#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
NRAS	4893	genome.wustl.edu	37	1	115256528	115256528	+	Missense_Mutation	SNP	T	T	A	rs121913255		TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr1:115256528T>A	ENST00000369535.4	-	3	436	c.183A>T	c.(181-183)caA>caT	p.Q61H		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61H(100)|p.Q61Q(3)|p.Q61L(3)|p.Q61R(2)|p.Q61K(1)|p.Q61_E62>HK(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTACTCTTCTTGTCCAGCTG	0.463	Q61H(ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61H(RD_SOFT_TISSUE)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												dbGAP		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	110	Substitution - Missense(106)|Substitution - coding silent(3)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(48)|skin(43)|soft_tissue(8)|thyroid(6)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|NS(1)	1											180.0	156.0	164.0					1																	115256528		2203	4300	6503	115058051	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.183A>T	1.37:g.115256528T>A	ENSP00000358548:p.Gln61His	Somatic	474	0.63	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	115058051	336	22.60	99	Q14971|Q15104|Q15282	Missense_Mutation	SNP	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.Q61H	ENST00000369535.4	37	c.183	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.695276	0.68386	.	.	ENSG00000213281	ENST00000369535	D	0.84146	-1.81	5.08	3.93	0.45458	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.87026	0.6075	H	0.94385	3.53	0.80722	D	1	B	0.30763	0.294	B	0.42087	0.375	D	0.89247	0.3588	10	0.72032	D	0.01	.	5.8174	0.18500	0.0:0.1721:0.0:0.8279	.	61	P01111	RASN_HUMAN	H	61	ENSP00000358548:Q61H	ENSP00000358548:Q61H	Q	-	3	2	NRAS	115058051	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.898000	0.28404	2.120000	0.65058	0.533000	0.62120	CAA	-	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.463	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	T	NM_002524		115058051	-1	no_errors	NM_002524.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
DNMT3A	1788	genome.wustl.edu	37	2	25463271	25463271	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr2:25463271G>A	ENST00000264709.3	-	19	2559	c.2222C>T	c.(2221-2223)gCg>gTg	p.A741V	DNMT3A_ENST00000402667.1_Missense_Mutation_p.A518V|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Missense_Mutation_p.A741V|DNMT3A_ENST00000380746.4_Missense_Mutation_p.A552V	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	741	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.A741V(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTGGGCCGCGCATCATGCAG	0.572			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											83.0	78.0	79.0					2																	25463271		2203	4300	6503	25316775	SO:0001583	missense	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2222C>T	2.37:g.25463271G>A	ENSP00000264709:p.Ala741Val	Somatic	212	0.47	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	25316775	143	47.83	132	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.A741V	ENST00000264709.3	37	c.2222	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.132405	0.77662	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92	5.38	5.38	0.77491	.	0.047415	0.85682	D	0.000000	D	0.91123	0.7205	N	0.15975	0.35	0.80722	D	1	P;D	0.69078	0.956;0.997	B;B	0.43889	0.256;0.435	D	0.91733	0.5398	10	0.41790	T	0.15	-11.9058	17.6755	0.88229	0.0:0.0:1.0:0.0	.	741;552	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	V	552;741;741;518	ENSP00000370122:A552V;ENSP00000324375:A741V;ENSP00000264709:A741V;ENSP00000384237:A518V	ENSP00000264709:A741V	A	-	2	0	DNMT3A	25316775	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.540000	0.85666	0.561000	0.74099	GCG	-	HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.572	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25316775	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
