#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	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_dbSNPPopFreq	i_dbSNP_AF	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_refseq_mrna_id	i_secondary_variant_classification
TRMT13	54482	hgsc.bcm.edu	37	1	100602441	100602441	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr1:100602441G>A	ENST00000370141.2	+	2	157	c.151G>A	c.(151-153)Gaa>Aaa	p.E51K	TRMT13_ENST00000370143.1_Missense_Mutation_p.E51K|TRMT13_ENST00000370139.1_Missense_Mutation_p.E20K	NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	51					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										TTATTAGGAAGAAGATGCTCG	0.323																																					p.E51K		Atlas-SNP	.											.	.	.	.	0			c.G151A						.						52.0	59.0	57.0					1																	100602441		2201	4298	6499	SO:0001583	missense	54482	exon2			TAGGAAGAAGATG	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.151G>A	chr1.hg19:g.100602441G>A	ENSP00000359160:p.Glu51Lys	123.0	0.0		190.0	12.0	NM_019083	Q5VVL0|Q9NW65	Missense_Mutation	SNP	ENST00000370141.2	hg19	CCDS765.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669791	0.47677	.	.	ENSG00000122435	ENST00000370143;ENST00000370141;ENST00000370139	T;T;T	0.43688	0.97;0.98;0.94	5.59	5.59	0.84812	.	0.150529	0.64402	D	0.000017	T	0.13157	0.0319	N	0.20766	0.605	0.52501	D	0.999951	B;B	0.31485	0.068;0.325	B;B	0.27796	0.014;0.083	T	0.06481	-1.0824	10	0.11182	T	0.66	-23.1678	14.7734	0.69696	0.0:0.1443:0.8557:0.0	.	51;51	B4DQS9;Q9NUP7	.;TRM13_HUMAN	K	51;51;20	ENSP00000359162:E51K;ENSP00000359160:E51K;ENSP00000359158:E20K	ENSP00000359158:E20K	E	+	1	0	CCDC76	100375029	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.204000	0.72143	2.611000	0.88343	0.650000	0.86243	GAA	.	.		0.323	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	
OBSCN	84033	hgsc.bcm.edu	37	1	228527773	228527773	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr1:228527773G>A	ENST00000422127.1	+	70	17430	c.17386G>A	c.(17386-17388)Gtc>Atc	p.V5796I	OBSCN_ENST00000366707.4_Missense_Mutation_p.V3430I|OBSCN_ENST00000570156.2_Missense_Mutation_p.V6753I|OBSCN_ENST00000284548.11_Missense_Mutation_p.V5796I|OBSCN_ENST00000366709.4_Missense_Mutation_p.V2915I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5796	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTCGGTGGTCGTCAGCACGGC	0.602																																					p.V6753I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G20257A						.						68.0	80.0	76.0					1																	228527773		2098	4202	6300	SO:0001583	missense	84033	exon81			GTGGTCGTCAGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17386G>A	chr1.hg19:g.228527773G>A	ENSP00000409493:p.Val5796Ile	61.0	0.0		89.0	4.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.74|19.74	3.884428|3.884428	0.72410|0.72410	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.62941	.|-0.01;-0.01;-0.01;-0.01	4.98|4.98	4.06|4.06	0.47325|0.47325	.|Dbl homology (DH) domain (4);	.|0.251783	.|0.33477	.|N	.|0.004879	T|T	0.56659|0.56659	0.2000|0.2000	L|L	0.31420|0.31420	0.93|0.93	0.28547|0.28547	N|N	0.911833|0.911833	.|D;D	.|0.59357	.|0.985;0.963	.|P;B	.|0.47786	.|0.557;0.281	T|T	0.58381|0.58381	-0.7646|-0.7646	5|10	.|0.87932	.|D	.|0	.|.	13.9957|13.9957	0.64397|0.64397	0.0:0.2891:0.7109:0.0|0.0:0.2891:0.7109:0.0	.|.	.|5796;5796	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	H|I	412|5796;5796;3430;2915	.|ENSP00000284548:V5796I;ENSP00000409493:V5796I;ENSP00000355668:V3430I;ENSP00000355670:V2915I	.|ENSP00000284548:V5796I	R|V	+|+	2|1	0|0	OBSCN|OBSCN	226594396|226594396	1.000000|1.000000	0.71417|0.71417	0.941000|0.941000	0.38009|0.38009	0.367000|0.367000	0.29736|0.29736	3.951000|3.951000	0.56684|0.56684	1.315000|1.315000	0.45114|0.45114	-0.502000|-0.502000	0.04539|0.04539	CGT|GTC	.	.		