#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_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_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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ERICH3	127254	hgsc.bcm.edu	37	1	75037489	75037489	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr1:75037489C>A	ENST00000326665.5	-	14	4123	c.3905G>T	c.(3904-3906)tGc>tTc	p.C1302F	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1302	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CTCCAGAGTGCACTCTTTGTC	0.542																																																	0													263.0	218.0	233.0					1																	75037489		2203	4300	6503	SO:0001583	missense	127254																														ENST00000326665.5:c.3905G>T	1.37:g.75037489C>A	ENSP00000322609:p.Cys1302Phe		Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.262562	0.23051	.	.	ENSG00000178965	ENST00000326665	T	0.12255	2.7	4.51	-3.12	0.05282	.	.	.	.	.	T	0.02494	0.0076	N	0.24115	0.695	0.09310	N	1	B	0.20671	0.047	B	0.18263	0.021	T	0.46541	-0.9184	9	0.51188	T	0.08	5.236	6.7233	0.23342	0.5174:0.2216:0.261:0.0	.	1302	Q5RHP9	CA173_HUMAN	F	1302	ENSP00000322609:C1302F	ENSP00000322609:C1302F	C	-	2	0	C1orf173	74810077	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.926000	0.00691	-0.340000	0.08388	0.462000	0.41574	TGC		0.542	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			
CHEK2	11200	hgsc.bcm.edu;ucsc.edu	37	22	29091808	29091808	+	Silent	SNP	G	G	A			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr22:29091808G>A	ENST00000405598.1	-	12	1340	c.1149C>T	c.(1147-1149)acC>acT	p.T383T	CHEK2_ENST00000403642.1_Silent_p.T292T|CHEK2_ENST00000328354.6_Silent_p.T383T|CHEK2_ENST00000544772.1_Silent_p.T162T|CHEK2_ENST00000382580.2_Silent_p.T426T|CHEK2_ENST00000402731.1_Silent_p.T354T|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382578.1_Silent_p.T292T|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000348295.3_Silent_p.T354T|CHEK2_ENST00000404276.1_Silent_p.T383T			O96017	CHK2_HUMAN	checkpoint kinase 2	383	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.T383T(5)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						TTCCACATAAGGTTCTCATGA	0.433			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																															yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	5	Substitution - coding silent(5)	central_nervous_system(5)											57.0	56.0	57.0					22																	29091808		2203	4300	6503	SO:0001819	synonymous_variant	11200			AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1149C>T	22.37:g.29091808G>A			A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	8.951	0.968314	0.18659	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-11.8	0.00035	.	.	.	.	.	T	0.43100	0.1232	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53585	-0.8418	4	.	.	.	-6.6972	7.2273	0.26022	0.624:0.0706:0.2037:0.1017	.	.	.	.	L	127	.	.	P	-	2	0	CHEK2	27421808	0.000000	0.05858	0.322000	0.25334	0.995000	0.86356	-3.768000	0.00371	-1.897000	0.01101	-0.143000	0.13931	CCT		0.433	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1		NM_001005735	
AGO1	26523	hgsc.bcm.edu	37	1	36358772	36358772	+	Silent	SNP	T	T	C			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr1:36358772T>C	ENST00000373204.4	+	4	618	c.405T>C	c.(403-405)atT>atC	p.I135I	AGO1_ENST00000373206.1_Silent_p.I60I	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	135					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										GGCTAGCCATTGTGAGCTGGC	0.557																																																	0													107.0	92.0	97.0					1																	36358772		2203	4300	6503	SO:0001819	synonymous_variant	26523			AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"""Argonaute/PIWI family"""	3262	protein-coding gene	gene with protein product	"""argonaute 1"""	606228	"""eukaryotic translation initiation factor 2C, 1"""	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.405T>C	1.37:g.36358772T>C			Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																				0.557	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			