DNMT3A	1788	genome.wustl.edu	37	2	25469029	25469029	+	Splice_Site	SNP	C	C	A			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr2:25469029C>A	ENST00000264709.3	-	11	1766	c.1429G>T	c.(1429-1431)Gag>Tag	p.E477*	DNMT3A_ENST00000402667.1_Splice_Site_p.E254*|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Splice_Site_p.E477*|DNMT3A_ENST00000380746.4_Splice_Site_p.E288*	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	477					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.E477*(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCCAACTACCTCTTGTGCGC	0.627			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	2											134.0	128.0	130.0					2																	25469029		2203	4300	6503	25322533	SO:0001630	splice_region_variant	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1429+1G>T	2.37:g.25469029C>A		Somatic	179	0.56	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	25322533	156	40.00	104	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.E477*	ENST00000264709.3	37	c.1429	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	41	8.570793	0.98868	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.42	5.42	0.78866	.	0.108387	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.0638	17.0771	0.86589	0.0:1.0:0.0:0.0	.	.	.	.	X	288;477;477;254	.	.	E	-	1	0	DNMT3A	25322533	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.165000	0.77544	2.700000	0.92200	0.643000	0.83706	GAG	-	NULL		0.627	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552	Nonsense_Mutation	25322533	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
DDX60	55601	genome.wustl.edu	37	4	169141819	169141819	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr4:169141819T>C	ENST00000393743.3	-	37	5317	c.5026A>G	c.(5026-5028)Att>Gtt	p.I1676V		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1676					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)	p.I1676V(2)		breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		ATAGATTTAATGGTGAGTGCA	0.234																																						dbGAP											2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	4											25.0	26.0	26.0					4																	169141819		2183	4284	6467	169378394	SO:0001583	missense	0			AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.5026A>G	4.37:g.169141819T>C	ENSP00000377344:p.Ile1676Val	Somatic	466	1.68	8		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	169378394	113	42.93	85	Q6PK35|Q9NVE3	Missense_Mutation	SNP	HMMPfam_Helicase_C,HMMSmart_SM00490,HMMPfam_DEAD,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.I1676V	ENST00000393743.3	37	c.5026	CCDS34097.1	4	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056589	0.36277	.	.	ENSG00000137628	ENST00000393743	T	0.19250	2.16	4.8	-4.93	0.03066	.	0.253891	0.27092	N	0.020972	T	0.19765	0.0475	L	0.57536	1.79	0.09310	N	1	B;P	0.47677	0.005;0.899	B;P	0.47528	0.007;0.549	T	0.10042	-1.0647	10	0.51188	T	0.08	.	6.7367	0.23413	0.0:0.2921:0.2831:0.4248	.	1676;168	Q8IY21;Q9NT91	DDX60_HUMAN;.	V	1676	ENSP00000377344:I1676V	ENSP00000377344:I1676V	I	-	1	0	DDX60	169378394	0.018000	0.18449	0.000000	0.03702	0.781000	0.44180	-0.097000	0.11042	-0.597000	0.05813	-0.605000	0.04089	ATT	-	NULL		0.234	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DDX60	protein_coding	OTTHUMT00000364622.1	T	NM_017631		169378394	-1	no_errors	NM_017631.5	genbank	human	validated	54_36p	missense	SNP	0.362	C
NIPBL	25836	genome.wustl.edu	37	5	37064105	37064105	+	Intron	SNP	A	A	G			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr5:37064105A>G	ENST00000282516.8	+	46	8548				NIPBL_ENST00000448238.2_Missense_Mutation_p.I2692V	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)						brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.I2692V(1)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	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)			GAGTCAACGTATTTCGCAGCG	0.388																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	5											197.0	214.0	208.0					5																	37064105		2203	4300	6503	37099862	SO:0001627	intron_variant	0			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.8049+25A>G	5.37:g.37064105A>G		Somatic	312	2.19	7		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	37099862	197	43.06	149	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.I2692V	ENST00000282516.8	37	c.8074	CCDS3920.1	5	.	.	.	.	.	.	.	.	.	.	A	8.452	0.853269	0.17106	.	.	ENSG00000164190	ENST00000448238	D	0.92595	-3.07	5.5	5.5	0.81552	.	.	.	.	.	T	0.82079	0.4959	N	0.08118	0	0.21802	N	0.99953	B	0.32968	0.392	B	0.25291	0.059	T	0.70641	-0.4816	8	.	.	.	.	14.1728	0.65522	1.0:0.0:0.0:0.0	.	2692	Q6KC79-2	.	V	2692	ENSP00000406266:I2692V	.	I	+	1	0	NIPBL	37099862	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.800000	0.55537	2.088000	0.63022	0.482000	0.46254	ATT	-	NULL		0.388	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NIPBL	protein_coding	OTTHUMT00000207582.1	A	NM_015384		37099862	+1	no_errors	NM_015384.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
