#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
USP24	23358	genome.wustl.edu	37	1	55589119	55589119	+	Splice_Site	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr1:55589119C>T	ENST00000294383.6	-	36	4276		c.e36+1		USP24_ENST00000407756.1_Splice_Site	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24						ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CTCCAGCATACCCAGTTGCTG	0.463																																						dbGAP											0			1											39.0	38.0	39.0					1																	55589119		1882	4109	5991	55361707	SO:0001630	splice_region_variant	0			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.4276+1G>A	1.37:g.55589119C>T		Somatic	97	2.02	2		1	96.00	96	WXS	Illumina HiSeq	Phase_IV	55361707	170	44.16	136	Q6ZSY2|Q8N2Y4|Q9NXD1	Splice_Site	SNP	-	e33+1	ENST00000294383.6	37	c.3796+1	CCDS44154.2	1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799962	0.70567	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4963	0.90866	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP24	55361707	1.000000	0.71417	0.998000	0.56505	0.528000	0.34623	7.487000	0.81328	2.347000	0.79759	0.563000	0.77884	.	-	-		0.463	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	USP24	protein_coding	OTTHUMT00000022275.2	C		Intron	55361707	-1	no_errors	NM_015306.1	genbank	human	validated	54_36p	splice_site	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25459803	25459803	+	Splice_Site	SNP	A	A	C			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr2:25459803A>C	ENST00000264709.3	-	21	2816		c.e21+1		DNMT3A_ENST00000380746.4_Splice_Site|DNMT3A_ENST00000321117.5_Splice_Site|DNMT3A_ENST00000474887.1_Intron|DNMT3A_ENST00000402667.1_Splice_Site	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha						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)			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)					GCTGGAGCTGACCTTGGCTAT	0.597			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											45.0	38.0	41.0					2																	25459803		2203	4300	6503	25313307	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.2478+1T>G	2.37:g.25459803A>C		Somatic	27	0.00	0		6	45.45	5	WXS	Illumina HiSeq	Phase_IV	25313307	14	46.43	13	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Splice_Site	SNP	-	e20+2	ENST00000264709.3	37	c.2478+2	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	A	21.5	4.162665	0.78226	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0536	0.58967	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNMT3A	25313307	1.000000	0.71417	0.912000	0.35992	0.909000	0.53808	8.966000	0.93397	2.031000	0.59945	0.533000	0.62120	.	-	-		0.597	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	A	NM_022552	Intron	25313307	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	splice_site	SNP	0.998	C
DNMT3A	1788	genome.wustl.edu	37	2	25462032	25462032	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr2:25462032C>T	ENST00000264709.3	-	20	2712	c.2375G>A	c.(2374-2376)cGc>cAc	p.R792H	DNMT3A_ENST00000380746.4_Missense_Mutation_p.R603H|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R792H|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R569H	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	792	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.R603H(1)|p.R792H(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)					CCAGAAGTAGCGGGCCCTGTG	0.557			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	2	Substitution - Missense(2)	lung(2)	2											68.0	61.0	64.0					2																	25462032		2203	4300	6503	25315536	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.2375G>A	2.37:g.25462032C>T	ENSP00000264709:p.Arg792His	Somatic	26	0.00	0		20	69.70	46	WXS	Illumina HiSeq	Phase_IV	25315536	26	42.22	19	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.R792H	ENST00000264709.3	37	c.2375	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	35	5.533263	0.96460	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.99557	-6.16;-6.16;-6.16;-6.16	5.64	5.64	0.86602	.	