#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_PopFreq	i_dbSNP_Strength	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
XPO1	7514	hgsc.bcm.edu	37	2	61709536	61709536	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:61709536G>A	ENST00000401558.2	-	23	3678	c.2951C>T	c.(2950-2952)tCg>tTg	p.S984L	XPO1_ENST00000404992.2_Missense_Mutation_p.S984L|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|XPO1_ENST00000406957.1_Missense_Mutation_p.S984L|RP11-355B11.2_ENST00000603652.1_RNA|RP11-355B11.2_ENST00000605437.1_RNA|RP11-355B11.2_ENST00000603199.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	984					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			AGGGAAGGCCGACTTAAGGAG	0.398			Mis		CLL																																p.S984L		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"""exportin 1 (CRM1 homolog, yeast)"""		L	.	XPO1	108	.	0			c.C2951T						PASS	.						129.0	130.0	129.0					2																	61709536		2203	4300	6503	SO:0001583	missense	7514	exon23			AAGGCCGACTTAA	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"""Exportins"""	12825	protein-coding gene	gene with protein product	"""chromosome region maintenance 1 homolog (yeast)"""	602559	"""exportin 1 (CRM1, yeast, homolog)"", ""exportin 1 (CRM1 homolog, yeast)"""			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.2951C>T	chr2.hg19:g.61709536G>A	ENSP00000384863:p.Ser984Leu	156.0	0.0	.		128.0	12.0	.	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953001	0.73902	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.68025	-0.3;-0.3;-0.3	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (2);Exportin 1, C-terminal (1);	0.055426	0.85682	D	0.000000	T	0.68366	0.2993	M	0.75615	2.305	0.58432	D	0.999998	B;B	0.31752	0.338;0.233	B;B	0.24848	0.034;0.056	T	0.70883	-0.4751	10	0.66056	D	0.02	-16.6961	19.6691	0.95903	0.0:0.0:1.0:0.0	.	631;984	B3KWD0;O14980	.;XPO1_HUMAN	L	984	ENSP00000384863:S984L;ENSP00000385942:S984L;ENSP00000385559:S984L	ENSP00000384863:S984L	S	-	2	0	XPO1	61563040	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.529000	0.81952	2.721000	0.93114	0.591000	0.81541	TCG	.	.	.	none		0.398	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400	
LRP1B	53353	hgsc.bcm.edu	37	2	141643776	141643776	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:141643776G>C	ENST00000389484.3	-	24	4866	c.3895C>G	c.(3895-3897)Caa>Gaa	p.Q1299E		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1299					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.Q1299K(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGTAAACTTTGATTGAAGTGA	0.328										TSP Lung(27;0.18)																											p.Q1299E	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,0,1	LRP1B	1315	.	1	Substitution - Missense(1)	endometrium(1)	c.C3895G						PASS	.						77.0	79.0	78.0					2																	141643776		2202	4299	6501	SO:0001583	missense	53353	exon24			AACTTTGATTGAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3895C>G	chr2.hg19:g.141643776G>C	ENSP00000374135:p.Gln1299Glu	97.0	0.0	.		97.0	80.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144239	0.57044	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90620	-2.7;-2.7	5.68	5.68	0.88126	Six-bladed beta-propeller, TolB-like (1);	0.140025	0.48767	D	0.000173	T	0.81597	0.4856	N	0.13043	0.29	0.42707	D	0.993639	B;B	0.34015	0.009;0.435	B;B	0.24974	0.009;0.057	T	0.79825	-0.1640	10	0.12430	T	0.62	.	19.7974	0.96491	0.0:0.0:1.0:0.0	.	482;1299	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	E	1299;1237;444	ENSP00000374135:Q1299E;ENSP00000413239:Q444E	ENSP00000374135:Q1299E	Q	-	1	0	LRP1B	141360246	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.640000	0.98453	2.673000	0.90976	0.650000	0.86243	CAA	.	.	.	none		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
