 Q7Z408;E7EUA6 CSMD2_HUMAN;. T 304 ENSP00000362479:S304T ENSP00000241312:S264T S - 1 0 CSMD2 34156292 1.000000 0.71417 1.000000 0.80357 0.934000 0.57294 3.738000 0.55067 2.095000 0.63458 0.391000 0.25812 TCC TCGA-3A-A9IZ-01A-12D-A40W-08 CSMD2-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 0 38 121 0 23 0 1.444715e-01 0 3 0 23 2 0 0 0 0 0 2 1 1.000000 37 120 0 23 2 -20.000000 1 1 0 0 1 1 2 3 2.063257 0 0.560000 1.960000 0.564873 0.860000 6.400000e-01 1.000000 1.000000 0.864874 0.860000 1 0.740000 1.000000 ZCCHC11 23318 broad.mit.edu 37 1 52933891 52933891 + Missense_Mutation SNP A A G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:52933891A>G ENST00000371544.3 - 15 3189 c.2927T>C c.(2926-2928)tTa>tCa p.L976S ZCCHC11_ENST00000257177.4_Missense_Mutation_p.L976S|ZCCHC11_ENST00000371541.1_5'UTR NM_001009881.2|NM_015269.2 NP_001009881.1|NP_056084.1 Q5TAX3 TUT4_HUMAN zinc finger, CCHC domain containing 11 58 CAAGCCAATTAAAATTTGCTC 0.308000 0 SO:0001583 missense ENST00000371544.3 0 1 hg19 CCDS30716.1 . . . . . . . . . . A 21.5 4.157006 0.78114 . . ENSG00000134744 ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723 T;T;T;T 0.49432 0.78;0.78;0.78;0.78 5.48 5.48 0.80851 . 0.076139 0.53938 D 0.000052 T 0.66346 0.2780 M 0.68952 2.095 0.80722 D 1 D;D 0.89917 0.994;1.0 D;D 0.91635 0.946;0.999 T 0.64980 -0.6279 10 0.34782 T 0.22 . 15.5436 0.76077 1.0:0.0:0.0:0.0 . 735;976 E9PKX1;Q5TAX3 .;TUT4_HUMAN S 976;976;905;735 ENSP00000257177:L976S;ENSP00000360599:L976S;ENSP00000433486:L905S;ENSP00000435256:L735S ENSP00000257177:L976S L - 2 0 ZCCHC11 52706479 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.449000 0.80643 2.076000 0.62316 0.378000 0.23410 TTA TCGA-3A-A9IZ-01A-12D-A40W-08 ZCCHC11-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000022462.1 0 0 0 4 226 0 46 0 3.009883e-02 0 12 0 46 2 0 0 0 0 0 2 1 0.889083 4 224 0 45 2 -6.044622 1 0 0 0 1 1 2 3 2.063257 0 0.560000 1.960000 0.564873 0.060000 1.000000e-02 1.000000 0.060000 0.104075 0.060000 0 0.030000 0.120000 ST6GALNAC5 81849 broad.mit.edu 37 1 77528872 77528872 + Missense_Mutation SNP A A G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr1:77528872A>G ENST00000477717.1 + 5 1227 c.992A>G c.(991-993)gAg>gGg p.E331G NM_030965.1 NP_112227.1 Q9BVH7 SIA7E_HUMAN ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 18 AATCATCCTGAGAATAAACCT 0.433000 0 SO:0001583 missense ENST00000477717.1 1 1 hg19 CCDS673.1 . . . . . . . . . . A 12.07 1.826269 0.32329 . . ENSG00000117069 ENST00000477717;ENST00000438953 T 0.34667 1.35 5.93 5.93 0.95920 . 0.501717 0.22376 N 0.060873 T 0.14960 0.0361 L 0.36672 1.1 0.36892 D 0.889957 B 0.21606 0.058 B 0.23419 0.046 T 0.08146 -1.0736 10 0.23302 T 0.38 -11.5623 11.4604 0.50206 0.8657:0.0:0.0:0.1343 . 331 Q9BVH7 SIA7E_HUMAN G 331;241 ENSP00000417583:E331G ENSP00000406658:E241G E + 2 0 ST6GALNAC5 77301460 1.000000 0.71417 1.000000 0.80357 0.368000 0.29767 3.139000 0.50577 2.267000 0.75376 0.533000 0.62120 GAG TCGA-3A-A9IZ-01A-12D-A40W-08 ST6GALNAC5-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026692.2 1 0 1 69 195 0 47 0 3.926561e-01 0 5 0 47 2 0 0 0 0 0 2 1 1.000000 65 194 0 47 2 -20.000000 1 1 0 0 1 1 2 3 2.063257 0 0.560000 1.960000 0.564873 0.940000 7.500000e-01 1.000000 1.000000 0.931131 0.940000 1 0.840000 1.000000 RBM12 10137 broad.mit.edu 37 20 34241168 34241168 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr20:34241168G>A ENST00000374114.3 - 3 2340 c.2077C>T c.(2077-2079)Ccc>Tcc p.P693S CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.P693S|RBM12_ENST00000359646.1_Missense_Mutation_p.P693S|CPNE1_ENST00000397445.1_Intron NM_001198838.1|NM_001198840.1|NM_006047.5 NP_001185767.1|NP_001185769.1|NP_006038.2 Q9NTZ6 RBM12_HUMAN RNA binding motif protein 12 36 Lung NSC(9;0.00608)|all_lung(11;0.00918) BRCA - Breast invasive adenocarcinoma(18;0.00953) CCTGCACTGGGCATTCCCGCA 0.557000 0 SO:0001583 missense ENST00000374114.3 0 1 hg19 CCDS13261.1 . . . . . . . . . . G 36 5.653504 0.96724 . . ENSG00000244462 ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942 T;T;T 0.22336 1.96;1.96;1.96 4.03 4.03 0.46877 . 0.000000 0.64402 D 0.000018 T 0.27663 0.0680 N 0.19112 0.55 0.80722 D 1 D 0.63880 0.993 D 0.70227 0.968 T 0.02365 -1.1170 10 0.19590 T 0.45 -3.377 14.4866 0.67622 0.0:0.0:1.0:0.0 . 693 Q9NTZ6 RBM12_HUMAN S 693;693;693;492 ENSP00000363228:P693S;ENSP00000352668:P693S;ENSP00000363217:P693S ENSP00000339879:P492S P - 1 0 RBM12 33704582 0.002000 0.14202 0.997000 0.53966 0.903000 0.53119 -0.160000 0.10041 2.528000 0.85240 0.563000 0.77884 CCC TCGA-3A-A9IZ-01A-12D-A40W-08 RBM12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078894.1 0 0 0 7 442 0 141 0 2.841551e-01 0 59 0 141 2 0 0 0 0 0 2 1 0.979506 7 435 0 138 2 -2.191687 0 1 0 0 1 0 0 0 2.022515 0 0.560000 1.960000 0.560000 0.050000 1.000000e-02 0.110000 0.060000 0.063263 0.050000 0 0.030000 0.090000 WDR33 55339 broad.mit.edu 37 2 128471486 128471486 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:128471486G>A ENST00000322313.4 - 18 3137 c.2979C>T c.(2977-2979)ggC>ggT p.G993G NM_018383.4 NP_060853.3 Q9C0J8 WDR33_HUMAN WD repeat domain 33 39 Colorectal(110;0.1) TGCAGTCCTGGCCACCCCGGA 0.662000 0 SO:0001819 synonymous_variant ENST00000322313.4 1 1 hg19 CCDS2150.1 TCGA-3A-A9IZ-01A-12D-A40W-08 WDR33-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331141.2 0 0 0 18 552 0 118 0 2.794856e-02 0 8 0 118 2 0 0 0 0 0 2 1 0.999980 17 544 0 116 2 -3.165678 1 1 0 0 1 1 2 3 2.031267 0 0.560000 1.960000 0.561229 0.110000 6.000000e-02 0.180000 0.120000 0.118802 0.110000 0 0.080000 0.150000 POTEE 445582 broad.mit.edu 37 2 131984442 131984442 + Missense_Mutation SNP A A C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:131984442A>C ENST00000356920.5 + 4 951 c.857A>C c.