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FSHR	2492	hgsc.bcm.edu	37	2	49295430	49295430	+	Splice_Site	SNP	C	C	T			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr2:49295430C>T	ENST00000406846.2	-	2	272		c.e2-1		FSHR_ENST00000304421.4_Splice_Site|FSHR_ENST00000346173.3_Splice_Site	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor						female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	GACAAACCTCCTGCAAAGAGA	0.383									Gonadal Dysgenesis, 46 XX																												.		Atlas-SNP	.											FSHR,NS,carcinoma,0,1	FSHR	164	.	0			c.153-1G>A						.						100.0	99.0	99.0					2																	49295430		2203	4299	6502	SO:0001630	splice_region_variant	2492	exon3	Familial Cancer Database		AACCTCCTGCAAA		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"""GPCR / Class A : Gonadotropin and TSH receptors"""	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.153-1G>A	chr2.hg19:g.49295430C>T		50.0	0.0		74.0	11.0	NM_181446	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Splice_Site	SNP	ENST00000406846.2	hg19	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.591742	0.66219	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000454032	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3532	0.60613	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FSHR	49148934	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.722000	0.54948	2.521000	0.84997	0.462000	0.41574	.	.	.		0.383	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		Intron
HK2	3099	hgsc.bcm.edu	37	2	75109363	75109363	+	Silent	SNP	C	C	T	rs200225889		TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr2:75109363C>T	ENST00000290573.2	+	12	2436	c.1836C>T	c.(1834-1836)gaC>gaT	p.D612D	HK2_ENST00000409174.1_Silent_p.D584D	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	612	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						ACAGCCTGGACGAGGTAACAG	0.547																																					p.D612D		Atlas-SNP	.											HK2,NS,carcinoma,0,1	HK2	85	.	0			c.C1836T						.	C		0,4406		0,0,2203	78.0	76.0	77.0		1836	-9.0	0.3	2		77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HK2	NM_000189.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		612/918	75109363	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon12			CCTGGACGAGGTA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1836C>T	chr2.hg19:g.75109363C>T		104.0	0.0		132.0	13.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	hg19	CCDS1956.1																																																																																			.	C|0.999;T|0.001		0.547	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
NDUFB3	4709	hgsc.bcm.edu	37	2	201943675	201943675	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr2:201943675A>G	ENST00000237889.4	+	2	393	c.70A>G	c.(70-72)Ata>Gta	p.I24V	RNU6-1206P_ENST00000516339.1_RNA|NDUFB3_ENST00000433898.1_Missense_Mutation_p.I24V|NDUFB3_ENST00000454214.1_Missense_Mutation_p.I24V	NM_001257102.1|NM_002491.2	NP_001244031.1|NP_002482.1	O43676	NDUB3_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa	24					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)|urinary_tract(1)	3						ACAATGGAAGATAGAAGGGAC	0.403																																					p.I24V		Atlas-SNP	.											.	NDUFB3	5	.	0			c.A70G						.						77.0	76.0	76.0					2																	201943675		2203	4300	6503	SO:0001583	missense	4709	exon3			TGGAAGATAGAAG	AF047183	CCDS2336.1	2q33.1	2011-07-04	2002-08-29		ENSG00000119013	ENSG00000119013		"""Mitochondrial respiratory chain complex / Complex I"""	7698	protein-coding gene	gene with protein product	"""complex I B12 subunit"""	603839	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3 (12kD, B12)"""			9425316, 11474204	Standard	NM_002491		Approved	B12	uc002uwx.4	O43676	OTTHUMG00000132820	ENST00000237889.4:c.70A>G	chr2.hg19:g.201943675A>G	ENSP00000237889:p.Ile24Val	225.0	0.0		290.0	24.0	NM_001257102	Q6IB80	Missense_Mutation	SNP	ENST00000237889.4	hg19	CCDS2336.