0.046266	0.85682	D	0.000000	D	0.99339	0.9768	M	0.88181	2.935	0.80722	D	1	D;B	0.65815	0.995;0.097	P;B	0.46275	0.51;0.004	D	0.99712	1.1007	10	0.62326	D	0.03	-8.3274	17.206	0.86918	0.0:1.0:0.0:0.0	.	792;603	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	H	603;792;792;569	ENSP00000370122:R603H;ENSP00000324375:R792H;ENSP00000264709:R792H;ENSP00000384237:R569H	ENSP00000264709:R792H	R	-	2	0	DNMT3A	25315536	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.681000	0.91329	0.561000	0.74099	CGC	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.557	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25315536	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
EPAS1	2034	genome.wustl.edu	37	2	46602890	46602890	+	Silent	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr2:46602890C>T	ENST00000263734.3	+	8	1458	c.948C>T	c.(946-948)taC>taT	p.Y316Y		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	316	PAC.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			ATGGGGGCTACGTGTGGCTGG	0.582																																						dbGAP											0			2											130.0	96.0	107.0					2																	46602890		2203	4300	6503	46456394	SO:0001819	synonymous_variant	0			U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.948C>T	2.37:g.46602890C>T		Somatic	126	1.56	2		8	0.00	0	WXS	Illumina HiSeq	Phase_IV	46456394	64	47.54	58	Q86VA2|Q99630	Silent	SNP	HMMSmart_PAS,HMMPfam_HLH,HMMSmart_HLH,HMMSmart_PAC,superfamily_HLH_basic,HMMPfam_PAS_3,HMMPfam_HIF-1a_CTAD,superfamily_SSF55785	p.Y316	ENST00000263734.3	37	c.948	CCDS1825.1	2																																																																																			-	HMMSmart_PAC,HMMPfam_PAS_3,superfamily_SSF55785		0.582	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPAS1	protein_coding	OTTHUMT00000250752.2	C	NM_001430		46456394	+1	no_errors	NM_001430.3	genbank	human	validated	54_36p	silent	SNP	0.901	T
PTPRN	5798	genome.wustl.edu	37	2	220166869	220166869	+	Silent	SNP	A	A	C			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr2:220166869A>C	ENST00000295718.2	-	6	1224	c.984T>G	c.(982-984)gcT>gcG	p.A328A	PTPRN_ENST00000409251.3_Silent_p.A328A|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Silent_p.A238A	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	328					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CTGGCTGCACAGCTGGGGAAG	0.602																																						dbGAP											0			2											61.0	60.0	60.0					2																	220166869		2203	4300	6503	219875113	SO:0001819	synonymous_variant	0				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.984T>G	2.37:g.220166869A>C		Somatic	98	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	219875113	127	41.10	90	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II	p.A328	ENST00000295718.2	37	c.984	CCDS2440.1	2																																																																																			-	NULL		0.602	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPRN	protein_coding	OTTHUMT00000256819.2	A			219875113	-1	no_errors	NM_002846.2	genbank	human	reviewed	54_36p	silent	SNP	0.007	C
ATP2C1	27032	genome.wustl.edu	37	3	130714936	130714936	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr3:130714936G>A	ENST00000510168.1	+	23	2657	c.2107G>A	c.(2107-2109)Gtt>Att	p.V703I	ATP2C1_ENST00000359644.3_Missense_Mutation_p.V703I|ATP2C1_ENST00000504948.1_Missense_Mutation_p.V687I|ATP2C1_ENST00000328560.8_Missense_Mutation_p.V703I|ATP2C1_ENST00000507488.2_Missense_Mutation_p.V687I|ATP2C1_ENST00000422190.2_Missense_Mutation_p.V703I|ATP2C1_ENST00000513801.1_Missense_Mutation_p.V687I|ATP2C1_ENST00000393221.4_Missense_Mutation_p.V737I|ATP2C1_ENST00000504381.1_Missense_Mutation_p.V648I|ATP2C1_ENST00000533801.2_Missense_Mutation_p.V698I|ATP2C1_ENST00000428331.2_Missense_Mutation_p.V703I|ATP2C1_ENST00000505330.1_Missense_Mutation_p.V687I|ATP2C1_ENST00000508532.1_Missense_Mutation_p.V703I			