(856-858)cAa>cCa p.Q286P POTEE_ENST00000358087.5_Missense_Mutation_p.Q296P|RNU6-127P_ENST00000390897.1_RNA|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron NM_001083538.1 NP_001077007.1 Q6S8J3 POTEE_HUMAN POTE ankyrin domain family, member E CAAAAACAGCAAGTCGTGAAA 0.328000 0 SO:0001583 missense ENST00000356920.5 0 1 hg19 CCDS46414.1 . . . . . . . . . . . 10.33 1.320219 0.23994 . . ENSG00000188219 ENST00000356920;ENST00000358087 T;T 0.63744 0.63;-0.06 1.16 1.16 0.20824 Ankyrin repeat-containing domain (4); 3.765040 0.01962 U 0.043420 T 0.60495 0.2273 L 0.33668 1.02 0.09310 N 1 D 0.63880 0.993 P 0.51355 0.667 T 0.51371 -0.8714 10 0.87932 D 0 . 4.5417 0.12061 1.0:0.0:0.0:0.0 . 286 Q6S8J3 POTEE_HUMAN P 286;296 ENSP00000439189:Q286P;ENSP00000443049:Q296P ENSP00000439189:Q286P Q + 2 0 AC131180.1 131700912 0.229000 0.23729 0.024000 0.17045 0.083000 0.17756 1.857000 0.39399 0.784000 0.33661 0.136000 0.15936 CAA TCGA-3A-A9IZ-01A-12D-A40W-08 POTEE-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 40 788 0 169 0 0 0 0 169 2 0 0 0 0 0 2 1 1.000000 30 595 0 180 2 -20.000000 1 1 0 0 1 1 2 3 2.031267 0 0.560000 1.960000 0.561229 0.170000 1.200000e-01 0.240000 0.180000 0.176745 0.170000 0 0.140000 0.200000 GALNT5 11227 broad.mit.edu 37 2 158157419 158157419 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:158157419C>G ENST00000259056.4 + 7 2832 c.2347C>G c.(2347-2349)Ctg>Gtg p.L783V GALNT5_ENST00000463418.1_3'UTR|RN7SKP281_ENST00000410472.1_RNA NM_014568.1 NP_055383.1 Q7Z7M9 GALT5_HUMAN polypeptide N-acetylgalactosaminyltransferase 5 56 GCAAAGGGAGCTGCGAAAGAA 0.498000 0 SO:0001583 missense ENST00000259056.4 1 1 hg19 CCDS2203.1 . . . . . . . . . . C 22.5 4.296112 0.81025 . . ENSG00000136542 ENST00000259056 T 0.57907 0.37 5.54 4.65 0.58169 . 0.069082 0.56097 D 0.000030 T 0.69646 0.3134 M 0.79011 2.435 0.53688 D 0.999977 D 0.63880 0.993 P 0.62435 0.902 T 0.74293 -0.3712 10 0.87932 D 0 . 13.1441 0.59450 0.0:0.921:0.0:0.079 . 783 Q7Z7M9 GALT5_HUMAN V 783 ENSP00000259056:L783V ENSP00000259056:L783V L + 1 2 GALNT5 157865665 0.998000 0.40836 0.970000 0.41538 0.994000 0.84299 3.340000 0.52143 1.305000 0.44909 0.563000 0.77884 CTG TCGA-3A-A9IZ-01A-12D-A40W-08 GALNT5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254925.2 1 0 1 52 127 0 31 1 9.999784e-01 21 22 0 31 2 0 0 0 0 0 2 1 1.000000 50 127 0 31 2 -20.000000 1 1 0 0 1 1 2 3 2.031267 0 0.560000 1.960000 0.561229 0.990000 8.100000e-01 1.000000 1.000000 0.971169 0.990000 1 0.910000 1.000000 GRB14 2888 broad.mit.edu 37 2 165353909 165353909 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:165353909G>A ENST00000263915.3 - 10 1734 c.1196C>T c.(1195-1197)gCg>gTg p.A399V GRB14_ENST00000497306.1_5'Flank|GRB14_ENST00000543549.1_Missense_Mutation_p.A312V NM_004490.2 NP_004481.2 Q14449 GRB14_HUMAN growth factor receptor-bound protein 14 32 TTCTTCAACCGCAACTGAAAG 0.393000 0 SO:0001583 missense ENST00000263915.3 0 1 hg19 CCDS2222.1 . . . . . . . . . . G 34 5.400675 0.96030 . . ENSG00000115290 ENST00000263915;ENST00000543549;ENST00000446413 T;T;T 0.39229 1.67;1.75;1.09 5.81 5.81 0.92471 BPS (Between PH and SH2) domain (1); 0.000000 0.85682 D 0.000000 T 0.67116 0.2859 M 0.79475 2.455 0.80722 D 1 D;D 0.71674 0.998;0.998 D;D 0.67900 0.954;0.954 T 0.68051 -0.5511 10 0.59425 D 0.04 -15.2997 20.0825 0.97783 0.0:0.0:1.0:0.0 . 312;399 B7Z7F9;Q14449 .;GRB14_HUMAN V 399;312;354 ENSP00000263915:A399V;ENSP00000443699:A312V;ENSP00000416786:A354V ENSP00000263915:A399V A - 2 0 GRB14 165062155 1.000000 0.71417 0.996000 0.52242 0.875000 0.50365 9.869000 0.99810 2.746000 0.94184 0.655000 0.94253 GCG TCGA-3A-A9IZ-01A-12D-A40W-08 GRB14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255180.2 0 0 0 5 501 1 95 0 2.327568e-03 0 6 1 95 2 0 0 0 0 0 2 0 0.004254 5 492 1 95 18 -2.049023 0 1 121412 1 31 1 1 2 3 2.031267 0 0.560000 1.960000 0.561229 0.030000 0 0.080000 0.040000 0.041869 0.030000 0 0.010000 0.060000 ATAD2B 54454 broad.mit.edu 37 2 24051724 24051724 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:24051724C>T ENST00000238789.5 - 15 2157 c.1814G>A c.(1813-1815)tGt>tAt p.C605Y ATAD2B_ENST00000474583.1_5'UTR NM_001242338.1|NM_017552.2 NP_001229267.1|NP_060022.1 Q9ULI0 ATD2B_HUMAN ATPase family, AAA domain containing 2B 1 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CTCACCAACACATTTTTCAGC 0.368000 0 SO:0001583 missense ENST00000238789.5 1 1 hg19 CCDS46227.1 . . . . . . . . . . C 22.4 4.287448 0.80803 . . ENSG00000119778 ENST00000238789;ENST00000458510 D;D 0.94862 -3.54;-1.68 4.85 4.85 0.62838 . . . . . D 0.96784 0.8950 M 0.82056 2.57 0.80722 D 1 P 0.52170 0.951 P 0.58077 0.832 D 0.97225 0.9880 9 0.72032 D 0.01 . 18.8549 0.92247 0.0:1.0:0.0:0.0 . 605 Q9ULI0 ATD2B_HUMAN Y 605;43 ENSP00000238789:C605Y;ENSP00000392764:C43Y ENSP00000238789:C605Y C - 2 0 ATAD2B 23905228 1.000000 0.71417 1.000000 0.80357 0.929000 0.56500 7.730000 0.84881 2.632000 0.89209 0.650000 0.86243 TGT TCGA-3A-A9IZ-01A-12D-A40W-08 ATAD2B-001 KNOWN mRNA_end_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324333.1 1 0 0 62 151 0 36 0 3.364988e-01 0 4 0 36 2 0 0 0 0 0 2 1 1.000000 62 150 0 36 2 -20.000000 1 1 0 0 1 1 2 3 2.029649 0 0.560000 1.960000 0.561229 0.990000 8.300000e-01 1.000000 1.000000 0.975261 0.990000 1 0.930000 1.000000 DNMT3A 1788 broad.mit.edu 37 2 25468126 25468126 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:25468126C>G ENST00000264709.3 - 13 1887 c.1550G>C c.