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.748465	0.30955	.	.	ENSG00000119013	ENST00000450023;ENST00000237889;ENST00000433898;ENST00000454214	T;T;T;T	0.75821	-0.97;-0.88;-0.88;-0.88	5.11	5.11	0.69529	.	0.214597	0.46758	N	0.000280	T	0.50326	0.1609	.	.	.	0.38465	D	0.947323	P	0.44006	0.824	B	0.34418	0.182	T	0.60182	-0.7313	9	0.05721	T	0.95	-0.9102	14.1733	0.65525	1.0:0.0:0.0:0.0	.	24	O43676	NDUB3_HUMAN	V	24	ENSP00000401834:I24V;ENSP00000237889:I24V;ENSP00000410600:I24V;ENSP00000407336:I24V	ENSP00000237889:I24V	I	+	1	0	NDUFB3	201651920	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.887000	0.48586	2.049000	0.60858	0.533000	0.62120	ATA	.	.		0.403	NDUFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256277.1	NM_002491	
SEL1L3	23231	hgsc.bcm.edu	37	4	25849364	25849364	+	Missense_Mutation	SNP	G	G	T	rs371579636		TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr4:25849364G>T	ENST00000399878.3	-	2	407	c.285C>A	c.(283-285)aaC>aaA	p.N95K	SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000264868.5_Missense_Mutation_p.N60K|SEL1L3_ENST00000502949.1_5'UTR	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	95						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						CTTCAGAAACGTTGCGAACGT	0.433																																					p.N95K		Atlas-SNP	.											.	SEL1L3	62	.	0			c.C285A						.						92.0	84.0	86.0					4																	25849364		1851	4112	5963	SO:0001583	missense	23231	exon2			AGAAACGTTGCGA	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.285C>A	chr4.hg19:g.25849364G>T	ENSP00000382767:p.Asn95Lys	148.0	0.0		176.0	30.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032919	0.54790	.	.	ENSG00000091490	ENST00000399878;ENST00000264868	T;T	0.16073	2.37;2.41	5.25	-3.42	0.04825	.	0.062148	0.64402	D	0.000005	T	0.28499	0.0705	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.66847	0.947	T	0.01839	-1.1263	10	0.72032	D	0.01	-22.1871	12.9132	0.58190	0.7017:0.0:0.2983:0.0	.	95	Q68CR1	SE1L3_HUMAN	K	95;60	ENSP00000382767:N95K;ENSP00000264868:N60K	ENSP00000264868:N60K	N	-	3	2	SEL1L3	25458462	0.048000	0.20356	0.325000	0.25375	0.894000	0.52154	-0.648000	0.05391	-0.595000	0.05828	-0.274000	0.10170	AAC	.	.		0.433	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
GZMA	3001	hgsc.bcm.edu	37	5	54404222	54404222	+	Splice_Site	SNP	T	T	C			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr5:54404222T>C	ENST00000274306.6	+	4	662	c.627T>C	c.(625-627)aaT>aaC	p.N209N		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	209	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				ACTCGTGCAATGTAAGTAAAA	0.393																																					p.N209N		Atlas-SNP	.											.	GZMA	60	.	0			c.T627C						.						67.0	69.0	68.0					5																	54404222		2203	4300	6503	SO:0001630	splice_region_variant	3001	exon4			GTGCAATGTAAGT		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"""CTL tryptase"", ""Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"""	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.627+1T>C	chr5.hg19:g.54404222T>C		106.0	0.0		143.0	20.0	NM_006144	A4PHN1|Q6IB36	Silent	SNP	ENST00000274306.6	hg19	CCDS3965.1																																																																																			.	.		0.393	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144	Silent
C6orf62	81688	hgsc.bcm.edu	37	6	24718778	24718778	+	Missense_Mutation	SNP	A	A	C			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr6:24718778A>C	ENST00000378119.4	-	1	2286	c.119T>G	c.(118-120)tTc>tGc	p.F40C	C6orf62_ENST00000378102.3_Intron|C6orf62_ENST00000540769.1_Intron	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	40						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						CTTCTCCTTGAATACAAAGGC	0.313																																					p.F40C		Atlas-SNP	.											.	C6orf62	18	.	0			c.T119G						.						