IQCF2	389123	hgsc.bcm.edu	37	3	51897176	51897176	+	Silent	SNP	C	C	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:51897176C>A	ENST00000333127.3	+	3	314	c.285C>A	c.(283-285)gcC>gcA	p.A95A	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	95										endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CTCTGATCGCCTACGCAACCA	0.582																																					p.A95A		Atlas-SNP	.											.	IQCF2	21	.	0			c.C285A						PASS	.						118.0	114.0	115.0					3																	51897176		2203	4300	6503	SO:0001819	synonymous_variant	389123	exon3			GATCGCCTACGCA	AK128883	CCDS2835.1	3p21.31	2008-02-05			ENSG00000184345	ENSG00000184345			31815	protein-coding gene	gene with protein product							Standard	NM_203424		Approved		uc003dbt.1	Q8IXL9	OTTHUMG00000156914	ENST00000333127.3:c.285C>A	chr3.hg19:g.51897176C>A		89.0	0.0	.		92.0	4.0	.	NM_203424		Silent	SNP	ENST00000333127.3	hg19	CCDS2835.1																																																																																			.	.	.	none		0.582	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424	
ACTL6A	86	hgsc.bcm.edu	37	3	179304341	179304341	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:179304341G>A	ENST00000429709.2	+	13	1343	c.1130G>A	c.(1129-1131)cGg>cAg	p.R377Q	RP11-15L13.4_ENST00000608818.1_RNA|RP11-145M9.6_ENST00000610007.1_RNA|ACTL6A_ENST00000392662.1_Missense_Mutation_p.R335Q|ACTL6A_ENST00000450518.2_Missense_Mutation_p.R335Q	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	377					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			CAGAGTATGCGGTTGAAATTG	0.348																																					p.R377Q		Atlas-SNP	.											.	ACTL6A	43	.	0			c.G1130A						PASS	.						88.0	88.0	88.0					3																	179304341		2203	4300	6503	SO:0001583	missense	86	exon13			GTATGCGGTTGAA	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"""INO80 complex subunits"""	24124	protein-coding gene	gene with protein product	"""BAF complex 53 kDa subunit"", ""BRG1-associated factor"", ""actin-related protein 4"", ""INO80 complex subunit K"""	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1130G>A	chr3.hg19:g.179304341G>A	ENSP00000397552:p.Arg377Gln	75.0	0.0	.		61.0	53.0	.	NM_004301	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	hg19	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140591	0.94560	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.94687	-3.49;-3.49;-3.49	5.91	4.07	0.47477	.	0.049963	0.85682	D	0.000000	D	0.95984	0.8692	L	0.59436	1.845	0.58432	D	0.999997	D	0.76494	0.999	D	0.64321	0.924	D	0.95826	0.8854	10	0.87932	D	0	.	15.2754	0.73737	0.0:0.0:0.7438:0.2562	.	377	O96019	ACL6A_HUMAN	Q	377;335;335	ENSP00000397552:R377Q;ENSP00000394014:R335Q;ENSP00000376430:R335Q	ENSP00000376430:R335Q	R	+	2	0	ACTL6A	180787035	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.371000	0.97162	0.789000	0.33779	0.655000	0.94253	CGG	.	.	.	none		0.348	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301	
KLHL3	26249	hgsc.bcm.edu	37	5	136963990	136963990	+	Silent	SNP	G	G	A	rs562736621		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:136963990G>A	ENST00000309755.4	-	13	2030	c.1587C>T	c.(1585-1587)aaC>aaT	p.N529N	KLHL3_ENST00000541417.1_3'UTR|KLHL3_ENST00000508657.1_Silent_p.N497N|KLHL3_ENST00000506491.1_Silent_p.N447N|KLHL3_ENST00000506873.1_5'UTR	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	529			N -> K (in PHA2D; impaired interaction with WNK1). {ECO:0000269|PubMed:22406640}.		distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		CATTACCTGCGTTGCGCCGGC	0.537																																					p.N529N		Atlas-SNP	.											.	KLHL3	54	.	0			c.C1587T						PASS	.						219.0	189.0	199.0					5																	136963990		2203	4300	6503	SO:0001819	synonymous_variant	26249	exon13			ACCTGCGTTGCGC	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1587C>T	chr5.hg19:g.136963990G>A		145.0	0.0	.		260.0	90.0	.	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	hg19	CCDS4192.1																																																																																			.	.	.	none		0.537	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711928	140711928	+	Silent	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:140711928G>A	ENST00000517417.1	+	1	1677	c.1677G>A	c.(1675-1677)gcG>gcA	p.A559A	PCDHGA1_ENST00000378105.3_Silent_p.A559A	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	559	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGACAACGCGCCCGAGATCC	0.647																																					p.A559A		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.G1677A						PASS	.						130.0	144.0	140.0					5																	140711928		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			CAACGCGCCCGAG	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1677G>A	chr5.hg19:g.140711928G>A		320.0	0.0	.		431.0	204.0	.	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.	.	none		0.647	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