(1549-1551)tGc>tCc p.C517S DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000380746.4_Missense_Mutation_p.C328S|DNMT3A_ENST00000402667.1_Missense_Mutation_p.C294S|DNMT3A_ENST00000321117.5_Missense_Mutation_p.C517S NM_175629.2 NP_783328.1 Q9Y6K1 DNM3A_HUMAN DNA (cytosine-5-)-methyltransferase 3 alpha 1021 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TCCTACCTTGCAGTTTTGGCA 0.597000 Mis, F, N, S AML Rec yes 2 2p23 1788 DNA (cytosine-5-)-methyltransferase 3 alpha L 0 SO:0001583 missense ENST00000264709.3 1 1 hg19 CCDS33157.1 . . . . . . . . . . C 31 5.078236 0.94000 . . ENSG00000119772 ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667 T;T;T;T 0.32515 1.45;1.45;1.45;1.45 5.27 5.27 0.74061 . 0.095869 0.64402 D 0.000001 T 0.57932 0.2087 M 0.79258 2.445 0.80722 D 1 D;D 0.89917 1.0;0.994 D;D 0.97110 1.0;0.981 T 0.61048 -0.7141 10 0.72032 D 0.01 -8.9535 16.4462 0.83935 0.0:1.0:0.0:0.0 . 517;328 Q9Y6K1;E9PEB8 DNM3A_HUMAN;. S 328;517;517;294 ENSP00000370122:C328S;ENSP00000324375:C517S;ENSP00000264709:C517S;ENSP00000384237:C294S ENSP00000264709:C517S C - 2 0 DNMT3A 25321630 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 5.788000 0.69020 2.735000 0.93741 0.655000 0.94253 TGC TCGA-3A-A9IZ-01A-12D-A40W-08 DNMT3A-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000211587.1 1 0 1 30 88 0 13 1 9.336265e-01 3 13 0 13 2 0 0 0 0 0 2 1 1.000000 29 85 0 13 2 -20.000000 1 1 0 0 1 1 2 3 2.029649 0 0.560000 1.960000 0.561229 0.900000 6.500000e-01 1.000000 1.000000 0.893152 0.900000 1 0.770000 1.000000 STON1 11037 broad.mit.edu 37 2 48808480 48808480 + Silent SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr2:48808480C>T ENST00000406226.1 + 3 903 c.708C>T c.(706-708)ctC>ctT p.L236L STON1_ENST00000404752.1_Silent_p.L236L|STON1-GTF2A1L_ENST00000394751.3_Silent_p.L236L|STON1-GTF2A1L_ENST00000405008.1_Silent_p.L236L|STON1-GTF2A1L_ENST00000394754.1_Silent_p.L236L|STON1-GTF2A1L_ENST00000402114.2_Silent_p.L236L|STON1_ENST00000309835.3_Silent_p.L236L|STON1-GTF2A1L_ENST00000309827.2_Silent_p.L236L NM_001198595.1 NP_001185524.1 Q9Y6Q2 STON1_HUMAN stonin 1 37 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) TTGAACATCTCCAGTCAGCTG 0.413000 0 SO:0001819 synonymous_variant ENST00000406226.1 1 1 hg19 CCDS1841.1 TCGA-3A-A9IZ-01A-12D-A40W-08 STON1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323848.2 1 0 0 46 412 0 92 0 1.059244e-02 0 2 0 92 2 0 0 0 0 0 2 1 1.000000 46 405 0 91 2 -3.142702 1 1 0 0 1 1 2 3 2.596143 1 0.560000 1.960000 0.654739 0.450000 3.300000e-01 0.610000 0.450000 0.469748 0.450000 0 0.390000 0.530000 MYH15 22989 broad.mit.edu 37 3 108149680 108149680 + Splice_Site SNP T T G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr3:108149680T>G ENST00000273353.3 - 27 3427 c.3371A>C c.(3370-3372)cAg>cCg p.Q1124P NM_014981.1 NP_055796.1 Q9Y2K3 MYH15_HUMAN myosin, heavy chain 15 105 ATTGATTACCTGAAGCTCTTT 0.368000 0 SO:0001630 splice_region_variant ENST00000273353.3 1 0 hg19 CCDS43127.1 . . . . . . . . . . T 13.03 2.116301 0.37339 . . ENSG00000144821 ENST00000273353 T 0.80214 -1.35 5.35 1.36 0.22044 Myosin tail (1); . . . . D 0.88844 0.6547 M 0.89534 3.04 0.42303 D 0.992189 D 0.89917 1.0 D 0.97110 1.0 D 0.86321 0.1692 9 0.87932 D 0 . 5.6809 0.17776 0.2619:0.0733:0.0:0.6647 . 1124 Q9Y2K3 MYH15_HUMAN P 1124 ENSP00000273353:Q1124P ENSP00000273353:Q1124P Q - 2 0 MYH15 109632370 1.000000 0.71417 0.061000 0.19648 0.016000 0.09150 3.060000 0.49955 0.412000 0.25729 0.528000 0.53228 CAG TCGA-3A-A9IZ-01A-12D-A40W-08 MYH15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353935.1 1 0 1 82 196 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1.000000 81 193 0 63 2 -20.000000 1 1 0 0 1 0 0 0 2.022823 0 0.560000 1.960000 0.560000 0.990000 8.600000e-01 1.000000 1.000000 0.983167 0.990000 1 0.950000 1.000000 XPC 7508 broad.mit.edu 37 3 14209834 14209834 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr3:14209834G>A ENST00000285021.7 - 4 673 c.459C>T c.(457-459)ttC>ttT p.F153F XPC_ENST00000449060.2_Intron NM_001145769.1|NM_004628.4 NP_001139241.1|NP_004619.3 Q01831 XPC_HUMAN xeroderma pigmentosum, complementation group C 22 GAGATCGAGAGAAGGCTGTAC 0.418000 Mis, N, F, S skin basal cell, skin squamous cell, melanoma Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (C) 3 3p25 7508 xeroderma pigmentosum, complementation group C E 0 SO:0001819 synonymous_variant Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000285021.7 1 1 hg19 CCDS46763.1 TCGA-3A-A9IZ-01A-12D-A40W-08 XPC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000340517.3 1 0 1 46 158 0 36 1 9.006246e-01 4 12 0 36 2 0 0 0 0 0 2 1 1.000000 45 156 0 36 2 -4.093461 1 1 0 0 1 0 0 0 2.025163 0 0.560000 1.960000 0.560000 0.800000 6.100000e-01 1.000000 1.000000 0.809842 0.800000 0 0.700000 0.910000 FNDC3B 64778 broad.mit.edu 37 3 172028627 172028627 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr3:172028627G>C ENST00000336824.4 + 11 1309 c.1210G>C c.(1210-1212)Gac>Cac p.D404H FNDC3B_ENST00000415807.2_Missense_Mutation_p.D404H|FNDC3B_ENST00000416957.1_Missense_Mutation_p.D404H NM_001135095.1 NP_001128567.1 Q53EP0 FND3B_HUMAN fibronectin type III domain containing 3B 69 all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) GGCACCAATTGACAACGGTTC 0.343000 0 SO:0001583 missense ENST00000336824.4 1 1 hg19 CCDS3217.1 . . . . . . . . . . G 26.6 4.754948 0.89843 . . ENSG00000075420 ENST00000415807;ENST00000336824;ENST00000416957 T;T;T 0.58940 0.3;0.3;0.3 5.9 5.9 0.94986 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.81950 0.4931 M 0.90483 3.12 0.80722 D 1 D;D 0.89917 1.0;0.993 D;D 0.91635 0.999;0.987 D 0.84606 0.0675 10 0.87932 D 0 -29.8321 19.8634 0.96793 0.0:0.0:1.0:0.0 . 404;404 Q53EP0-2;Q53EP0 .;FND3B_HUMAN H 404 ENSP00000411242:D404H;ENSP00000338523:D404H;ENSP00000389094:D404H ENSP00000338523:D404H D + 1 0 FNDC3B 173511321 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 8.709000 0.91379 2.800000 0.96347 0.591000 0.81541 GAC TCGA-3A-A9IZ-01A-12D-A40W-08 FNDC3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345618.2 0 0 0 31 752 1 117 0 3.389468e-01 4 112 1 117 6 0 0 0 0 0 2 1 0.911797 31 743 1 113 22 -4.086988 1 1 0 0 1 1 2 3 2.633929 1 0.560000 1.960000 0.656250 0.170000 1.100000e-01 0.250000 0.180000 0.186221 0.170000 0 0.140000 0.220000 RPL15 6138 broad.mit.edu 37 3 23959499 23959499 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr3:23959499G>C ENST00000307839.5 + 2 788 c.149G>C c.