MFSD10	10227	hgsc.bcm.edu	37	4	2934201	2934201	+	Silent	SNP	C	C	G	rs373159516		TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr4:2934201C>G	ENST00000329687.4	-	5	1104	c.570G>C	c.(568-570)ctG>ctC	p.L190L	NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000508221.1_Silent_p.L190L|MFSD10_ENST00000355443.4_Silent_p.L190L|MFSD10_ENST00000507555.1_Silent_p.L190L|MFSD10_ENST00000514800.1_Silent_p.L190L|NOP14-AS1_ENST00000507999.1_RNA	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	190					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GCATAGGGCCCAGGGTGAAGC	0.632																																																	0								C	,	0,4406		0,0,2203	58.0	67.0	64.0		570,570	2.2	1.0	4		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	MFSD10	NM_001120.4,NM_001146069.1	,	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	,	190/456,190/456	2934201	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10227			L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"""tetracycline transporter like protein"""	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.570G>C	4.37:g.2934201C>G			Q07706	Silent	SNP	ENST00000329687.4	37	CCDS3365.1																																																																																				0.632	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2		NM_001120	
MFSD6L	162387	hgsc.bcm.edu	37	17	8701341	8701341	+	Silent	SNP	G	G	A			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr17:8701341G>A	ENST00000329805.4	-	1	1326	c.1098C>T	c.(1096-1098)ccC>ccT	p.P366P		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	366						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						GAATGAGGTGGGGGTCACCCC	0.557																																																	0													86.0	90.0	88.0					17																	8701341		2203	4300	6503	SO:0001819	synonymous_variant	162387			AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.1098C>T	17.37:g.8701341G>A			Q6YL34|Q8NA76	Silent	SNP	ENST00000329805.4	37	CCDS11146.1																																																																																				0.557	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1		NM_152599	
MTMR8	55613	hgsc.bcm.edu	37	X	63548772	63548772	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chrX:63548772T>C	ENST00000374852.3	-	12	1428	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	MTMR8_ENST00000453546.1_Intron|MTMR8_ENST00000478487.1_5'Flank	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	454	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.		E -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						ATGTGTTTTCTCATAGACTCT	0.378																																																	1	Whole gene deletion(1)	ovary(1)											64.0	55.0	58.0					X																	63548772		2203	4300	6503	SO:0001583	missense	55613			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1361A>G	X.37:g.63548772T>C	ENSP00000363985:p.Glu454Gly		Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.39|17.39	3.377465|3.377465	0.61735|0.61735	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000374852;ENST00000247400|ENST00000442913	D|.	0.90563|.	-2.69|.	2.93|2.93	2.93|2.93	0.34026|0.34026	Myotubularin phosphatase domain (1);|.	0.000000|.	0.43747|.	U|.	0.000540|.	T|.	0.74329|.	0.3702|.	M|M	0.85197|0.85197	2.74|2.74	0.80722|0.80722	D|D	1|1	D|.	0.61080|.	0.989|.	P|.	0.57468|.	0.821|.	T|.	0.75659|.	-0.3241|.	10|.	0.72032|.	D|.	0.01|.	.|.	9.6367|9.6367	0.39811|0.39811	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	454|.	Q96EF0|.	MTMR8_HUMAN|.	G|W	454;340|257	ENSP00000363985:E454G|.	ENSP00000247400:E340G|.	E|X	-|-	2|3	0|0	MTMR8|MTMR8	63465497|63465497	1.000000|1.000000	0.71417|0.71417	0.626000|0.626000	0.29213|0.29213	0.914000|0.914000	0.54420|0.54420	5.936000|5.936000	0.70153|0.70153	1.188000|1.188000	0.43014|0.43014	0.412000|0.412000	0.27726|0.27726	GAG|TGA		0.378	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2		NM_017677	