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	703					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TAAAAATTTCGTTAGATTCCA	0.303									Hailey-Hailey disease																												Esophageal Squamous(99;456 1443 27647 34099 42636)	dbGAP											0			3											87.0	101.0	96.0					3																	130714936		2203	4300	6503	132197626	SO:0001583	missense	0	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"""ATPases / P-type"""	13211	protein-coding gene	gene with protein product	"""secretory pathway Ca2+/Mn2+ ATPase 1"", ""calcium-transporting ATPase type 2C member 1"""	604384	"""benign chronic pemphigus (Hailey-Hailey disease)"""	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.2107G>A	3.37:g.130714936G>A	ENSP00000427461:p.Val703Ile	Somatic	76	0.00	0		66	37.14	39	WXS	Illumina HiSeq	Phase_IV	132197626	56	47.17	50	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Missense_Mutation	SNP	HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M	p.V703I	ENST00000510168.1	37	c.2107	CCDS46914.1	3	.	.	.	.	.	.	.	.	.	.	G	15.95	2.983218	0.53827	.	.	ENSG00000017260	ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421	D;D;D;D;D;D;D;D;D;D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11	5.75	5.75	0.90469	ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	T	0.79435	0.4445	N	0.04820	-0.15	0.80722	D	1	D;P;B;P;B;P;P	0.54047	0.964;0.871;0.33;0.921;0.33;0.809;0.94	P;B;B;B;B;B;B	0.49953	0.627;0.33;0.089;0.38;0.153;0.275;0.285	T	0.76580	-0.2907	10	0.02654	T	1	.	19.9312	0.97120	0.0:0.0:1.0:0.0	.	737;698;737;703;737;703;703	G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194	.;.;.;.;.;.;AT2C1_HUMAN	I	687;648;687;737;698;703;703;687;687;703;703;703;703;702	ENSP00000423774:V687I;ENSP00000425320:V648I;ENSP00000421326:V687I;ENSP00000376914:V737I;ENSP00000432956:V698I;ENSP00000427461:V703I;ENSP00000424783:V703I;ENSP00000423330:V687I;ENSP00000422872:V687I;ENSP00000329664:V703I;ENSP00000395809:V703I;ENSP00000352665:V703I;ENSP00000402677:V703I	ENSP00000329664:V703I	V	+	1	0	ATP2C1	132197626	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.689000	0.98673	2.720000	0.93068	0.491000	0.48974	GTT	-	superfamily_Calcium ATPase transmembrane domain M		0.303	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ATP2C1	protein_coding	OTTHUMT00000356648.2	G	NM_001001486		132197626	+1	no_errors	NM_001001486.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
FAM193A	8603	genome.wustl.edu	37	4	2698284	2698284	+	Silent	SNP	G	G	A			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr4:2698284G>A	ENST00000324666.5	+	16	2949	c.2598G>A	c.(2596-2598)acG>acA	p.T866T	FAM193A_ENST00000505311.1_Silent_p.T866T|FAM193A_ENST00000382839.3_Silent_p.T866T|FAM193A_ENST00000502458.1_Silent_p.T888T|FAM193A_ENST00000545951.1_Silent_p.T866T	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	866										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						TGAGCAGCACGCGTGCAGCGA	0.542																																						dbGAP											0			4											75.0	71.0	72.0					4																	2698284		2203	4300	6503	2668082	SO:0001819	synonymous_variant	0			AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.2598G>A	4.37:g.2698284G>A		Somatic	91	0.00	0		26	29.73	11	WXS	Illumina HiSeq	Phase_IV	2668082	89	43.31	68	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Silent	SNP	NULL	p.T866	ENST00000324666.5	37	c.2598	CCDS58875.1	4																																																																																			-	NULL		0.542	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C4orf8	protein_coding	OTTHUMT00000360903.1	G	NM_003704		2668082	+1	no_errors	NM_003704.3	genbank	human	validated	54_36p	silent	SNP	0.983	A