72.0	73.0	73.0					6																	24718778		2203	4300	6503	SO:0001583	missense	81688	exon1			TCCTTGAATACAA	AL136632	CCDS4559.1	6p22.1	2011-12-13			ENSG00000112308	ENSG00000112308			20998	protein-coding gene	gene with protein product	"""HBV X-transactivated protein 12"""					11230166	Standard	NM_030939		Approved	FLJ12619, DKFZP564G182, XTP12	uc003nel.3	Q9GZU0	OTTHUMG00000014361	ENST00000378119.4:c.119T>G	chr6.hg19:g.24718778A>C	ENSP00000367359:p.Phe40Cys	109.0	0.0		127.0	16.0	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	hg19	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.752550	0.69533	.	.	ENSG00000112308	ENST00000378119	T	0.41400	1.0	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.51733	-0.8668	10	0.87932	D	0	-9.8903	15.9584	0.79906	1.0:0.0:0.0:0.0	.	40	Q9GZU0	CF062_HUMAN	C	40	ENSP00000367359:F40C	ENSP00000367359:F40C	F	-	2	0	C6orf62	24826757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.678000	0.91211	2.165000	0.68154	0.528000	0.53228	TTC	.	.		0.313	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939	
TIGD3	220359	hgsc.bcm.edu	37	11	65124527	65124527	+	Silent	SNP	C	C	T			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr11:65124527C>T	ENST00000309880.5	+	2	1455	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D		NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	416						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						GCACTGAAGACGAGAAGGGGG	0.607																																					p.D416D		Atlas-SNP	.											.	TIGD3	32	.	0			c.C1248T						.						106.0	100.0	102.0					11																	65124527		2201	4297	6498	SO:0001819	synonymous_variant	220359	exon2			TGAAGACGAGAAG		CCDS8101.1	11q13.1	2008-07-21				ENSG00000173825			18334	protein-coding gene	gene with protein product							Standard	NM_145719		Approved		uc001odo.4	Q6B0B8		ENST00000309880.5:c.1248C>T	chr11.hg19:g.65124527C>T		87.0	0.0		111.0	9.0	NM_145719		Silent	SNP	ENST00000309880.5	hg19	CCDS8101.1																																																																																			.	.		0.607	TIGD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387310.1	NM_145719	
DDX47	51202	hgsc.bcm.edu	37	12	12974309	12974309	+	Missense_Mutation	SNP	T	T	G			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr12:12974309T>G	ENST00000358007.3	+	3	371	c.349T>G	c.(349-351)Tcc>Gcc	p.S117A	DDX47_ENST00000352940.4_Missense_Mutation_p.S117A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	117	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		AGCCCTGGGGTCCTCTATTGG	0.532																																					p.S117A		Atlas-SNP	.											.	DDX47	37	.	0			c.T349G						.						110.0	110.0	110.0					12																	12974309		2203	4300	6503	SO:0001583	missense	51202	exon3			CTGGGGTCCTCTA	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.349T>G	chr12.hg19:g.12974309T>G	ENSP00000350698:p.Ser117Ala	63.0	0.0		101.0	18.0	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	hg19	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.973325	0.53614	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.15256	2.44;2.44	5.6	5.6	0.85130	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.08492	0.0211	N	0.02275	-0.615	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.12156	0.004;0.004;0.003;0.007	T	0.29243	-1.0018	10	0.30854	T	0.27	-14.6871	15.7878	0.78322	0.0:0.0:0.0:1.0	.	117;117;117;117	B4DYP6;Q9H4E3;G5E955;Q9H0S4	.;.;.;DDX47_HUMAN	A	117	ENSP00000319578:S117A;ENSP00000350698:S117A	ENSP00000319578:S117A	S	+	1	0	DDX47	12865576	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.506000	0.81665	2.135000	0.66039	0.454000	0.30748	TCC	.	.		0.532	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