DRD1	1812	hgsc.bcm.edu	37	5	174870046	174870046	+	Silent	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:174870046G>A	ENST00000393752.2	-	2	1049	c.57C>T	c.(55-57)gaC>gaT	p.D19D		NM_000794.3	NP_000785.1	P21728	DRD1_HUMAN	dopamine receptor D1	19					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult walking behavior (GO:0007628)|astrocyte development (GO:0014002)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|cellular response to catecholamine stimulus (GO:0071870)|cerebral cortex GABAergic interneuron migration (GO:0021853)|conditioned taste aversion (GO:0001661)|dentate gyrus development (GO:0021542)|dopamine metabolic process (GO:0042417)|dopamine transport (GO:0015872)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose import (GO:0046323)|grooming behavior (GO:0007625)|habituation (GO:0046959)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|maternal behavior (GO:0042711)|mating behavior (GO:0007617)|memory (GO:0007613)|neuronal action potential (GO:0019228)|operant conditioning (GO:0035106)|peristalsis (GO:0030432)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|prepulse inhibition (GO:0060134)|protein import into nucleus (GO:0006606)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|sensitization (GO:0046960)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|transmission of nerve impulse (GO:0019226)|vasodilation (GO:0042311)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GAACAGAGAAGTCCCTCTCCA	0.572																																					p.D19D		Atlas-SNP	.											.	DRD1	56	.	0			c.C57T						PASS	.						106.0	108.0	107.0					5																	174870046		2203	4300	6503	SO:0001819	synonymous_variant	1812	exon2			AGAGAAGTCCCTC	X55760	CCDS4393.1	5q34-q35	2012-08-08			ENSG00000184845	ENSG00000184845		"""GPCR / Class A : Dopamine receptors"""	3020	protein-coding gene	gene with protein product		126449					Standard	NM_000794		Approved		uc003mcz.3	P21728	OTTHUMG00000130557	ENST00000393752.2:c.57C>T	chr5.hg19:g.174870046G>A		122.0	0.0	.		190.0	77.0	.	NM_000794	B2RA44|Q4QRJ0	Silent	SNP	ENST00000393752.2	hg19	CCDS4393.1																																																																																			.	.	.	none		0.572	DRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252982.2	NM_000794	
UBR2	23304	hgsc.bcm.edu	37	6	42657391	42657391	+	Silent	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:42657391G>A	ENST00000372899.1	+	46	5367	c.5109G>A	c.(5107-5109)gaG>gaA	p.E1703E	UBR2_ENST00000372901.1_Silent_p.E1703E|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1703					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			ACTATGGGGAGACCGACCAGG	0.517																																					p.E1703E		Atlas-SNP	.											.	UBR2	134	.	0			c.G5109A						PASS	.						254.0	259.0	257.0					6																	42657391		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon46			TGGGGAGACCGAC	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.5109G>A	chr6.hg19:g.42657391G>A		495.0	0.0	.		393.0	351.0	.	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	hg19	CCDS4870.1																																																																																			.	.	.	none		0.517	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