CRISPLD1	83690	genome.wustl.edu	37	8	75929669	75929669	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr8:75929669G>A	ENST00000262207.4	+	10	1579	c.1111G>A	c.(1111-1113)Ggt>Agt	p.G371S	CRISPLD1_ENST00000523524.1_Missense_Mutation_p.G183S|CRISPLD1_ENST00000517786.1_Missense_Mutation_p.G185S	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	371	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			CAATAGAAATGGTATTCAAAC	0.323																																						dbGAP											0			8											114.0	123.0	120.0					8																	75929669		2203	4298	6501	76092224	SO:0001583	missense	0			AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"""LCCL domain containing cysteine-rich secretory protein 1"""	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1111G>A	8.37:g.75929669G>A	ENSP00000262207:p.Gly371Ser	Somatic	64	0.00	0		7	56.25	9	WXS	Illumina HiSeq	Phase_IV	76092224	38	62.38	63	B2RA60|B7Z929	Missense_Mutation	SNP	HMMSmart_SM00198,HMMPfam_LCCL,HMMSmart_SM00603,superfamily_LCCL domain,HMMPfam_SCP,superfamily_PR-1-like,PatternScan_CRISP_2	p.G371S	ENST00000262207.4	37	c.1111	CCDS6219.1	8	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203050	0.58234	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	D;D;D	0.91740	-2.9;-2.9;-2.9	5.29	5.29	0.74685	LCCL (5);	0.057288	0.64402	D	0.000001	D	0.96408	0.8828	M	0.83118	2.625	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.97110	1.0;0.926	D	0.96448	0.9332	10	0.66056	D	0.02	.	19.1314	0.93408	0.0:0.0:1.0:0.0	.	185;371	B7Z929;Q9H336	.;CRLD1_HUMAN	S	371;183;185	ENSP00000262207:G371S;ENSP00000430105:G183S;ENSP00000429746:G185S	ENSP00000262207:G371S	G	+	1	0	CRISPLD1	76092224	1.000000	0.71417	0.988000	0.46212	0.017000	0.09413	7.377000	0.79668	2.753000	0.94483	0.557000	0.71058	GGT	-	HMMPfam_LCCL,HMMSmart_SM00603,superfamily_LCCL domain		0.323	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CRISPLD1	protein_coding	OTTHUMT00000379117.1	G	NM_031461		76092224	+1	no_errors	NM_031461.4	genbank	human	validated	54_36p	missense	SNP	1.000	A
PCDH15	65217	genome.wustl.edu	37	10	55587268	55587268	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr10:55587268C>T	ENST00000320301.6	-	32	4646	c.4252G>A	c.(4252-4254)Gca>Aca	p.A1418T	PCDH15_ENST00000395433.1_Missense_Mutation_p.A1393T|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.A1425T|PCDH15_ENST00000395438.1_Missense_Mutation_p.A1418T|PCDH15_ENST00000361849.3_Missense_Mutation_p.A1418T|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000437009.1_Missense_Mutation_p.A1347T|PCDH15_ENST00000409834.1_Missense_Mutation_p.A1029T|PCDH15_ENST00000395445.1_Missense_Mutation_p.A1425T|PCDH15_ENST00000414778.1_Missense_Mutation_p.A1420T|PCDH15_ENST00000395432.2_Missense_Mutation_p.A1378T|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395430.1_Missense_Mutation_p.A1415T	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1418					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCGGGTAATGCGGCCTGAATT	0.532										HNSCC(58;0.16)																												dbGAP											0			10											81.0	85.0	84.0					10																	55587268		2203	4300	6503	55257274	SO:0001583	missense	0			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4252G>A	10.37:g.55587268C>T	ENSP00000322604:p.Ala1418Thr	Somatic	62	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	55257274	22	50.00	22	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like	p.A1418T	ENST00000320301.6	37	c.4252	CCDS7248.1	10	.	.	.	.	.	.	.	.	.	.	C	20.8	4.057177	0.76074	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.67523	0.36;0.44;0.34;0.23;0.21;0.14;-0.06;0.17;-0.08;0.1;-0.27	5.17	4.27	0.50696	.	.	.	.	.	T	0.71626	0.3362	L	0.34521	1.04	0.58432	D	0.999997	P;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.95;0.998;0.973;0.996;1.0;0.998;0.972;0.995;0.986;0.986;0.999;0.999;0.985	P;P;P;P;D;P;P;P;P;P;P;P;P	0.71414	0.53;0.887;0.53;0.83;0.973;0.887;0.747;0.801;0.691;0.691;0.856;0.887;0.747	T	0.73748	-0.3885	9	0.56958	D	0.05	.	12.7244	0.57162	0.0:0.9211:0.0:0.0789	.	1393;1418;1418;1423;1347;1378;1415;1418;1425;1425;1418;1420;1418	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	T	1425;1420;1418;1418;1029;1425;1378;1418;1393;1418;1415;1423;1347	ENSP00000363076:A1425T;ENSP00000410304:A1420T;ENSP00000378826:A1418T;ENSP00000386693:A1029T;ENSP00000378832:A1425T;ENSP00000378820:A1378T;ENSP00000354950:A1418T;ENSP00000378821:A1393T;ENSP00000322604:A1418T;ENSP00000378818:A1415T;ENSP00000412628:A1347T	ENSP00000322604:A1418T	A	-	1	0	PCDH15	55257274	1.000000	0.71417	0.060000	0.19600	0.466000	0.32739	5.173000	0.65010	1.497000	0.48584	0.561000	0.74099	GCA	-	NULL		0.532	PCDH15-001	KNOWN	basic|CCDS	protein_coding	PCDH15	protein_coding	OTTHUMT00000048121.2	C	NM_033056		55257274	-1	no_errors	NM_033056.1	genbank	human	reviewed	54_36p	missense	SNP	0.977	T