EXOC2	55770	genome.wustl.edu	37	6	592581	592581	+	Silent	SNP	C	C	G			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr6:592581C>G	ENST00000230449.4	-	11	1215	c.1080G>C	c.(1078-1080)ctG>ctC	p.L360L	EXOC2_ENST00000448181.3_Intron	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	360					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L360L(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GAAGGTCAGACAGGTACCTGA	0.433																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	6											96.0	84.0	88.0					6																	592581		2203	4300	6503	537581	SO:0001819	synonymous_variant	0			AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1080G>C	6.37:g.592581C>G		Somatic	348	0.57	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	537581	180	41.37	127	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Silent	SNP	HMMPfam_TIG,superfamily_Ig_E-set	p.L360	ENST00000230449.4	37	c.1080	CCDS34327.1	6																																																																																			-	NULL		0.433	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	EXOC2	protein_coding	OTTHUMT00000039627.1	C	NM_018303		537581	-1	no_errors	NM_018303.4	genbank	human	reviewed	54_36p	silent	SNP	1.000	G
FBXL18	80028	genome.wustl.edu	37	7	5540409	5540409	+	Silent	SNP	G	G	A	rs371160878		TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr7:5540409G>A	ENST00000382368.3	-	3	1614	c.1491C>T	c.(1489-1491)tcC>tcT	p.S497S	FBXL18_ENST00000453700.3_Silent_p.S497S	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	497								p.S497S(1)	FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GGGGCATGGCGGAGGAGAAGT	0.682																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	7						G		1,4203		0,1,2101	14.0	17.0	16.0		1491	-6.1	0.8	7		16	10,8428		0,10,4209	no	coding-synonymous	FBXL18	NM_024963.4		0,11,6310	AA,AG,GG		0.1185,0.0238,0.087		497/719	5540409	11,12631	2102	4219	6321	5506935	SO:0001819	synonymous_variant	0			AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.1491C>T	7.37:g.5540409G>A		Somatic	130	1.52	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	5506935	100	42.20	73	Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	NULL	p.R56C	ENST00000382368.3	37	c.166	CCDS43546.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.789|5.789	0.329975|0.329975	0.10956|0.10956	2.38E-4|2.38E-4	0.001185|0.001185	ENSG00000155034|ENSG00000155034	ENST00000458142|ENST00000297035	.|.	.|.	.|.	5.29|5.29	-6.12|-6.12	0.02124|0.02124	.|.	.|.	.|.	.|.	.|.	T|T	0.52629|0.52629	0.1746|0.1746	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.59467|0.59467	-0.7449|-0.7449	4|5	.|0.87932	.|D	.|0	.|.	3.4703|3.4703	0.07565|0.07565	0.5312:0.1728:0.1894:0.1066|0.5312:0.1728:0.1894:0.1066	.|.	.|.	.|.	.|.	L|C	381|57	.|.	.|ENSP00000297035:R57C	P|R	-|-	2|1	0|0	FBXL18|FBXL18	5506935|5506935	0.000000|0.000000	0.05858|0.05858	0.815000|0.815000	0.32552|0.32552	0.963000|0.963000	0.63663|0.63663	-4.391000|-4.391000	0.00241|0.00241	-1.283000|-1.283000	0.02393|0.02393	-0.225000|-0.225000	0.12378|0.12378	CCG|CGC	-	NULL		0.682	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	FBXL18	protein_coding	OTTHUMT00000324093.1	G	NM_024963		5506935	-1	no_errors	ENST00000297035	ensembl	human	known	54_36p	missense	SNP	0.174	A