DOPEY1	23033	hgsc.bcm.edu	37	6	83862077	83862077	+	Silent	SNP	A	A	G			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:83862077A>G	ENST00000349129.2	+	30	6380	c.6120A>G	c.(6118-6120)ttA>ttG	p.L2040L	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Silent_p.L2031L|DOPEY1_ENST00000237163.5_Intron	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2040					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CATTGACATTACTCTCTGAGG	0.294																																					p.L2040L		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A6120G						PASS	.						62.0	63.0	63.0					6																	83862077		2203	4291	6494	SO:0001819	synonymous_variant	23033	exon30			GACATTACTCTCT	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6120A>G	chr6.hg19:g.83862077A>G		62.0	0.0	.		66.0	4.0	.	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	hg19	CCDS4996.1																																																																																			.	.	.	none		0.294	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
USP45	85015	hgsc.bcm.edu	37	6	99930682	99930682	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:99930682C>A	ENST00000327681.6	-	8	1324	c.792G>T	c.(790-792)gaG>gaT	p.E264D	USP45_ENST00000329966.6_Missense_Mutation_p.E264D|USP45_ENST00000500704.2_Missense_Mutation_p.E264D|USP45_ENST00000392738.2_Intron|USP45_ENST00000369233.2_Missense_Mutation_p.E264D|USP45_ENST00000472914.2_Missense_Mutation_p.E264D	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	264	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTTTTCAGTCTCCTTCATGC	0.383																																					p.E264D		Atlas-SNP	.											.	USP45	56	.	0			c.G792T						PASS	.						82.0	85.0	84.0					6																	99930682		2203	4300	6503	SO:0001583	missense	85015	exon8			TTCAGTCTCCTTC	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"""Ubiquitin-specific peptidases"""	20080	protein-coding gene	gene with protein product			"""ubiquitin specific protease 45"""			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.792G>T	chr6.hg19:g.99930682C>A	ENSP00000333376:p.Glu264Asp	100.0	0.0	.		86.0	80.0	.	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	hg19	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.164251	0.38217	.	.	ENSG00000123552	ENST00000500704;ENST00000327681;ENST00000369233;ENST00000511403;ENST00000329966;ENST00000472914	T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47	5.32	3.4	0.38934	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.16257	0.0391	L	0.41961	1.31	0.80722	D	1	B;B	0.30482	0.039;0.281	B;B	0.39185	0.039;0.293	T	0.03630	-1.1018	10	0.42905	T	0.14	.	9.9212	0.41466	0.0:0.7614:0.0:0.2386	.	264;264	D6RBV3;Q70EL2	.;UBP45_HUMAN	D	264;264;264;20;264;264	ENSP00000424372:E264D;ENSP00000333376:E264D;ENSP00000358236:E264D;ENSP00000423374:E20D;ENSP00000330540:E264D;ENSP00000423993:E264D	ENSP00000333376:E264D	E	-	3	2	USP45	100037403	0.155000	0.22806	0.998000	0.56505	0.743000	0.42351	-0.128000	0.10531	0.616000	0.30141	0.557000	0.71058	GAG	.	.	.	none		0.383	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
IRF5	3663	hgsc.bcm.edu	37	7	128587532	128587532	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr7:128587532C>T	ENST00000402030.2	+	6	754	c.682C>T	c.(682-684)Ccc>Tcc	p.P228S	IRF5_ENST00000249375.4_Missense_Mutation_p.P228S|IRF5_ENST00000473745.1_Missense_Mutation_p.P228S|IRF5_ENST00000477535.1_Intron|IRF5_ENST00000357234.5_Missense_Mutation_p.P244S	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	228					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						TGCCAGCCTGCCCCCTGCAGG	0.682																																					p.P244S		Atlas-SNP	.											.	IRF5	40	.	0			c.C730T						PASS	.						15.0	18.0	17.0					7																	128587532		2120	4170	6290	SO:0001583	missense	3663	exon6			AGCCTGCCCCCTG		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.682C>T	chr7.hg19:g.128587532C>T	ENSP00000385352:p.Pro228Ser	40.0	0.0	.		54.0	23.0	.	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	hg19	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630932	0.67015	.	.	ENSG00000128604	ENST00000357234;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D	0.97529	-4.4;-4.42;-4.42;-4.42	5.26	2.02	0.26589	.	0.848323	0.10423	N	0.676477	D	0.95175	0.8436	L	0.53249	1.67	0.36808	D	0.885713	B;B	0.30634	0.043;0.288	B;B	0.35413	0.027;0.202	D	0.93066	0.6478	10	0.56958	D	0.05	-11.2851	8.0991	0.30846	0.1597:0.4338:0.4065:0.0	.	228;244	Q13568;Q13568-2	IRF5_HUMAN;.	S	244;228;228;228;218	ENSP00000349770:P244S;ENSP00000385352:P228S;ENSP00000249375:P228S;ENSP00000419149:P228S	ENSP00000249375:P228S	P	+	1	0	IRF5	128374768	0.309000	0.24518	0.269000	0.24586	0.935000	0.57460	0.974000	0.29436	0.667000	0.31107	0.561000	0.74099	CCC	.	.	.	none		0.682	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