TET1	80312	genome.wustl.edu	37	10	70405604	70405604	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr10:70405604C>T	ENST00000373644.4	+	4	3327	c.3118C>T	c.(3118-3120)Cca>Tca	p.P1040S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1040					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TCAGTTGCCACCAAGAAATAA	0.368																																						dbGAP											0			10											89.0	88.0	88.0					10																	70405604		2203	4300	6503	70075610	SO:0001583	missense	0			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.3118C>T	10.37:g.70405604C>T	ENSP00000362748:p.Pro1040Ser	Somatic	152	0.00	0		3	25.00	1	WXS	Illumina HiSeq	Phase_IV	70075610	78	43.66	62	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	HMMPfam_zf-CXXC	p.P1040S	ENST00000373644.4	37	c.3118	CCDS7281.1	10	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.459843	0.01062	.	.	ENSG00000138336	ENST00000373644	T	0.05649	3.41	5.4	-2.82	0.05787	.	3.201200	0.00777	N	0.001249	T	0.03390	0.0098	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.30909	-0.9962	10	0.02654	T	1	.	2.9932	0.05989	0.4868:0.2666:0.109:0.1376	.	1040	Q8NFU7	TET1_HUMAN	S	1040	ENSP00000362748:P1040S	ENSP00000362748:P1040S	P	+	1	0	TET1	70075610	0.000000	0.05858	0.000000	0.03702	0.193000	0.23685	-0.037000	0.12164	-0.619000	0.05648	0.563000	0.77884	CCA	-	NULL		0.368	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TET1	protein_coding	OTTHUMT00000048354.1	C	NM_030625		70075610	+1	no_errors	NM_030625.2	genbank	human	validated	54_36p	missense	SNP	0.000	T
MYO16	23026	genome.wustl.edu	37	13	109379889	109379889	+	Silent	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr13:109379889C>T	ENST00000357550.2	+	3	440	c.399C>T	c.(397-399)gcC>gcT	p.A133A	MYO16_ENST00000356711.2_Silent_p.A133A|MYO16_ENST00000251041.5_Silent_p.A133A	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TGCACATTGCCTGTGCCTGCG	0.423																																						dbGAP											0			13											201.0	177.0	185.0					13																	109379889		2203	4300	6503	108177890	SO:0001819	synonymous_variant	0				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.399C>T	13.37:g.109379889C>T		Somatic	284	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	108177890	84	43.79	67		Silent	SNP	HMMPfam_IQ,HMMPfam_Myosin_head,HMMSmart_SM00242,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.A133	ENST00000357550.2	37	c.399	CCDS32008.1	13																																																																																			-	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat		0.423	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYO16	protein_coding	OTTHUMT00000045746.1	C	NM_015011		108177890	+1	no_errors	NM_015011.1	genbank	human	validated	54_36p	silent	SNP	1.000	T
ACAN	176	genome.wustl.edu	37	15	89401084	89401084	+	Silent	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr15:89401084C>T	ENST00000561243.1	+	11	5268	c.5268C>T	c.