(148-150)cGa>cCa p.R50P NKIRAS1_ENST00000437230.1_5'Flank|NKIRAS1_ENST00000412028.1_5'Flank|RPL15_ENST00000435882.1_Missense_Mutation_p.R50P|RPL15_ENST00000415719.1_Missense_Mutation_p.R50P|NKIRAS1_ENST00000415901.2_5'Flank|NKIRAS1_ENST00000421515.2_Intron|NKIRAS1_ENST00000416026.2_5'Flank|NKIRAS1_ENST00000388759.3_5'Flank|RPL15_ENST00000456530.2_Missense_Mutation_p.R50P|NKIRAS1_ENST00000425478.2_5'Flank|RPL15_ENST00000354811.5_Missense_Mutation_p.R50P|RPL15_ENST00000413699.1_Missense_Mutation_p.R50P|NKIRAS1_ENST00000443659.2_5'Flank NM_001253379.1|NM_001253380.1|NM_002948.3 NP_001240308.1|NP_001240309.1|NP_002939.2 P61313 RL15_HUMAN ribosomal protein L15 7 AAAGCGCGCCGACTGGGCTAC 0.557000 0 SO:0001583 missense ENST00000307839.5 0 1 hg19 CCDS2640.1 . . . . . . . . . . G 21.3 4.133108 0.77662 . . ENSG00000174748 ENST00000307839;ENST00000422218;ENST00000434031;ENST00000413699;ENST00000456530;ENST00000412097;ENST00000510788;ENST00000435882;ENST00000415719;ENST00000354811 . . . 5.77 5.77 0.91146 Ribosomal protein L15e, conserved site (1);Ribosomal protein L23/L15e (1); 0.000000 0.85682 U 0.000000 D 0.90068 0.6898 H 0.96720 3.87 0.80722 D 1 B;D;B;D 0.60160 0.013;0.987;0.092;0.965 B;D;B;D 0.71656 0.094;0.97;0.155;0.974 D 0.92718 0.6189 9 0.87932 D 0 . 20.0007 0.97408 0.0:0.0:1.0:0.0 . 50;50;50;50 B4DEN1;B4DLP4;Q642I1;P61313 .;.;.;RL15_HUMAN P 50 . ENSP00000309334:R50P R + 2 0 RPL15 23934503 1.000000 0.71417 0.995000 0.50966 0.515000 0.34225 7.956000 0.87863 2.726000 0.93360 0.650000 0.86243 CGA TCGA-3A-A9IZ-01A-12D-A40W-08 RPL15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252885.3 0 0 0 5 201 0 36 1 9.999850e-01 31 1533 0 36 2 0 0 0 0 0 2 1 0.932476 4 195 0 39 2 -6.459283 1 0 0 0 1 0 0 0 2.025163 0 0.560000 1.960000 0.560000 0.090000 3.000000e-02 0.190000 0.080000 0.102615 0.090000 0 0.050000 0.140000 SEMA3G 56920 broad.mit.edu 37 3 52471991 52471991 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr3:52471991C>G ENST00000231721.2 - 14 1733 c.1734G>C c.(1732-1734)caG>caC p.Q578H NM_020163.1 NP_064548.1 Q9NS98 SEM3G_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G 18 ACTCACCTTCCTGGCTCTGGC 0.672000 0 SO:0001583 missense ENST00000231721.2 0 1 hg19 CCDS2856.1 . . . . . . . . . . C 12.01 1.809149 0.31961 . . ENSG00000010319 ENST00000231721 T 0.30714 1.52 5.09 3.22 0.36961 Immunoglobulin-like (1); 0.329295 0.29225 N 0.012777 T 0.15565 0.0375 N 0.08118 0 0.22266 N 0.999244 B 0.02656 0.0 B 0.10450 0.005 T 0.17561 -1.0365 10 0.38643 T 0.18 . 10.4033 0.44241 0.0:0.7738:0.146:0.0801 . 578 Q9NS98 SEM3G_HUMAN H 578 ENSP00000231721:Q578H ENSP00000231721:Q578H Q - 3 2 SEMA3G 52447031 0.001000 0.12720 0.978000 0.43139 0.977000 0.68977 0.311000 0.19380 1.388000 0.46506 0.655000 0.94253 CAG TCGA-3A-A9IZ-01A-12D-A40W-08 SEMA3G-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351354.1 1 0 0 4 118 0 24 0 1.060836e-02 1 3 0 24 2 0 0 0 0 0 2 1 0.885718 4 116 0 23 2 -6.992705 1 1 0 0 1 0 0 0 2.022823 0 0.560000 1.960000 0.560000 0.120000 4.000000e-02 0.280000 0.120000 0.143070 0.120000 0 0.070000 0.200000 SLC12A2 6558 broad.mit.edu 37 5 127488461 127488461 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:127488461G>A ENST00000262461.2 + 15 2516 c.2327G>A c.(2326-2328)cGt>cAt p.R776H SLC12A2_ENST00000343225.4_Missense_Mutation_p.R776H NM_001046.2 NP_001037.1 P55011 S12A2_HUMAN solute carrier family 12 (sodium/potassium/chloride transporter), member 2 48 all_cancers(142;0.0972)|Prostate(80;0.151) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325) CATTCAATTCGTCTTTCTGGA 0.413000 0 SO:0001583 missense ENST00000262461.2 1 1 hg19 CCDS4144.1 . . . . . . . . . . G 16.25 3.070173 0.55539 4.54E-4 0.0 ENSG00000064651 ENST00000262461;ENST00000343225 D;D 0.98792 -5.14;-5.14 5.27 5.27 0.74061 Amino acid permease domain (1); 0.215343 0.46758 D 0.000270 D 0.97383 0.9144 L 0.56199 1.76 0.58432 D 0.999999 B;B 0.19445 0.029;0.036 B;B 0.19148 0.014;0.024 D 0.95103 0.8232 10 0.42905 T 0.14 . 19.0718 0.93140 0.0:0.0:1.0:0.0 . 776;776 P55011-3;P55011 .;S12A2_HUMAN H 776 ENSP00000262461:R776H;ENSP00000340878:R776H ENSP00000262461:R776H R + 2 0 SLC12A2 127516360 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 3.777000 0.55364 2.746000 0.94184 0.460000 0.39030 CGT TCGA-3A-A9IZ-01A-12D-A40W-08 SLC12A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250972.1 1 0 1 93 291 0 84 1 9.999978e-01 27 34 0 84 2 0 0 0 0 0 2 1 1.000000 91 286 0 82 2 -20.000000 1 1 121412 3 38 1 1 2 3 2.046659 0 0.560000 1.960000 0.562450 0.860000 7.100000e-01 1.000000 1.000000 0.872082 0.860000 1 0.790000 0.950000 PCDHGB7 56099 broad.mit.edu 37 5 140799066 140799066 + Missense_Mutation SNP G G C TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:140799066G>C ENST00000398594.2 + 1 1640 c.1640G>C c.(1639-1641)aGc>aCc p.S547T PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank NM_018927.3 NP_061750.1 Q9Y5F8 PCDGJ_HUMAN protocadherin gamma subfamily B, 7 56 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCCAATGTGAGCCTGCGCGTG 0.711000 0 SO:0001583 missense ENST00000398594.2 1 1 hg19 CCDS47293.1 . . . . . . . . . . g 8.119 0.780447 0.16120 . . ENSG00000254122 ENST00000398594 T 0.46819 0.86 5.38 4.49 0.54785 Cadherin (5);Cadherin-like (1); 0.234553 0.20219 U 0.096729 T 0.20170 0.0485 N 0.01424 -0.875 0.21325 N 0.999726 P;B 0.35107 0.484;0.208 B;B 0.38225 0.268;0.108 T 0.13845 -1.0494 10 0.16896 T 0.51 . 8.4342 0.32778 0.0:0.3785:0.4932:0.1283 . 