PIK3CG	5294	hgsc.bcm.edu	37	7	106526717	106526717	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr7:106526717C>A	ENST00000359195.3	+	10	3320	c.3010C>A	c.(3010-3012)Cca>Aca	p.P1004T	PIK3CG_ENST00000496166.1_Missense_Mutation_p.P1004T|PIK3CG_ENST00000440650.2_Missense_Mutation_p.P1004T	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	1004	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GAAGACAAGCCCACACTTCCA	0.478																																																	0													72.0	69.0	70.0					7																	106526717		2203	4300	6503	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.3010C>A	7.37:g.106526717C>A	ENSP00000352121:p.Pro1004Thr		A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.867849	0.51588	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.74315	-0.83;-0.83;-0.83	5.64	4.71	0.59529	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.515416	0.23910	N	0.043359	T	0.63307	0.2500	L	0.29908	0.895	0.46564	D	0.9991	B	0.10296	0.003	B	0.16722	0.016	T	0.56165	-0.8024	10	0.19590	T	0.45	0.5226	15.7056	0.77577	0.1374:0.8626:0.0:0.0	.	1004	P48736	PK3CG_HUMAN	T	1004	ENSP00000392258:P1004T;ENSP00000419260:P1004T;ENSP00000352121:P1004T	ENSP00000352121:P1004T	P	+	1	0	PIK3CG	106313953	0.999000	0.42202	0.980000	0.43619	0.925000	0.55904	4.839000	0.62810	2.820000	0.97059	0.650000	0.86243	CCA		0.478	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			
PKD1L2	114780	hgsc.bcm.edu	37	16	81242151	81242151	+	RNA	SNP	T	T	C	rs5818326|rs532218091|rs386792900	byFrequency	TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr16:81242151T>C	ENST00000525539.1	-	0	704				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.G235G(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GACACAGGTTTCCAAAGTAGG	0.562													T|||	2211	0.441494	0.1717	0.4625	5008	,	,		20463	0.8026		0.4205	False		,,,				2504	0.4407																2	Substitution - coding silent(2)	lung(2)											86.0	82.0	83.0					16																	81242151		2123	4226	6349			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242151T>C			Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																					0.562	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			
PTPRT	11122	hgsc.bcm.edu	37	20	40714466	40714466	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr20:40714466T>C	ENST00000373187.1	-	28	3873	c.3874A>G	c.(3874-3876)Acc>Gcc	p.T1292A	PTPRT_ENST00000356100.2_Missense_Mutation_p.T1301A|PTPRT_ENST00000373201.1_Missense_Mutation_p.T1282A|PTPRT_ENST00000373193.3_Missense_Mutation_p.T1295A|PTPRT_ENST00000373184.1_Missense_Mutation_p.T1302A|PTPRT_ENST00000373190.1_Missense_Mutation_p.T1291A|PTPRT_ENST00000373198.4_Missense_Mutation_p.T1311A			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1292	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.T1314A(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CACCCGGAGGTCTTCTCAGGC	0.522																																																	1	Substitution - Missense(1)	ovary(1)											72.0	74.0	73.0					20																	40714466		1943	4139	6082	SO:0001583	missense	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3874A>G	20.37:g.40714466T>C	ENSP00000362283:p.Thr1292Ala		A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.561626	0.45590	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58;2.58	5.31	5.31	0.75309	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.113243	0.64402	D	0.000011	T	0.13372	0.0324	N	0.25825	0.765	0.44417	D	0.997339	B;B	0.24258	0.1;0.072	B;B	0.30029	0.067;0.11	T	0.06215	-1.0839	10	0.66056	D	0.02	.	15.4285	0.75072	0.0:0.0:0.0:1.0	.	1314;1292	O14522-1;O14522	.;PTPRT_HUMAN	A	1291;1292;1295;1301;1314;1302;1282	ENSP00000362286:T1291A;ENSP00000362283:T1292A;ENSP00000362289:T1295A;ENSP00000348408:T1301A;ENSP00000362294:T1314A;ENSP00000362280:T1302A;ENSP00000362297:T1282A	ENSP00000348408:T1301A	T	-	1	0	PTPRT	40147880	0.999000	0.42202	1.000000	0.80357	0.936000	0.57629	2.539000	0.45718	2.232000	0.73038	0.533000	0.62120	ACC		0.522	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			