DLGAP2	9228	genome.wustl.edu	37	8	1604152	1604152	+	Intron	SNP	C	C	G			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr8:1604152C>G	ENST00000421627.2	+	6	1704					NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2						neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GCGTGTGCCGCAGAGGAACCC	0.532																																						dbGAP											0			8																																								1591559	SO:0001627	intron_variant	0			AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1571-12343C>G	8.37:g.1604152C>G		Somatic	309	1.28	4		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	1591559	196	46.51	173	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	NULL	p.C456S	ENST00000421627.2	37	c.1367	CCDS47760.1	8																																																																																			-	NULL		0.532	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100133915	protein_coding	OTTHUMT00000374478.1	C	NM_004745		1591559	-1	no_start_codon:pseudogene:no_stop_codon	XM_001715423.1	genbank	human	model	54_36p	missense	SNP	0.000	G
COMMD5	28991	genome.wustl.edu	37	8	146076709	146076709	+	Silent	SNP	C	C	G			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr8:146076709C>G	ENST00000305103.3	-	2	267	c.15G>C	c.(13-15)ggG>ggC	p.G5G	AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000402718.3_Silent_p.G5G|COMMD5_ENST00000450361.2_Silent_p.G5G|ZNF250_ENST00000543949.1_3'UTR	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	5						nucleus (GO:0005634)		p.G5G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GAGTTGCAGCCCCCACAGCAG	0.597																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	8											63.0	66.0	65.0					8																	146076709		2203	4300	6503	146047513	SO:0001819	synonymous_variant	0			AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.15G>C	8.37:g.146076709C>G		Somatic	169	3.43	6		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	146047513	103	41.14	72	D3DWN7|Q9NVN6|Q9UHX5	Silent	SNP	HMMPfam_HCaRG	p.G5	ENST00000305103.3	37	c.15	CCDS6436.1	8																																																																																			-	NULL		0.597	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	COMMD5	protein_coding	OTTHUMT00000382962.1	C	NM_014066		146047513	-1	no_errors	NM_001081003.1	genbank	human	validated	54_36p	silent	SNP	0.745	G
PTCH1	5727	genome.wustl.edu	37	9	98229498	98229498	+	Silent	SNP	G	G	A			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr9:98229498G>A	ENST00000331920.6	-	15	2759	c.2460C>T	c.(2458-2460)taC>taT	p.Y820Y	PTCH1_ENST00000430669.2_Silent_p.Y754Y|PTCH1_ENST00000418258.1_Silent_p.Y669Y|PTCH1_ENST00000421141.1_Silent_p.Y669Y|PTCH1_ENST00000429896.2_Silent_p.Y669Y|PTCH1_ENST00000375274.2_Silent_p.Y819Y|PTCH1_ENST00000437951.1_Silent_p.Y754Y	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	820					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.Y820Y(4)|p.Y819Y(2)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TGTGTAGGTCGTAAAGTAAGT	0.398																																						dbGAP											6	Substitution - coding silent(6)	large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)	9											190.0	179.0	182.0					9																	98229498		2203	4300	6503	97269319	SO:0001819	synonymous_variant	0			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2460C>T	9.37:g.98229498G>A		Somatic	445	1.11	5		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	97269319	171	32.68	83	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	HMMPfam_Patched,superfamily_SSF82866	p.Y820	ENST00000331920.6	37	c.2460	CCDS6714.1	9																																																																																			-	HMMPfam_Patched		0.398	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTCH1	protein_coding	OTTHUMT00000053229.2	G	NM_000264		97269319	-1	no_errors	NM_000264.3	genbank	human	reviewed	54_36p	silent	SNP	0.971	A
Unknown	0	genome.wustl.edu	37	11	127811108	127811108	+	IGR	SNP	G	G	A			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr11:127811108G>A								RN7SKP279 (533065 upstream) : RP11-702B10.2 (239213 downstream)																							TCTAAAAGACGGAAATCCACT	0.478																																						dbGAP											0			11																																								127316318	SO:0001628	intergenic_variant	0																															11.37:g.127811108G>A		Somatic	286	1.38	4		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	127316318	140	26.32	50		RNA	SNP	-	NULL		37	NULL		11																																																																																			-	-	0	0.478					LOC387820			G			127316318	-1	pseudogene	XR_017453.2	genbank	human	model	54_36p	rna	SNP	0.997	A