547;547 Q9Y5F8;Q9Y5F8-2 PCDGJ_HUMAN;. T 547 ENSP00000381594:S547T ENSP00000381594:S547T S + 2 0 PCDHGB7 140779250 0.000000 0.05858 1.000000 0.80357 0.968000 0.65278 0.243000 0.18106 2.513000 0.84729 0.491000 0.48974 AGC TCGA-3A-A9IZ-01A-12D-A40W-08 PCDHGB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376973.1 1 0 1 58 169 0 55 0 0 0 1 0 55 2 0 0 0 0 0 2 1 1.000000 58 166 0 53 2 -20.000000 1 1 0 0 1 1 2 3 2.046659 0 0.560000 1.960000 0.562450 0.910000 7.200000e-01 1.000000 1.000000 0.908974 0.910000 1 0.810000 1.000000 DOCK2 1794 broad.mit.edu 37 5 169267840 169267840 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:169267840G>A ENST00000256935.8 + 27 2863 c.2783G>A c.(2782-2784)cGg>cAg p.R928Q DOCK2_ENST00000520908.1_Missense_Mutation_p.R420Q|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_5'UTR NM_004946.2 NP_004937.1 Q92608 DOCK2_HUMAN dedicator of cytokinesis 2 160 Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) ACCATGGGCCGGGATCACATT 0.453000 0 SO:0001583 missense ENST00000256935.8 1 1 hg19 CCDS4371.1 . . . . . . . . . . G 22.9 4.350030 0.82132 . . ENSG00000134516 ENST00000256935;ENST00000343291;ENST00000520908;ENST00000519628 T;T 0.68331 -0.32;-0.32 5.28 5.28 0.74379 . 0.120890 0.56097 D 0.000022 T 0.65481 0.2695 M 0.71036 2.16 0.80722 D 1 P;P 0.52061 0.95;0.67 B;B 0.40864 0.342;0.098 T 0.67597 -0.5630 10 0.30854 T 0.27 . 15.8081 0.78531 0.0:0.0:1.0:0.0 . 420;928 E7ERW7;Q92608 .;DOCK2_HUMAN Q 928;309;420;132 ENSP00000256935:R928Q;ENSP00000429283:R420Q ENSP00000256935:R928Q R + 2 0 DOCK2 169200418 1.000000 0.71417 0.998000 0.56505 0.726000 0.41606 6.268000 0.72552 2.460000 0.83146 0.585000 0.79938 CGG TCGA-3A-A9IZ-01A-12D-A40W-08 DOCK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252828.2 1 0 1 38 123 0 30 0 5.835703e-02 0 2 0 30 2 0 0 0 0 0 2 1 1.000000 37 122 0 30 2 -3.899043 1 1 121402 2 29 1 1 2 3 2.046659 0 0.560000 1.960000 0.562450 0.840000 6.200000e-01 1.000000 1.000000 0.849328 0.840000 0 0.730000 0.980000 ADAMTS2 9509 broad.mit.edu 37 5 178585787 178585787 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:178585787C>T ENST00000251582.7 - 6 1170 c.1069G>A c.(1069-1071)Gat>Aat p.D357N ADAMTS2_ENST00000274609.5_Missense_Mutation_p.D357N NM_014244.4 NP_055059.2 O95450 ATS2_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 2 72 all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326) all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) TGGTATTCATCGTGGCCCGTG 0.612000 0 SO:0001583 missense ENST00000251582.7 1 1 hg19 CCDS4444.1 . . . . . . . . . . C 11.91 1.780745 0.31502 . . ENSG00000087116 ENST00000251582;ENST00000274609 T;T 0.62788 0.0;0.0 5.73 5.73 0.89815 Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2); 0.373747 0.22328 N 0.061514 T 0.51686 0.1689 L 0.31476 0.935 0.41488 D 0.988209 D;P 0.56035 0.974;0.874 B;B 0.39503 0.301;0.254 T 0.54200 -0.8329 10 0.35671 T 0.21 . 18.8826 0.92362 0.0:1.0:0.0:0.0 . 357;357 O95450-2;O95450 .;ATS2_HUMAN N 357 ENSP00000251582:D357N;ENSP00000274609:D357N ENSP00000251582:D357N D - 1 0 ADAMTS2 178518393 1.000000 0.71417 0.556000 0.28293 0.068000 0.16541 5.858000 0.69532 2.695000 0.91970 0.650000 0.86243 GAT TCGA-3A-A9IZ-01A-12D-A40W-08 ADAMTS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253507.1 1 0 1 105 273 0 73 1 9.999998e-01 2 60 0 73 2 0 0 0 0 0 2 1 1.000000 100 269 0 70 2 -7.055285 1 0 121412 5 39 1 1 2 3 2.046659 0 0.560000 1.960000 0.562450 0.990000 8.300000e-01 1.000000 1.000000 0.967202 0.990000 1 0.910000 1.000000 ADAMTS12 81792 broad.mit.edu 37 5 33881302 33881302 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:33881302G>A ENST00000504830.1 - 2 746 c.411C>T c.(409-411)ccC>ccT p.P137P ADAMTS12_ENST00000352040.3_Silent_p.P137P|ADAMTS12_ENST00000515401.1_Silent_p.P137P NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 216 GATGGCAGAGGGGGGCAGAGG 0.532000 HNSCC(64;0.19) 0 SO:0001819 synonymous_variant ENST00000504830.1 0 1 hg19 CCDS34140.1 TCGA-3A-A9IZ-01A-12D-A40W-08 ADAMTS12-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367164.2 0 0 0 5 229 0 46 0 1.467768e-01 0 26 0 46 2 0 0 0 0 0 2 1 0.933862 5 223 0 44 2 -3.287924 1 1 121412 2 35 1 1 2 3 2.049225 0 0.560000 1.960000 0.562450 0.080000 2.000000e-02 0.190000 0.080000 0.099910 0.080000 0 0.040000 0.130000 NIPBL 25836 broad.mit.edu 37 5 37022228 37022228 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:37022228G>A ENST00000282516.8 + 28 5903 c.5404G>A c.(5404-5406)Gta>Ata p.V1802I NIPBL_ENST00000448238.2_Missense_Mutation_p.V1802I NM_015384.4|NM_133433.3 NP_056199.2|NP_597677.2 Q6KC79 NIPBL_HUMAN Nipped-B homolog (Drosophila) 128 all_lung(31;0.000447)|Hepatocellular(1;0.108) Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202) GGTTGTTGCTGTAGACCCCAG 0.358000 0 SO:0001583 missense ENST00000282516.8 0 1 hg19 CCDS3920.1 . . . . . . . . . . G 22.9 4.353414 0.82243 . . ENSG00000164190 ENST00000282516;ENST00000448238 D;D 0.87334 -2.24;-2.24 5.24 4.35 0.52113 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 D 0.89818 0.6825 L 0.40543 1.245 0.58432 D 0.999992 D;D 0.64830 0.992;0.994 D;D 0.68483 0.958;0.948 D 0.88745 0.3246 10 0.34782 T 0.22 . 16.1087 0.81244 0.0:0.1342:0.8658:0.0 . 1802;1802 Q6KC79;Q6KC79-2 NIPBL_HUMAN;. I 1802 ENSP00000282516:V1802I;ENSP00000406266:V1802I ENSP00000282516:V1802I V + 1 0 NIPBL 37057985 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.384000 0.97219 1.300000 0.44818 0.650000 0.86243 GTA TCGA-3A-A9IZ-01A-12D-A40W-08 NIPBL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207582.1 0 0 0 5 212 0 50 0 2.500449e-01 0 35 0 50 2 0 0 0 0 0 2 1 0.937507 5 211 0 47 2 -3.336058 1 1 0 0 1 1 2 3 2.049225 0 0.560000 1.960000 0.562450 0.080000 2.000000e-02 0.200000 0.080000 0.106880 0.080000 0 0.050000 0.140000 HCN1 348980 broad.mit.edu 37 5 45262090 45262090 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:45262090C>T ENST00000303230.4 - 8 2663 c.2606G>A c.