(5266-5268)agC>agT	p.S1756S	ACAN_ENST00000559004.1_Silent_p.S1756S|ACAN_ENST00000439576.2_Silent_p.S1756S|ACAN_ENST00000352105.7_Silent_p.S1756S			P16112	PGCA_HUMAN	aggrecan	1780	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.S1642S(2)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CTGAGCTTAGCGGGCTGTCCT	0.493																																						dbGAP											2	Substitution - coding silent(2)	lung(2)	15											72.0	74.0	73.0					15																	89401084		1913	4117	6030	87202088	SO:0001819	synonymous_variant	0			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.5268C>T	15.37:g.89401084C>T		Somatic	36	2.70	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	87202088	29	38.30	18	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin	p.S1642	ENST00000561243.1	37	c.4926	CCDS53970.1	15																																																																																			-	NULL		0.493	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	ACAN	protein_coding	OTTHUMT00000416267.2	C	NM_001135		87202088	+1	no_errors	NM_013227.2	genbank	human	reviewed	54_36p	silent	SNP	0.969	T
IDH2	3418	genome.wustl.edu	37	15	90631838	90631838	+	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr15:90631838C>T	ENST00000330062.3	-	4	628	c.515G>A	c.(514-516)aGg>aAg	p.R172K	IDH2_ENST00000539790.1_Missense_Mutation_p.R42K|IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.R120K	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172K(116)|p.R172M(21)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			ATGGGCGTGCCTGCCAATGGT	0.632			M		GBM																																	dbGAP		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	138	Substitution - Missense(138)	haematopoietic_and_lymphoid_tissue(67)|central_nervous_system(65)|biliary_tract(6)	15											85.0	81.0	82.0					15																	90631838		2200	4298	6498	88432842	SO:0001583	missense	0				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.515G>A	15.37:g.90631838C>T	ENSP00000331897:p.Arg172Lys	Somatic	78	0.00	0		80	50.31	81	WXS	Illumina HiSeq	Phase_IV	88432842	43	42.11	32	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	p.R172K	ENST00000330062.3	37	c.515	CCDS10359.1	15	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957149	0.53293	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86432	-2.12;-2.12;-2.12	5.93	4.07	0.47477	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96889	3.9	0.49687	D	0.999812	D	0.89917	1.0	D	0.91635	0.999	D	0.95096	0.8226	10	0.87932	D	0	.	10.781	0.46377	0.0:0.8464:0.0:0.1536	.	172	P48735	IDHP_HUMAN	K	172;42;120	ENSP00000331897:R172K;ENSP00000438457:R42K;ENSP00000446147:R120K	ENSP00000331897:R172K	R	-	2	0	IDH2	88432842	1.000000	0.71417	0.025000	0.17156	0.001000	0.01503	7.797000	0.85911	0.862000	0.35528	-0.258000	0.10820	AGG	-	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like		0.632	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IDH2	protein_coding	OTTHUMT00000313426.1	C			88432842	-1	no_errors	NM_002168.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
CUEDC1	404093	genome.wustl.edu	37	17	55962593	55962593	+	Silent	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr17:55962593C>T	ENST00000577830.1	-	2	746	c.333G>A	c.(331-333)ccG>ccA	p.P111P	CUEDC1_ENST00000407144.2_Silent_p.P111P|CUEDC1_ENST00000360238.2_Silent_p.P111P|CUEDC1_ENST00000577840.1_Intron	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	111	Pro-rich.									endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						CCCCTACCTCCGGGGGGATGC	0.662																																						dbGAP											0			17											38.0	44.0	42.0					17																	55962593		2184	4257	6441	53317592	SO:0001819	synonymous_variant	0			AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.333G>A	17.37:g.55962593C>T		Somatic	18	0.00	0		7	30.00	3	WXS	Illumina HiSeq	Phase_IV	53317592	32	34.69	17	D3DTZ2|Q9NWD0	Silent	SNP	HMMPfam_CUE,HMMSmart_SM00546,superfamily_UBA-like	p.P111	ENST00000577830.1	37	c.333	CCDS11599.1	17																																																																																			-	NULL		0.662	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CUEDC1	protein_coding	OTTHUMT00000443305.1	C	NM_017949		53317592	-1	no_errors	NM_017949.1	genbank	human	provisional	54_36p	silent	SNP	0.274	T