SETD2	29072	hgsc.bcm.edu;ucsc.edu	37	3	47142969	47142969	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr3:47142969T>A	ENST00000409792.3	-	8	5036	c.4994A>T	c.(4993-4995)gAc>gTc	p.D1665V		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1665	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GAACTGATAGTCAAACGTTAA	0.378			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0													163.0	166.0	165.0					3																	47142969		2203	4300	6503	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4994A>T	3.37:g.47142969T>A	ENSP00000386759:p.Asp1665Val		O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	27.1	4.804649	0.90623	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.84873	-1.91	5.94	5.94	0.96194	SET domain (3);	0.000000	0.56097	D	0.000028	D	0.96166	0.8750	H	0.99590	4.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98154	1.0443	10	0.87932	D	0	.	16.4075	0.83691	0.0:0.0:0.0:1.0	.	1665;1665	F2Z317;Q9BYW2	.;SETD2_HUMAN	V	1665	ENSP00000386759:D1665V	ENSP00000386759:D1665V	D	-	2	0	SETD2	47117973	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.955000	0.87856	2.275000	0.75901	0.528000	0.53228	GAC		0.378	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC26A8	116369	hgsc.bcm.edu	37	6	35922962	35922962	+	Silent	SNP	G	G	A			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr6:35922962G>A	ENST00000490799.1	-	17	2552	c.2199C>T	c.(2197-2199)taC>taT	p.Y733Y	SLC26A8_ENST00000355574.2_Silent_p.Y733Y|SLC26A8_ENST00000394602.2_Silent_p.Y628Y	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8									p.Y733Y(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						GTGAATCCACGTAGTGTACCA	0.547																																																	1	Substitution - coding silent(1)	prostate(1)											115.0	105.0	108.0					6																	35922962		2203	4300	6503	SO:0001819	synonymous_variant	116369			AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2199C>T	6.37:g.35922962G>A				Silent	SNP	ENST00000490799.1	37	CCDS4813.1																																																																																				0.547	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			
TAF1C	9013	hgsc.bcm.edu	37	16	84213194	84213194	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr16:84213194C>T	ENST00000567759.1	-	14	2145	c.1963G>A	c.(1963-1965)Gca>Aca	p.A655T	TAF1C_ENST00000570117.1_Missense_Mutation_p.A323T|TAF1C_ENST00000541676.1_Missense_Mutation_p.A562T|TAF1C_ENST00000566732.1_Missense_Mutation_p.A629T|TAF1C_ENST00000341690.6_Missense_Mutation_p.A561T|TAF1C_ENST00000378541.4_Missense_Mutation_p.A655T	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	655					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						AAGGTGGGTGCTGTCCACACA	0.672																																																	0													27.0	28.0	27.0					16																	84213194		2200	4298	6498	SO:0001583	missense	9013			L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.1963G>A	16.37:g.84213194C>T	ENSP00000455265:p.Ala655Thr		B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047977	0.36085	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.04317	3.75;3.65;3.65	4.95	3.97	0.46021	.	0.494210	0.17937	N	0.156970	T	0.16896	0.0406	M	0.68317	2.08	0.09310	N	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;0.996	D;D;D;D	0.87578	0.998;0.998;0.998;0.993	T	0.01444	-1.1353	10	0.54805	T	0.06	-1.8941	9.8811	0.41233	0.0:0.7252:0.2748:0.0	.	629;178;655;561	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	T	655;562;561;178	ENSP00000367802:A655T;ENSP00000437900:A562T;ENSP00000345305:A561T	ENSP00000345305:A561T	A	-	1	0	TAF1C	82770695	0.427000	0.25514	0.104000	0.21259	0.010000	0.07245	1.016000	0.29976	2.287000	0.76781	0.561000	0.74099	GCA		0.672	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2		NM_139353	