PLCZ1	89869	genome.wustl.edu	37	12	18865835	18865835	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr12:18865835G>A	ENST00000266505.7	-	6	918	c.655C>T	c.(655-657)Ctc>Ttc	p.L219F	PLCZ1_ENST00000447925.2_Missense_Mutation_p.L217F|PLCZ1_ENST00000542762.1_5'UTR|PLCZ1_ENST00000435379.1_Intron|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000538330.1_5'UTR|PLCZ1_ENST00000539875.1_Intron|PLCZ1_ENST00000541695.1_Missense_Mutation_p.L82F					phospholipase C, zeta 1									p.L219F(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					TTGCTTGTGAGTGTGTAGCCA	0.383																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12											158.0	134.0	142.0					12																	18865835		2203	4300	6503	18757102	SO:0001583	missense	0			AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"""EF-hand domain containing"""	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.655C>T	12.37:g.18865835G>A	ENSP00000266505:p.Leu219Phe	Somatic	744	1.20	9		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	18757102	296	46.38	256		Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_SM00239,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand	p.L219F	ENST00000266505.7	37	c.655	CCDS8680.1	12	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615982	0.46631	.	.	ENSG00000139151	ENST00000266505;ENST00000447925;ENST00000541695;ENST00000540421	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.26	5.19	3.31	0.37934	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.149249	0.46145	N	0.000313	T	0.61515	0.2353	L	0.55017	1.72	0.39775	D	0.972219	B	0.30482	0.281	B	0.38020	0.263	T	0.56432	-0.7980	10	0.30854	T	0.27	.	8.1764	0.31285	0.2862:0.0:0.7138:0.0	.	219	Q86YW0	PLCZ1_HUMAN	F	219;217;82;4	ENSP00000266505:L219F;ENSP00000402358:L217F;ENSP00000443349:L82F;ENSP00000445889:L4F	ENSP00000266505:L219F	L	-	1	0	PLCZ1	18757102	0.999000	0.42202	0.996000	0.52242	0.973000	0.67179	2.991000	0.49409	0.715000	0.32103	0.591000	0.81541	CTC	-	HMMPfam_PI-PLC-X,HMMSmart_SM00148,superfamily_PLC-like phosphodiesterases		0.383	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	PLCZ1	protein_coding	OTTHUMT00000401667.3	G	NM_033123		18757102	-1	no_errors	NM_033123.2	genbank	human	provisional	54_36p	missense	SNP	0.998	A
EIF4B	1975	genome.wustl.edu	37	12	53413723	53413723	+	Silent	SNP	C	C	G			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr12:53413723C>G	ENST00000262056.9	+	4	716	c.390C>G	c.(388-390)ccC>ccG	p.P130P	EIF4B_ENST00000420463.3_Silent_p.P130P|RP11-983P16.4_ENST00000549388.1_RNA|EIF4B_ENST00000551527.1_3'UTR|EIF4B_ENST00000416762.3_Intron|RP11-983P16.4_ENST00000552905.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	130	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)	p.P130P(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						CACGTGAACCCAGCAATCCAG	0.418																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	12											105.0	98.0	100.0					12																	53413723		1856	4091	5947	51699990	SO:0001819	synonymous_variant	0			X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"""RNA binding motif (RRM) containing"""	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.390C>G	12.37:g.53413723C>G		Somatic	337	1.75	6		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	51699990	127	40.38	86	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Silent	SNP	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928	p.P130	ENST00000262056.9	37	c.390	CCDS41788.1	12																																																																																			-	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928		0.418	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	EIF4B	protein_coding	OTTHUMT00000404852.2	C	NM_001417		51699990	+1	no_errors	NM_001417.4	genbank	human	validated	54_36p	silent	SNP	1.000	G