(2605-2607)aGa>aAa p.R869K NM_021072.3 NP_066550.2 O60741 HCN1_HUMAN hyperpolarization activated cyclic nucleotide-gated potassium channel 1 156 GGAAGATTCTCTTGGAAGAGC 0.537000 0 SO:0001583 missense ENST00000303230.4 1 1 hg19 CCDS3952.1 . . . . . . . . . . c 9.791 1.177962 0.21787 2.27E-4 0.0 ENSG00000164588 ENST00000303230 D 0.97575 -4.44 4.87 4.87 0.63330 . 0.082787 0.49305 D 0.000148 D 0.90865 0.7130 N 0.04880 -0.145 0.36584 D 0.873737 B 0.09022 0.002 B 0.09377 0.004 D 0.88891 0.3346 10 0.36615 T 0.2 . 11.8404 0.52350 0.0:0.9193:0.0:0.0807 . 869 O60741 HCN1_HUMAN K 869 ENSP00000307342:R869K ENSP00000307342:R869K R - 2 0 HCN1 45297847 1.000000 0.71417 0.996000 0.52242 0.361000 0.29550 1.995000 0.40767 2.399000 0.81585 0.651000 0.88453 AGA TCGA-3A-A9IZ-01A-12D-A40W-08 HCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253847.1 1 0 1 173 392 0 105 0 0 0 0 105 2 0 0 0 0 0 2 1 1.000000 170 382 0 101 2 -11.834740 1 1 121412 3 38 1 1 2 3 2.049225 0 0.560000 1.960000 0.562450 0.990000 9.600000e-01 1.000000 1.000000 0.997852 0.990000 1 0.990000 1.000000 SLC9A3 6550 broad.mit.edu 37 5 476656 476656 + Splice_Site SNP A A G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr5:476656A>G ENST00000264938.3 - 12 1900 c.e12+1 CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|SLC9A3_ENST00000514375.1_Splice_Site|CTD-2228K2.7_ENST00000606288.1_RNA NM_004174.2 NP_004165.2 P48764 SL9A3_HUMAN solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 37 Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863) CGCAGTGCCCACCTCCTGCCG 0.701000 0 SO:0001630 splice_region_variant ENST00000264938.3 1 1 hg19 CCDS3855.1 . . . . . . . . . . A 11.92 1.781915 0.31502 . . ENSG00000066230 ENST00000264938;ENST00000514375 . . . 4.8 4.8 0.61643 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.0046 0.64456 1.0:0.0:0.0:0.0 . . . . . -1 . . . - . . SLC9A3 529656 1.000000 0.71417 0.988000 0.46212 0.288000 0.27193 4.943000 0.63554 1.799000 0.52666 0.459000 0.35465 . TCGA-3A-A9IZ-01A-12D-A40W-08 SLC9A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206677.2 0 0 0 8 139 0 22 0 8.434371e-02 0 8 0 22 2 0 0 0 0 0 2 1 0.987794 7 133 0 21 2 -12.020620 1 1 0 0 1 1 2 3 2.603320 1 0.560000 1.960000 0.656250 0.260000 1.200000e-01 0.460000 0.240000 0.275145 0.260000 0 0.180000 0.360000 KIAA0319 9856 broad.mit.edu 37 6 24582552 24582552 + Nonsense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr6:24582552C>T ENST00000378214.3 - 6 1640 c.1116G>A c.(1114-1116)tgG>tgA p.W372* KIAA0319_ENST00000430948.2_Nonsense_Mutation_p.W327*|KIAA0319_ENST00000535378.1_Nonsense_Mutation_p.W363*|KIAA0319_ENST00000543707.1_Nonsense_Mutation_p.W372*|KIAA0319_ENST00000537886.1_Nonsense_Mutation_p.W372* NM_001168375.1|NM_014809.3 NP_001161847.1|NP_055624.2 Q5VV43 K0319_HUMAN KIAA0319 53 TTATTAAATTCCATTCATAGT 0.388000 0 SO:0001587 stop_gained ENST00000378214.3 0 1 hg19 CCDS34348.1 . . . . . . . . . . C 39 7.560686 0.98358 . . ENSG00000137261 ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707 . . . 4.22 4.22 0.49857 . 0.084787 0.50627 D 0.000107 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -8.3723 16.7793 0.85559 0.0:1.0:0.0:0.0 . . . . X 372;363;327;372;372 . ENSP00000367459:W372X W - 3 0 KIAA0319 24690531 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 6.029000 0.70895 2.156000 0.67533 0.484000 0.47621 TGG TCGA-3A-A9IZ-01A-12D-A40W-08 KIAA0319-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040009.1 1 0 0 134 355 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 1.000000 133 351 0 91 2 -20.000000 1 1 0 0 1 0 0 0 2.023190 0 0.560000 1.960000 0.560000 0.970000 8.300000e-01 1.000000 1.000000 0.960227 0.970000 1 0.900000 1.000000 PPP1R3A 5506 broad.mit.edu 37 7 113518053 113518053 + Missense_Mutation SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr7:113518053C>G ENST00000284601.3 - 4 3162 c.3094G>C c.(3094-3096)Gta>Cta p.V1032L NM_002711.3 NP_002702.2 Q16821 PPR3A_HUMAN protein phosphatase 1, regulatory subunit 3A 121 CCAGAGCTTACTAATCCTTCA 0.403000 0 SO:0001583 missense ENST00000284601.3 1 1 hg19 CCDS5759.1 . . . . . . . . . . C 0.015 -1.552420 0.00918 . . ENSG00000154415 ENST00000284601 T 0.14391 2.51 5.71 -1.44 0.08856 . 0.595751 0.16550 N 0.209508 T 0.04861 0.0131 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.28299 -1.0048 10 0.56958 D 0.05 0.0241 0.9691 0.01412 0.2108:0.1318:0.2531:0.4042 . 1032 Q16821 PPR3A_HUMAN L 1032 ENSP00000284601:V1032L ENSP00000284601:V1032L V - 1 0 PPP1R3A 113305289 0.002000 0.14202 0.000000 0.03702 0.120000 0.20174 -0.006000 0.12833 -0.436000 0.07254 -0.300000 0.09419 GTA TCGA-3A-A9IZ-01A-12D-A40W-08 PPP1R3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346724.1 1 0 1 163 484 0 150 0 0 0 0 150 2 0 0 0 0 0 2 1 1.000000 160 478 0 148 2 -20.000000 1 1 0 0 1 0 0 0 2.017843 0 0.560000 1.960000 0.560000 0.890000 7.700000e-01 1.000000 1.000000 0.899845 0.890000 1 0.830000 0.960000 CREB5 9586 broad.mit.edu 37 7 28610110 28610110 + Missense_Mutation SNP C C A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr7:28610110C>A ENST00000357727.2 + 5 809 c.419C>A c.(418-420)tCc>tAc p.S140Y CREB5_ENST00000396300.2_Missense_Mutation_p.S133Y|CREB5_ENST00000409603.1_Missense_Mutation_p.S107Y|CREB5_ENST00000396299.2_Missense_Mutation_p.S107Y NM_182898.2 NP_878901.2 Q02930 CREB5_HUMAN cAMP responsive element binding protein 5 32 TCGCCTCAGTCCAGCTCTGTC 0.622000 0 SO:0001583 missense ENST00000357727.2 1 1 hg19 CCDS5417.1 . . . . . . . . . . C 19.92 3.916836 0.73098 . . ENSG00000146592 ENST00000396299;ENST00000357727;ENST00000396300;ENST00000409603 T;T;T;T 0.66460 -0.21;-0.21;-0.2;-0.21 5.45 5.45 0.79879 . 