MTA1	9112	hgsc.bcm.edu	37	14	105929876	105929876	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr14:105929876A>G	ENST00000331320.7	+	12	1278	c.1064A>G	c.(1063-1065)tAt>tGt	p.Y355C	MTA1_ENST00000435036.2_5'UTR|MTA1_ENST00000406191.1_Missense_Mutation_p.Y355C|MTA1_ENST00000405646.1_Missense_Mutation_p.Y338C	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	355					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AAGCAAGTTTATATTCCCAAC	0.582																																					p.Y355C		Atlas-SNP	.											.	MTA1	61	.	0			c.A1064G						.						64.0	66.0	66.0					14																	105929876		2203	4300	6503	SO:0001583	missense	9112	exon12			AAGTTTATATTCC	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1064A>G	chr14.hg19:g.105929876A>G	ENSP00000333633:p.Tyr355Cys	99.0	0.0		115.0	12.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.145321	0.77888	.	.	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050	T;T;T;T	0.36699	1.26;1.25;1.25;1.24	4.11	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.60340	0.2261	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.984	T	0.66333	-0.5950	10	0.87932	D	0	-8.3006	12.2357	0.54514	1.0:0.0:0.0:0.0	.	147;355	Q59FW1;Q13330	.;MTA1_HUMAN	C	264;355;355;338;147	ENSP00000333633:Y355C;ENSP00000385702:Y355C;ENSP00000384180:Y338C;ENSP00000394106:Y147C	ENSP00000333633:Y355C	Y	+	2	0	MTA1	105000921	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.181000	0.94874	1.632000	0.50472	0.460000	0.39030	TAT	.	.		0.582	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
SMARCD2	6603	hgsc.bcm.edu	37	17	61911595	61911595	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr17:61911595T>C	ENST00000448276.2	-	8	1280	c.1015A>G	c.(1015-1017)Atc>Gtc	p.I339V	SMARCD2_ENST00000323347.10_Missense_Mutation_p.I291V|SMARCD2_ENST00000225742.9_Missense_Mutation_p.I264V	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	339	SWIB.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						TTGTGCTTGATGTAAAGCCAC	0.597											OREG0024642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I339V		Atlas-SNP	.											.	SMARCD2	29	.	0			c.A1015G						.						34.0	35.0	34.0					17																	61911595		2083	4196	6279	SO:0001583	missense	6603	exon8			GCTTGATGTAAAG	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60B"", ""Swp73-like protein"", ""chromatin remodeling complex BAF60B subunit"", ""SWI/SNF complex 60 kDa subunit B"""	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.1015A>G	chr17.hg19:g.61911595T>C	ENSP00000392617:p.Ile339Val	102.0	0.0	1057	119.0	21.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	5.438	0.266022	0.10294	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T	0.56941	0.43;0.46	5.55	4.48	0.54585	SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.49457	0.1558	L	0.54863	1.705	0.80722	D	1	B;B;B	0.27286	0.007;0.04;0.174	B;B;B	0.36092	0.003;0.036;0.217	T	0.40156	-0.9578	10	0.25751	T	0.34	-8.4759	9.6059	0.39632	0.0:0.0816:0.0:0.9184	.	291;302;339	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	V	339;281;302;291	ENSP00000392617:I339V;ENSP00000318451:I291V	ENSP00000225742:I281V	I	-	1	0	SMARCD2	59265327	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	4.987000	0.63857	1.130000	0.42092	-0.250000	0.11733	ATC	.	.		0.597	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426	
RNF213	57674	hgsc.bcm.edu	37	17	78363961	78363961	+	Missense_Mutation	SNP	A	A	C			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chr17:78363961A>C	ENST00000582970.1	+	67	15578	c.15435A>C	c.(15433-15435)caA>caC	p.Q5145H	RNF213_ENST00000508628.2_Missense_Mutation_p.Q5194H|RNF213_ENST00000427003.3_3'UTR|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.Q3218H	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5145					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGAACCCCCAAACCCAAACCG	0.507																																					p.Q5145H		Atlas-SNP	.											.	RNF213	766	.	0			c.A15435C						.						78.0	89.0	85.0					17																	78363961		2202	4300	6502	SO:0001583	missense	57674	exon67			CCCCCAAACCCAA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.15435A>C	chr17.hg19:g.78363961A>C	ENSP00000464087:p.Gln5145His	122.0	0.0		158.0	23.