KSR2	283455	genome.wustl.edu	37	12	117922266	117922266	+	Missense_Mutation	SNP	G	G	A	rs563602140		TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr12:117922266G>A	ENST00000339824.5	-	16	3132	c.2405C>T	c.(2404-2406)aCg>aTg	p.T802M	KSR2_ENST00000425217.1_Missense_Mutation_p.T773M|KSR2_ENST00000302438.5_3'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	802	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.T834M(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCCAAAGTCCGTGATGACCAC	0.542													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19917	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12											96.0	99.0	98.0					12																	117922266		2020	4190	6210	116406649	SO:0001583	missense	0			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2405C>T	12.37:g.117922266G>A	ENSP00000339952:p.Thr802Met	Somatic	462	2.12	10		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	116406649	240	44.08	190	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	HMMSmart_SM00219,HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase,superfamily_Cysteine-rich domain	p.T681M	ENST00000339824.5	37	c.2042		12	.	.	.	.	.	.	.	.	.	.	G	29.4	5.000619	0.93227	.	.	ENSG00000171435	ENST00000425217;ENST00000339824	D;D	0.83419	-1.72;-1.72	5.55	5.55	0.83447	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91314	0.7261	M	0.76727	2.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91727	0.5393	10	0.72032	D	0.01	.	19.5084	0.95130	0.0:0.0:1.0:0.0	.	802	Q6VAB6	KSR2_HUMAN	M	773;802	ENSP00000389715:T773M;ENSP00000339952:T802M	ENSP00000339952:T802M	T	-	2	0	KSR2	116406649	1.000000	0.71417	0.965000	0.40720	0.948000	0.59901	9.837000	0.99465	2.612000	0.88384	0.655000	0.94253	ACG	-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase		0.542	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	KSR2	protein_coding	OTTHUMT00000401987.2	G	NM_173598		116406649	-1	no_errors	NM_173598.4	genbank	human	validated	54_36p	missense	SNP	1.000	A
MTUS2	23281	genome.wustl.edu	37	13	29855919	29855919	+	Missense_Mutation	SNP	G	G	A	rs542576593		TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr13:29855919G>A	ENST00000431530.3	+	4	2811	c.2753G>A	c.(2752-2754)cGg>cAg	p.R918Q		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	908	Localization to the growing distal tip of microtubules.|Mediates interaction with MAPRE1.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.R918Q(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GGGGCCGGCCGGGTGGCCCCT	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		13858	0.0		0.0	False		,,,				2504	0.001					dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	13											34.0	37.0	36.0					13																	29855919		1864	4097	5961	28753919	SO:0001583	missense	0			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2753G>A	13.37:g.29855919G>A	ENSP00000392057:p.Arg918Gln	Somatic	259	0.77	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	28753919	247	42.82	185	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	NULL	p.R918Q	ENST00000431530.3	37	c.2753	CCDS45022.1	13	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730298	0.48939	.	.	ENSG00000132938	ENST00000431530	T	0.17691	2.26	4.85	4.85	0.62838	.	0.225856	0.28171	N	0.016339	T	0.32912	0.0845	L	0.53249	1.67	0.44079	D	0.996832	D	0.89917	1.0	D	0.69824	0.966	T	0.00630	-1.1636	9	.	.	.	.	10.765	0.46288	0.0962:0.0:0.9038:0.0	.	908	Q5JR59	MTUS2_HUMAN	Q	918	ENSP00000392057:R918Q	.	R	+	2	0	MTUS2	28753919	0.387000	0.25188	0.294000	0.24946	0.072000	0.16883	3.061000	0.49963	2.692000	0.91855	0.655000	0.94253	CGG	-	NULL		0.577	MTUS2-002	KNOWN	basic|CCDS	protein_coding	KIAA0774	protein_coding	OTTHUMT00000044336.3	G	XM_166270		28753919	+1	no_errors	NM_001033602.2	genbank	human	validated	54_36p	missense	SNP	0.496	A
BPTF	2186	genome.wustl.edu	37	17	65907983	65907983	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr17:65907983T>G	ENST00000321892.4	+	13	4422	c.4361T>G	c.