0.100681 0.64402 D 0.000001 D 0.82318 0.5011 M 0.73962 2.25 0.80722 D 1 D 0.65815 0.995 D 0.72982 0.979 D 0.83827 0.0250 10 0.72032 D 0.01 -14.944 19.2936 0.94112 0.0:1.0:0.0:0.0 . 140 Q02930 CREB5_HUMAN Y 107;140;133;107 ENSP00000379593:S107Y;ENSP00000350359:S140Y;ENSP00000379594:S133Y;ENSP00000387197:S107Y ENSP00000350359:S140Y S + 2 0 CREB5 28576635 1.000000 0.71417 1.000000 0.80357 0.918000 0.54935 7.205000 0.77881 2.583000 0.87209 0.650000 0.86243 TCC TCGA-3A-A9IZ-01A-12D-A40W-08 CREB5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000214204.4 0 0 0 79 222 1 45 0 2.861770e-01 0 4 1 45 2 0 0 0 0 0 2 1 1.000000 76 214 0 41 2 -20.000000 1 1 0 0 1 1 2 3 2.035720 0 0.560000 1.960000 0.561229 0.930000 7.600000e-01 1.000000 1.000000 0.928154 0.930000 1 0.840000 1.000000 OXR1 55074 broad.mit.edu 37 8 107705020 107705020 + Missense_Mutation SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr8:107705020G>A ENST00000442977.2 + 6 692 c.593G>A c.(592-594)cGa>cAa p.R198Q OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000312046.6_Missense_Mutation_p.R190Q|OXR1_ENST00000445937.1_Missense_Mutation_p.R197Q|OXR1_ENST00000531443.1_Missense_Mutation_p.R197Q|OXR1_ENST00000497705.1_Missense_Mutation_p.R130Q|OXR1_ENST00000517566.2_Missense_Mutation_p.R197Q NM_001198532.1 NP_001185461.1 Q8N573 OXR1_HUMAN oxidation resistance 1 31 OV - Ovarian serous cystadenocarcinoma(57;1.81e-09) CGACCTGCACGAGTTGTATCT 0.348000 0 SO:0001583 missense ENST00000442977.2 1 1 hg19 CCDS56548.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 20.5|20.5 4.008905|4.008905 0.75046|0.75046 .|. .|. ENSG00000164830|ENSG00000164830 ENST00000517455|ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977;ENST00000497705;ENST00000312046 .|T;T;T;T;T;T .|0.25414 .|2.62;2.62;2.61;2.61;1.8;2.64 5.06|5.06 5.06|5.06 0.68205|0.68205 .|. .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.33323|0.33323 0.0859|0.0859 L|L 0.52573|0.52573 1.65|1.65 0.80722|0.80722 D|D 1|1 .|P;P;P;P .|0.52692 .|0.903;0.843;0.955;0.955 .|B;B;P;B .|0.47299 .|0.283;0.147;0.543;0.392 T|T 0.06338|0.06338 -1.0832|-1.0832 5|10 .|0.46703 .|T .|0.11 -14.7806|-14.7806 17.9993|17.9993 0.89194|0.89194 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|190;198;130;197 .|Q8N573-2;Q8N573;Q8N573-3;Q8N573-5 .|.;OXR1_HUMAN;.;. K|Q 114|197;197;197;198;130;190 .|ENSP00000402918:R197Q;ENSP00000431966:R197Q;ENSP00000429205:R197Q;ENSP00000405424:R198Q;ENSP00000431014:R130Q;ENSP00000311026:R190Q .|ENSP00000311026:R190Q E|R +|+ 1|2 0|0 OXR1|OXR1 107774196|107774196 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.329000|0.329000 0.28539|0.28539 7.352000|7.352000 0.79404|0.79404 2.336000|2.336000 0.79503|0.79503 0.467000|0.467000 0.42956|0.42956 GAG|CGA TCGA-3A-A9IZ-01A-12D-A40W-08 OXR1-201 KNOWN basic|CCDS protein_coding protein_coding 0 0 1 89 336 1 57 1 9.720256e-01 17 29 1 57 5 0 0 0 0 0 2 1 1.000000 89 328 0 57 2 -3.145317 1 1 121412 5 36 1 1 2 3 2.535813 1 0.560000 1.960000 0.651678 0.940000 7.700000e-01 1.000000 1.000000 0.936374 0.940000 1 0.850000 1.000000 ABRA 137735 broad.mit.edu 37 8 107782407 107782407 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr8:107782407G>A ENST00000311955.3 - 1 66 c.12C>T c.(10-12)ggC>ggT p.G4G NM_139166.4 NP_631905.1 actin-binding Rho activating protein 27 OV - Ovarian serous cystadenocarcinoma(57;3.83e-09) TTTCCTTTTCGCCCGGAGCCA 0.592000 0 SO:0001819 synonymous_variant ENST00000311955.3 1 1 hg19 CCDS6305.1 TCGA-3A-A9IZ-01A-12D-A40W-08 ABRA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380416.1 0 0 0 9 325 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.993893 9 320 0 46 2 -3.422836 1 1 121364 1 29 1 1 2 3 2.535813 1 0.560000 1.960000 0.651678 0.120000 5.000000e-02 1.000000 0.120000 0.174723 0.120000 0 0.080000 0.190000 FBXL6 26233 broad.mit.edu 37 8 145580308 145580308 + Silent SNP G G A rs148685592 TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr8:145580308G>A ENST00000331890.5 - 6 1009 c.945C>T c.(943-945)ccC>ccT p.P315P SLC52A2_ENST00000329994.2_5'Flank|SLC52A2_ENST00000532887.1_5'Flank|FBXL6_ENST00000455319.2_Silent_p.P309P|TMEM249_ENST00000531225.1_5'Flank|FBXL6_ENST00000526524.1_5'UTR|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000527078.1_5'Flank|SLC52A2_ENST00000530047.1_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|SLC52A2_ENST00000540505.1_5'Flank|SLC52A2_ENST00000526752.1_5'Flank NM_012162.2 NP_036294.2 Q8N531 FBXL6_HUMAN F-box and leucine-rich repeat protein 6 5 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055) GCAGCTGAAGGGGAATGCTAT 0.647000 0 SO:0001819 synonymous_variant ENST00000331890.5 0 1 hg19 CCDS6422.1 TCGA-3A-A9IZ-01A-12D-A40W-08 FBXL6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000382413.1 0 0 0 6 576 0 102 0 1.707104e-02 0 16 0 102 2 0 0 0 0 0 2 1 0.962599 6 563 0 97 2 -2.538992 1 1 121392 2 34 1 1 2 3 2.520403 1 0.560000 1.960000 0.645390 0.050000 0 1.000000 0.060000 0.158073 0.050000 0 0.020000 0.090000 ERI1 90459 broad.mit.edu 37 8 8875864 8875864 + Missense_Mutation SNP A A T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr8:8875864A>T ENST00000523898.1 + 6 1319 c.640A>T c.(640-642)Atg>Ttg p.M214L ERI1_ENST00000520332.1_3'UTR|ERI1_ENST00000250263.7_Missense_Mutation_p.M214L|ERI1_ENST00000519292.1_Missense_Mutation_p.M214L Q8IV48 ERI1_HUMAN exoribonuclease 1 11 AATTGACTGGATGAAATTGAA 0.308000 0 SO:0001583 missense ENST00000523898.1 1 1 hg19 CCDS5972.1 . . . . . . . . . . A 9.693 1.152316 0.21371 . . ENSG00000104626 ENST00000523898;ENST00000250263;ENST00000519292 T;T;T 0.32753 1.44;1.44;1.44 5.83 5.83 0.93111 Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1); 0.040723 0.85682 D 0.000000 T 0.11495 0.0280 N 0.01446 -0.86 0.80722 D 1 B 0.11235 0.004 B 0.16289 0.015 T 0.18681 -1.0329 10 0.02654 T 1 -25.2268 15.3806 0.74651 1.0:0.0:0.0:0.0 . 