TET1	80312	hgsc.bcm.edu	37	10	70450816	70450816	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr10:70450816G>T	ENST00000373644.4	+	12	5865	c.5656G>T	c.(5656-5658)Gga>Tga	p.G1886*		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1886					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)	p.G1886R(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GATGCCTTCGGGAAGACTCAG	0.567																																																	2	Substitution - Missense(2)	lung(2)											74.0	67.0	69.0					10																	70450816		2203	4300	6503	SO:0001587	stop_gained	80312			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.5656G>T	10.37:g.70450816G>T	ENSP00000362748:p.Gly1886*		Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Nonsense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	42	9.620891	0.99221	.	.	ENSG00000138336	ENST00000373644	.	.	.	5.55	2.21	0.28008	.	8.812420	0.00166	N	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	3.2751	0.06896	0.1305:0.1605:0.5446:0.1644	.	.	.	.	X	1886	.	ENSP00000362748:G1886X	G	+	1	0	TET1	70120822	0.094000	0.21725	0.050000	0.19076	0.046000	0.14306	0.570000	0.23653	1.306000	0.44926	0.655000	0.94253	GGA		0.567	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1		NM_030625	
TNR	7143	hgsc.bcm.edu	37	1	175334171	175334171	+	Silent	SNP	C	C	T			TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr1:175334171C>T	ENST00000367674.2	-	12	3270	c.2562G>A	c.(2560-2562)gaG>gaA	p.E854E	TNR_ENST00000263525.2_Silent_p.E854E			Q92752	TENR_HUMAN	tenascin R	854	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CCACAATGGGCTCAGAGGTCA	0.522																																																	0													77.0	75.0	76.0					1																	175334171		2203	4300	6503	SO:0001819	synonymous_variant	7143			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2562G>A	1.37:g.175334171C>T			C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.522	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4		NM_003285	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937854	88937854	+	Missense_Mutation	SNP	T	T	A	rs58050565|rs77621374|rs397759922	byFrequency	TCGA-CJ-4891-01A-01D-1373-10	TCGA-CJ-4891-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	4176dd2a-f3b8-44bd-866f-cd5835080b2b	84b5374a-2e42-43e0-bed9-5d9a000398e2	g.chr9:88937854T>A	ENST00000375963.3	-	13	2983	c.2811A>T	c.(2809-2811)aaA>aaT	p.K937N	ZCCHC6_ENST00000277141.6_Missense_Mutation_p.K226N|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.K937N|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.K814N|ZCCHC6_ENST00000469004.1_5'Flank	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	937				Missing (in Ref. 1; CAI45944/CAH56219). {ECO:0000305}.	RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						CAGGTGAATTTTTTTCTTCAC	0.343																																																	0													29.0	32.0	31.0					9																	88937854		2059	4076	6135	SO:0001583	missense	79670			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2811A>T	9.37:g.88937854T>A	ENSP00000365130:p.Lys937Asn		Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	-	4.685	0.127420	0.08981	.	.	ENSG00000083223	ENST00000277141;ENST00000375960;ENST00000375961;ENST00000375963	T;T;T;T	0.56611	0.45;0.9;0.87;0.88	5.24	2.89	0.33648	.	0.839607	0.08576	U	0.925223	T	0.32285	0.0824	N	0.08118	0	0.09310	N	1	B;P	0.39094	0.003;0.659	B;B	0.42959	0.0;0.403	T	0.17167	-1.0378	10	0.19590	T	0.45	.	3.5944	0.08001	0.2793:0.1598:0.0:0.5609	.	814;937	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	N	226;814;937;937	ENSP00000277141:K226N;ENSP00000365127:K814N;ENSP00000365128:K937N;ENSP00000365130:K937N	ENSP00000277141:K226N	K	-	3	2	ZCCHC6	88127674	0.000000	0.05858	0.997000	0.53966	0.445000	0.32107	-0.165000	0.09968	0.453000	0.26858	0.528000	0.53228	AAA		0.343	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1		NM_024617	