(4360-4362)gTc>gGc	p.V1454G	BPTF_ENST00000306378.6_Missense_Mutation_p.V1328G|BPTF_ENST00000335221.5_Missense_Mutation_p.V1454G|BPTF_ENST00000424123.3_Missense_Mutation_p.V1315G			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1454					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.V1328G(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATGTTGAAGTCTTGGAGCCG	0.438																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	17											69.0	70.0	69.0					17																	65907983		2203	4300	6503	63338445	SO:0001583	missense	0			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.4361T>G	17.37:g.65907983T>G	ENSP00000315454:p.Val1454Gly	Somatic	407	1.21	5		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	63338445	236	38.06	145	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,HMMSmart_PHD,HMMPfam_DDT,superfamily_FYVE_PHD_ZnF,HMMPfam_FYDLN_acid,PatternScan_EGF_2,PatternScan_BROMODOMAIN_1,HMMSmart_DDT,PatternScan_ZF_PHD_1,HMMPfam_PHD	p.V1328G	ENST00000321892.4	37	c.3983		17	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.776141	0.00640	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.61510	0.11;0.1;0.1	5.26	1.88	0.25563	.	.	.	.	.	T	0.25754	0.0627	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22521	-1.0214	9	0.13470	T	0.59	0.3078	5.4901	0.16771	0.3798:0.0:0.4952:0.125	.	1328;1454	Q12830-2;Q12830-4	.;.	G	1328;1454;1454	ENSP00000307208:V1328G;ENSP00000334351:V1454G;ENSP00000315454:V1454G	ENSP00000307208:V1328G	V	+	2	0	BPTF	63338445	0.001000	0.12720	0.030000	0.17652	0.003000	0.03518	-0.160000	0.10041	0.001000	0.14605	-0.744000	0.03518	GTC	-	NULL		0.438	BPTF-201	KNOWN	basic	protein_coding	BPTF	protein_coding		T	NM_182641, NM_004459		63338445	+1	no_errors	NM_182641.6	genbank	human	reviewed	54_36p	missense	SNP	0.020	G
PRODH2	58510	genome.wustl.edu	37	19	36303651	36303651	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr19:36303651C>T	ENST00000301175.3	-	2	302	c.285G>A	c.(283-285)tgG>tgA	p.W95*		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	95					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)	p.W95*(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TCAGGGACTGCCAGCCCCTGG	0.652																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	19											40.0	41.0	41.0					19																	36303651		2203	4300	6503	40995491	SO:0001587	stop_gained	0			U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.285G>A	19.37:g.36303651C>T	ENSP00000301175:p.Trp95*	Somatic	537	1.47	8		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	40995491	181	44.98	148		Nonsense_Mutation	SNP	HMMPfam_Pro_dh,superfamily_SSF51730	p.W95*	ENST00000301175.3	37	c.285	CCDS12478.1	19	.	.	.	.	.	.	.	.	.	.	C	15.44	2.834998	0.50951	.	.	ENSG00000250799	ENST00000301175	.	.	.	5.01	3.97	0.46021	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	12.672	0.56872	0.1661:0.8339:0.0:0.0	.	.	.	.	X	95	.	ENSP00000301175:W95X	W	-	3	0	PRODH2	40995491	0.976000	0.34144	0.999000	0.59377	0.041000	0.13682	2.092000	0.41700	1.330000	0.45394	-0.230000	0.12252	TGG	-	NULL		0.652	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRODH2	protein_coding	OTTHUMT00000452552.2	C	NM_021232		40995491	-1	no_errors	NM_021232.1	genbank	human	reviewed	54_36p	nonsense	SNP	0.998	T
U2AF1	7307	genome.wustl.edu	37	21	44524456	44524456	+	Missense_Mutation	SNP	G	G	A	rs371769427		TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr21:44524456G>A	ENST00000291552.4	-	2	193	c.101C>T	c.(100-102)tCt>tTt	p.S34F	U2AF1_ENST00000380276.2_Missense_Mutation_p.S34F|U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000398137.1_5'UTR	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	34					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S34F(45)|p.S34Y(12)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GTGCAACCGAGAGCACCTGTC	0.358			Mis		"""CLL, MDS"""																																	dbGAP		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	57	Substitution - Missense(57)	haematopoietic_and_lymphoid_tissue(43)|lung(12)|endometrium(2)	21						G	PHE/SER,PHE/SER,	1,4405		0,1,2202	67.0	64.0	65.0		101,101,	5.5	1.0	21		65	0,8600		0,0,4300	no	missense,missense,utr-5	U2AF1	NM_001025203.1,NM_006758.2,NM_001025204.1	155,155,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,	34/241,34/241,	44524456	1,13005	2203	4300	6503	43397525	SO:0001583	missense	0			BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"""RNA binding motif (RRM) containing"""	12453	protein-coding gene	gene with protein product		191317	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein"", ""U2(RNU2) small nuclear RNA auxiliary factor 1"""	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.101C>T	21.37:g.44524456G>A	ENSP00000291552:p.Ser34Phe	Somatic	252	3.82	10		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	43397525	77	44.60	62	Q701P4|Q71RF1	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	p.S34F	ENST00000291552.4	37	c.101	CCDS13694.1	21	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025187	0.93518	2.27E-4	0.0	ENSG00000160201	ENST00000380276;ENST00000291552	T;T	0.46063	0.88;0.88	5.47	5.47	0.80525	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	H	0.96430	3.