MEGF8	1954	genome.wustl.edu	37	19	42873053	42873053	+	Silent	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr19:42873053C>T	ENST00000251268.6	+	37	6540	c.6540C>T	c.(6538-6540)gaC>gaT	p.D2180D	MEGF8_ENST00000378073.4_5'Flank|MEGF8_ENST00000334370.4_Silent_p.D2113D	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2180	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCCCTGAGGACGAGTGTGCAA	0.612																																						dbGAP											0			19											85.0	91.0	89.0					19																	42873053		2203	4300	6503	47564893	SO:0001819	synonymous_variant	0			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.6540C>T	19.37:g.42873053C>T		Somatic	84	0.00	0		12	33.33	6	WXS	Illumina HiSeq	Phase_IV	47564893	15	48.28	14	A8KAY0|O75097	Silent	SNP	PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_CUB,superfamily_CUB,HMMSmart_EGF_CA,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,HMMPfam_PSI,HMMSmart_PSI,HMMSmart_EGF,HMMPfam_Kelch_1,superfamily_Gal_oxid_central,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_SSF57196	p.D2113	ENST00000251268.6	37	c.6339		19																																																																																			-	NULL		0.612	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	MEGF8	protein_coding	OTTHUMT00000463854.1	C	NM_001410		47564893	+1	no_errors	NM_001410.2	genbank	human	validated	54_36p	silent	SNP	1.000	T
SEL1L2	80343	genome.wustl.edu	37	20	13858170	13858170	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr20:13858170C>T	ENST00000284951.5	-	11	1096	c.1022G>A	c.(1021-1023)gGa>gAa	p.G341E	SEL1L2_ENST00000378072.5_Missense_Mutation_p.G341E|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	341						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						ATGTACCTTTCCTATAAATGC	0.408																																						dbGAP											0			20											95.0	89.0	91.0					20																	13858170		1853	4091	5944	13806170	SO:0001583	missense	0			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1022G>A	20.37:g.13858170C>T	ENSP00000284951:p.Gly341Glu	Somatic	143	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	13806170	81	49.38	79	B4DXX5	Missense_Mutation	SNP	HMMPfam_Sel1,HMMSmart_SEL1,superfamily_SSF81901	p.G341E	ENST00000284951.5	37	c.1022		20	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156739	0.78114	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.58940	0.3;0.3	5.32	5.32	0.75619	Tetratricopeptide-like helical (1);	0.000000	0.56097	D	0.000021	D	0.83156	0.5193	H	0.96269	3.795	0.51233	D	0.99991	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88051	0.2787	10	0.87932	D	0	-14.9364	14.8541	0.70323	0.0:1.0:0.0:0.0	.	341;341	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	E	341	ENSP00000367312:G341E;ENSP00000284951:G341E	ENSP00000284951:G341E	G	-	2	0	SEL1L2	13806170	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.345000	0.65987	2.648000	0.89879	0.655000	0.94253	GGA	-	HMMPfam_Sel1,HMMSmart_SEL1,superfamily_SSF81901		0.408	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	SEL1L2	protein_coding	OTTHUMT00000078067.3	C	NM_025229		13806170	-1	no_errors	NM_025229.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
DOPEY2	9980	genome.wustl.edu	37	21	37600135	37600135	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr21:37600135C>A	ENST00000399151.3	+	13	1710	c.1625C>A	c.(1624-1626)cCt>cAt	p.P542H		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	542					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GTCCAGATGCCTCCTTCCTAC	0.547																																						dbGAP											0			21											74.0	57.0	62.0					21																	37600135		2203	4300	6503	36522005	SO:0001583	missense	0			AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.1625C>A	21.37:g.37600135C>A	ENSP00000382104:p.Pro542His	Somatic	126	0.00	0		18	45.45	15	WXS	Illumina HiSeq	Phase_IV	36522005	40	41.18	28	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	HMMPfam_Dopey_N	p.P542H	ENST00000399151.3	37	c.1625	CCDS13643.1	21	.	.	.	.	.	.	.	.	.	.	C	27.9	4.873924	0.91664	.	.	