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	6.357	0.433998	0.12045	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.23348	1.91	.	.	.	.	.	.	.	.	T	0.14356	0.0347	N	0.25144	0.715	0.09310	N	1	P;P	0.39940	0.696;0.676	B;B	0.36030	0.056;0.216	T	0.15009	-1.0452	7	0.72032	D	0.01	.	.	.	.	.	5145;3218	D6RI12;Q63HN8	.;RN213_HUMAN	H	5145;5194;3218;495	ENSP00000338218:Q3218H	ENSP00000338218:Q3218H	Q	+	3	2	RNF213	75978556	0.012000	0.17670	0.002000	0.10522	0.072000	0.16883	-0.267000	0.08619	0.077000	0.16863	0.076000	0.15429	CAA	.	.		0.507	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
FANCB	2187	hgsc.bcm.edu	37	X	14862009	14862009	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chrX:14862009A>T	ENST00000324138.3	-	9	2413	c.2260T>A	c.(2260-2262)Ttc>Atc	p.F754I	FANCB_ENST00000398334.1_Missense_Mutation_p.F754I	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	754					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					TCAATTAGGAAATTCTCACTT	0.343								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.F754I		Atlas-SNP	.											.	FANCB	78	.	0			c.T2260A						.						75.0	73.0	74.0					X																	14862009		2203	4299	6502	SO:0001583	missense	2187	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTAGGAAATTCTC	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"""Fanconi anemia, complementation groups"""	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.2260T>A	chrX.hg19:g.14862009A>T	ENSP00000326819:p.Phe754Ile	29.0	0.0		44.0	6.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Missense_Mutation	SNP	ENST00000324138.3	hg19	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	A	1.827	-0.470744	0.04445	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.6	1.66	0.24008	.	0.756841	0.13152	N	0.409779	T	0.24005	0.0581	L	0.31926	0.97	0.09310	N	1	B	0.17268	0.021	B	0.16722	0.016	T	0.27226	-1.0080	9	0.12430	T	0.62	-0.7611	1.9414	0.03347	0.5002:0.19:0.0784:0.2314	.	754	Q8NB91	FANCB_HUMAN	I	754	.	ENSP00000326819:F754I	F	-	1	0	FANCB	14771930	0.000000	0.05858	0.031000	0.17742	0.138000	0.21146	-0.110000	0.10824	-0.063000	0.13065	0.481000	0.45027	TTC	.	.		0.343	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633	
MT-ND4	4538	hgsc.bcm.edu	37	M	11087	11087	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chrM:11087T>C	ENST00000361381.2	+	1	328	c.328T>C	c.(328-330)Ttc>Ctc	p.F110L	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	110					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TAATTATAACATTCACAGCCA	0.428																																					p.F110L		Atlas-SNP	.											.	.	.	.	0			c.T328C						.																																			SO:0001583	missense	0	exon1			ATAACATTCACAG			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.328T>C	chrM.hg19:g.11087T>C	ENSP00000354961:p.Phe110Leu	28.0	0.0		26.0	16.0	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	hg19																																																																																				.	.		0.428	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
MT-ND5	4540	hgsc.bcm.edu	37	M	13976	13976	+	Missense_Mutation	SNP	A	A	C			TCGA-CC-A9FV-01A-11D-A36X-10	TCGA-CC-A9FV-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee96f017-533b-4dfc-bd2a-bac5a8e505ab	e96de230-4a53-4be9-8595-1da88b23b989	g.chrM:13976A>C	ENST00000361567.2	+	1	1640	c.1640A>C	c.(1639-1641)aAc>aCc	p.N547T	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	547					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TACGAGCCAAAACCTGCCCCT	0.453																																					p.N547T		Atlas-SNP	.											.	.	.	.	0			c.A1640C						.																																			SO:0001583	missense	0	exon1			GCCAAAACCTGCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1640A>C	chrM.hg19:g.13976A>C	ENSP00000354813:p.Asn547Thr	49.0	0.0		33.0	9.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.453	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