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	D	0.84864	0.0821	10	0.87932	D	0	-15.7954	19.3169	0.94218	0.0:0.0:1.0:0.0	.	34;34;34	Q69YM7;Q01081;Q701P4	.;U2AF1_HUMAN;.	F	34	ENSP00000369629:S34F;ENSP00000291552:S34F	ENSP00000291552:S34F	S	-	2	0	U2AF1	43397525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.864000	0.92294	2.560000	0.86352	0.563000	0.77884	TCT	-	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1		0.358	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	U2AF1	protein_coding	OTTHUMT00000195541.1	G	NM_006758		43397525	-1	no_errors	NM_001025203.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
BCOR	54880	genome.wustl.edu	37	X	39932084	39932085	+	Frame_Shift_Ins	INS	-	-	G	rs147497014	byFrequency	TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	-	-	-	G	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chrX:39932084_39932085insG	ENST00000378444.4	-	4	2742_2743	c.2514_2515insC	c.(2512-2517)cccaagfs	p.K839fs	BCOR_ENST00000397354.3_Frame_Shift_Ins_p.K839fs|BCOR_ENST00000378455.4_Frame_Shift_Ins_p.K839fs|BCOR_ENST00000342274.4_Frame_Shift_Ins_p.K839fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	839					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						ACTGAGGGCTTGGGGGGCTCAG	0.545			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																															dbGAP		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		0			X																																								39817029	SO:0001589	frameshift_variant	0			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.2515dupC	X.37:g.39932090_39932090dupG	ENSP00000367705:p.Lys839fs	Somatic	89	2.20	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	39817028	42	62.16	69	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Ins	INS	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK	p.K838fs	ENST00000378444.4	37	c.2515_2514	CCDS48093.1	X																																																																																			-	NULL		0.545	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BCOR	protein_coding	OTTHUMT00000060666.2	-	NM_017745		39817029	-1	no_errors	NM_017745.1	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.579:0.203	G
CCNG2	901	genome.wustl.edu	37	4	78087044	78087044	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2968-03A-01D-0739-09	TCGA-AB-2968-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	85d9ba67-6bb0-440d-8d9f-1c9582697ba6	2f3495f2-e136-437c-8c9a-a2e01db92a3e	g.chr4:78087044delC	ENST00000316355.5	+	8	1358	c.1002delC	c.(1000-1002)ttcfs	p.F334fs	CCNG2_ENST00000395640.1_Frame_Shift_Del_p.F334fs|CCNG2_ENST00000502280.1_Frame_Shift_Del_p.F334fs|CCNG2_ENST00000354403.5_Intron|CCNG2_ENST00000497512.1_Intron	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	334					cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)		p.F334F(1)		breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						TTTTCAACTTCAAAGTGGCAC	0.403																																						dbGAP											1	Substitution - coding silent(1)	ovary(1)	4											103.0	101.0	102.0					4																	78087044		2203	4300	6503	78306068	SO:0001589	frameshift_variant	0			BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.1002delC	4.37:g.78087044delC	ENSP00000315743:p.Phe334fs	Somatic	551	1.78	10		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	78306068	254	40.44	184	B4DF25|Q6FGA7|Q6FGC6	Frame_Shift_Del	DEL	HMMSmart_SM00385,HMMPfam_Cyclin_N,superfamily_Cyclin-like	p.F334fs	ENST00000316355.5	37	c.1002	CCDS3581.1	4																																																																																			-	NULL		0.403	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCNG2	protein_coding	OTTHUMT00000252404.3	C	NM_004354		78306068	+1	no_errors	NM_004354.2	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.971	-