ENSG00000142197	ENST00000399151	T	0.16743	2.32	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.44808	0.1311	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	T	0.17684	-1.0361	10	0.87932	D	0	-24.1069	20.5596	0.99324	0.0:1.0:0.0:0.0	.	542;542	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	H	542	ENSP00000382104:P542H	ENSP00000382104:P542H	P	+	2	0	DOPEY2	36522005	1.000000	0.71417	0.971000	0.41717	0.827000	0.46813	7.395000	0.79876	2.868000	0.98415	0.555000	0.69702	CCT	-	NULL		0.547	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOPEY2	protein_coding	OTTHUMT00000194636.1	C	NM_005128		36522005	+1	no_errors	NM_005128.2	genbank	human	validated	54_36p	missense	SNP	1.000	A
ASXL2	55252	genome.wustl.edu	37	2	25967233	25967234	+	Frame_Shift_Ins	INS	-	-	CT	rs569929404		TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	-	-	-	CT	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr2:25967233_25967234insCT	ENST00000435504.4	-	13	2265_2266	c.1972_1973insAG	c.(1972-1974)gcafs	p.A658fs	ASXL2_ENST00000272341.4_Frame_Shift_Ins_p.A398fs|ASXL2_ENST00000404843.1_Frame_Shift_Ins_p.A398fs|ASXL2_ENST00000336112.4_Frame_Shift_Ins_p.A630fs			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	658	Ala-rich.				adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTGATGTCTGCAAGAGTTCTG	0.574																																						dbGAP											0			2																																								25820738	SO:0001589	frameshift_variant	0					2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.1972_1973insAG	2.37:g.25967233_25967234insCT	ENSP00000391447:p.Ala658fs	Somatic	319	0.00	0		13	23.53	4	WXS	Illumina HiSeq	Phase_IV	25820737	68	36.45	39	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Frame_Shift_Ins	INS	NULL	p.A658fs	ENST00000435504.4	37	c.1973_1972		2																																																																																			-	NULL		0.574	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	ASXL2	protein_coding	OTTHUMT00000325593.3	-	NM_018263		25820738	-1	no_errors	NM_018263.4	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	CT
MPI	4351	genome.wustl.edu	37	15	75185119	75185121	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-AB-2898-03A-01W-0733-08	TCGA-AB-2898-11A-01W-0732-08	GAG	GAG	GAG	-	GAG	GAG	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	cebc6078-57bf-4866-a96d-a9e4fdaaf44d	e0e506a6-aeda-49ac-9ce5-46792b9b8c25	g.chr15:75185119_75185121delGAG	ENST00000352410.4	+	4	530_532	c.463_465delGAG	c.(463-465)gagdel	p.E156del	MPI_ENST00000563786.1_In_Frame_Del_p.E136del|MPI_ENST00000566377.1_In_Frame_Del_p.E156del|MPI_ENST00000563422.1_In_Frame_Del_p.E156del|MPI_ENST00000323744.6_In_Frame_Del_p.E156del|MPI_ENST00000565576.1_In_Frame_Del_p.E156del|MPI_ENST00000535694.1_In_Frame_Del_p.E106del|MPI_ENST00000564003.1_In_Frame_Del_p.E106del|MPI_ENST00000562606.1_In_Frame_Del_p.E136del			P34949	MPI_HUMAN	mannose phosphate isomerase	156					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						CCGGCCAGTTGAGGAGATTGTAA	0.567																																						dbGAP											0			15																																								72972174	SO:0001651	inframe_deletion	0				CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"""mannose-6-phosphate isomerase"""	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.463_465delGAG	15.37:g.75185122_75185124delGAG	ENSP00000318318:p.Glu156del	Somatic	0	0.00	0		0	15.00	3	WXS	Illumina HiSeq	Phase_IV	72972172	0	20.63	13	A8K8K9|Q96AB0	In_Frame_Del	DEL	HMMPfam_PMI_typeI,superfamily_RmlC-like cupins,PatternScan_PMI_I_1,PatternScan_PMI_I_2	p.E156in_frame_del	ENST00000352410.4	37	c.463_465	CCDS10272.1	15																																																																																			-	HMMPfam_PMI_typeI,superfamily_RmlC-like cupins		0.567	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MPI	protein_coding	OTTHUMT00000286418.4	GAG			72972174	+1	no_errors	NM_002435.1	genbank	human	reviewed	54_36p	in_frame_del	DEL	0.983:0.998:1.000	-