214 Q8IV48 ERI1_HUMAN L 214 ENSP00000429615:M214L;ENSP00000250263:M214L;ENSP00000430190:M214L ENSP00000250263:M214L M + 1 0 ERI1 8913274 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.856000 0.69518 2.220000 0.72140 0.459000 0.35465 ATG TCGA-3A-A9IZ-01A-12D-A40W-08 ERI1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251471.2 1 0 1 55 179 0 47 1 9.894830e-01 2 24 0 47 2 0 0 0 0 0 2 1 1.000000 55 178 0 47 2 -20.000000 1 1 0 0 1 1 2 3 2.044957 0 0.560000 1.960000 0.562450 0.840000 6.500000e-01 1.000000 1.000000 0.847618 0.840000 0 0.740000 0.950000 PTDSS1 9791 broad.mit.edu 37 8 97342493 97342493 + Missense_Mutation SNP A A G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr8:97342493A>G ENST00000517309.1 + 11 1552 c.1226A>G c.(1225-1227)tAt>tGt p.Y409C PTDSS1_ENST00000522072.1_Missense_Mutation_p.Y206C|PTDSS1_ENST00000455950.2_Missense_Mutation_p.Y263C NM_014754.1 NP_055569.1 P48651 PTSS1_HUMAN phosphatidylserine synthase 1 29 Breast(36;6.18e-05) Phosphatidylserine(DB00144) GCAGAACACTATGGTCACCGA 0.463000 0 SO:0001583 missense ENST00000517309.1 1 1 hg19 CCDS6271.1 . . . . . . . . . . A 8.633 0.894173 0.17613 . . ENSG00000156471 ENST00000517309;ENST00000455950;ENST00000522072 T;T;T 0.46451 0.93;0.93;0.87 5.6 0.454 0.16644 . 0.185282 0.49916 N 0.000121 T 0.19005 0.0456 N 0.04959 -0.14 0.48185 D 0.999601 B 0.06786 0.001 B 0.06405 0.002 T 0.03922 -1.0992 10 0.38643 T 0.18 -3.7125 8.5488 0.33438 0.5948:0.0:0.4052:0.0 . 409 P48651 PTSS1_HUMAN C 409;263;206 ENSP00000430548:Y409C;ENSP00000401248:Y263C;ENSP00000430928:Y206C ENSP00000401248:Y263C Y + 2 0 PTDSS1 97411669 0.554000 0.26522 0.933000 0.37362 0.785000 0.44390 0.481000 0.22260 0.080000 0.16959 -0.411000 0.06167 TAT TCGA-3A-A9IZ-01A-12D-A40W-08 PTDSS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379743.2 1 0 1 51 240 0 29 1 9.999999e-01 25 96 0 29 2 0 0 0 0 0 2 1 1.000000 50 233 0 28 2 -20.000000 1 1 121412 1 30 1 1 2 3 2.535813 1 0.560000 1.960000 0.651678 0.790000 6.000000e-01 1.000000 0.790000 0.807436 0.790000 0 0.690000 0.920000 NOTCH1 4851 broad.mit.edu 37 9 139412288 139412288 + Missense_Mutation SNP C C T TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr9:139412288C>T ENST00000277541.6 - 8 1432 c.1357G>A c.(1357-1359)Gtc>Atc p.V453I MIR4673_ENST00000584777.1_RNA NM_017617.3 NP_060087.3 P46531 NOTC1_HUMAN notch 1 1359 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) CACTCGTTGACGTCGATCTCG 0.657000 T, Mis, O TRB@ T-ALL HNSCC(8;0.001) Dom yes 9 9q34.3 4851 Notch homolog 1, translocation-associated (Drosophila) (TAN1) L 0 SO:0001583 missense ENST00000277541.6 1 1 hg19 CCDS43905.1 . . . . . . . . . . C 5.036 0.192406 0.09599 . . ENSG00000148400 ENST00000277541 D 0.87103 -2.21 4.57 4.57 0.56435 EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.202030 0.42682 D 0.000678 T 0.67249 0.2873 N 0.02120 -0.675 0.43588 D 0.995933 P 0.35363 0.497 B 0.34418 0.182 T 0.72953 -0.4135 10 0.02654 T 1 . 16.3317 0.83023 0.0:1.0:0.0:0.0 . 453 P46531 NOTC1_HUMAN I 453 ENSP00000277541:V453I ENSP00000277541:V453I V - 1 0 NOTCH1 138532109 0.997000 0.39634 0.990000 0.47175 0.788000 0.44548 0.789000 0.26886 2.088000 0.63022 0.462000 0.41574 GTC TCGA-3A-A9IZ-01A-12D-A40W-08 NOTCH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055087.1 1 0 1 76 240 0 63 1 7.316790e-01 4 6 0 63 2 0 0 0 0 0 2 1 1.000000 73 234 0 58 2 -20.000000 1 1 120904 2 35 1 1 2 3 2.043119 0 0.560000 1.960000 0.562450 0.860000 6.900000e-01 1.000000 1.000000 0.866137 0.860000 1 0.770000 0.960000 PRUNE2 158471 broad.mit.edu 37 9 79318726 79318726 + Silent SNP G G A TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chr9:79318726G>A ENST00000376718.3 - 9 7926 c.7803C>T c.(7801-7803)gcC>gcT p.A2601A PRUNE2_ENST00000428286.1_Silent_p.A2242A NM_015225.2 NP_056040.2 Q8WUY3 PRUN2_HUMAN prune homolog 2 (Drosophila) 16 CATTTAAGGAGGCTGGCTGAC 0.428000 0 SO:0001819 synonymous_variant ENST00000376718.3 1 1 hg19 CCDS47982.1 . . . . . . . . . . G 2.478 -0.320244 0.05386 . . ENSG00000106772 ENST00000426088 . . . 5.61 -1.16 0.09678 . . . . . T 0.18635 0.0447 . . . 0.09310 N 1 . . . . . . T 0.23190 -1.0195 4 . . . -2.112 0.8443 0.01157 0.2855:0.1178:0.3678:0.229 . . . . F 1923 . . L - 1 0 PRUNE2 78508546 0.010000 0.17322 0.001000 0.08648 0.460000 0.32559 0.028000 0.13644 -0.216000 0.10048 -0.218000 0.12543 CTC TCGA-3A-A9IZ-01A-12D-A40W-08 PRUNE2-003 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052730.2 1 0 1 78 225 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1.000000 78 225 0 62 2 -20.000000 1 1 0 0 1 0 0 0 2.024122 0 0.560000 1.960000 0.560000 0.910000 7.400000e-01 1.000000 1.000000 0.912633 0.910000 1 0.820000 1.000000 PNMA5 114824 broad.mit.edu 37 X 152159333 152159333 + Silent SNP C C G TCGA-3A-A9IZ-01A-12D-A40W-08 TCGA-3A-A9IZ-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6baafe4a-8cdb-4775-8f5b-575d68e9d1ba 33790505-3f29-412f-ad68-7dbe0943b342 g.chrX:152159333C>G ENST00000439251.1 - 2 1248 c.810G>C c.(808-810)ctG>ctC p.L270L PNMA5_ENST00000535214.1_Silent_p.L270L|PNMA5_ENST00000361887.5_Silent_p.L270L|PNMA5_ENST00000452693.1_Silent_p.L270L NM_001103150.1 NP_001096620.1 Q96PV4 PNMA5_HUMAN paraneoplastic Ma antigen family member 5 25 Acute lymphoblastic leukemia(192;6.56e-05) CGGCTTTCTGCAGCAGGGGCT 0.542000 0 SO:0001819 synonymous_variant ENST00000439251.1 1 1 hg19 CCDS14718.1 TCGA-3A-A9IZ-01A-12D-A40W-08 PNMA5-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060925.1 1 0 1 47 219 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 1.000000 47 216 0 36 2 -20.000000 1 1 0 0 1 0 1 1 0.560000 1.960000 0.560000 0.310000 2.300000e-01 0.400000 0.310000 0.318885 0.310000 0 0.270000 0.360000