SORCS1	114815	hgsc.bcm.edu	37	10	108427534	108427534	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr10:108427534T>C	ENST00000263054.6	-	17	2223	c.2216A>G	c.(2215-2217)aAt>aGt	p.N739S	SORCS1_ENST00000344440.6_Missense_Mutation_p.N739S|SORCS1_ENST00000369698.1_Missense_Mutation_p.N274S	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	739					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GCACTGGCCATTGCTGTGTCG	0.458																																					p.N739S		Atlas-SNP	.											.	SORCS1	534	.	0			c.A2216G						PASS	.						69.0	62.0	65.0					10																	108427534		2203	4300	6503	SO:0001583	missense	114815	exon17			TGGCCATTGCTGT	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2216A>G	chr10.hg19:g.108427534T>C	ENSP00000263054:p.Asn739Ser	36.0	0.0	.		34.0	31.0	.	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	T	7.105	0.574795	0.13623	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.23348	1.91;2.47;2.47	5.49	4.33	0.51752	VPS10 (1);	0.111999	0.64402	N	0.000012	T	0.12433	0.0302	N	0.05031	-0.125	0.39169	D	0.962557	B;B;B;B;B	0.25206	0.073;0.054;0.12;0.073;0.007	B;B;B;B;B	0.25506	0.028;0.061;0.061;0.028;0.02	T	0.13548	-1.0505	9	.	.	.	-18.7721	11.8351	0.52319	0.0:0.0698:0.0:0.9302	.	739;739;739;739;739	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	S	274;739;739	ENSP00000358712:N274S;ENSP00000263054:N739S;ENSP00000345964:N739S	.	N	-	2	0	SORCS1	108417524	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	3.928000	0.56506	0.982000	0.38575	0.379000	0.24179	AAT	.	.	.	none		0.458	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
OR52J3	119679	hgsc.bcm.edu	37	11	5068288	5068288	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr11:5068288A>T	ENST00000380370.1	+	1	533	c.533A>T	c.(532-534)cAt>cTt	p.H178L		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATAATAGCCCATTCCTACTGT	0.418																																					p.H178L		Atlas-SNP	.											OR52J3,NS,carcinoma,0,1	OR52J3	77	.	0			c.A533T						PASS	.						191.0	162.0	172.0					11																	5068288		2201	4298	6499	SO:0001583	missense	119679	exon1			TAGCCCATTCCTA	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.533A>T	chr11.hg19:g.5068288A>T	ENSP00000369728:p.His178Leu	163.0	0.0	.		117.0	112.0	.	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	hg19	CCDS31370.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.387131	0.61956	.	.	ENSG00000205495	ENST00000380370	T	0.00183	8.6	3.89	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000183	T	0.01061	0.0035	H	0.98769	4.325	0.37287	D	0.908099	D	0.89917	1.0	D	0.97110	1.0	T	0.13019	-1.0525	10	0.87932	D	0	.	11.9816	0.53123	1.0:0.0:0.0:0.0	.	178	Q8NH60	O52J3_HUMAN	L	178	ENSP00000369728:H178L	ENSP00000369728:H178L	H	+	2	0	OR52J3	5024864	0.235000	0.23794	0.989000	0.46669	0.817000	0.46193	3.921000	0.56454	1.742000	0.51746	0.533000	0.62120	CAT	.	.	.	none		0.418	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
IL10RA	3587	hgsc.bcm.edu	37	11	117866403	117866403	+	Missense_Mutation	SNP	G	G	A	rs145975996		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr11:117866403G>A	ENST00000227752.3	+	6	908	c.788G>A	c.(787-789)cGa>cAa	p.R263Q	IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000545409.1_Missense_Mutation_p.R114Q|IL10RA_ENST00000541785.1_Missense_Mutation_p.R243Q	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	263					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		GTGCGGCGCCGAAAGAAGCTA	0.602																																					p.R263Q		Atlas-SNP	.											.	IL10RA	46	.	0			c.G788A						PASS	.	G	GLN/ARG	0,4400		0,0,2200	96.0	76.0	83.0		788	-1.2	0.0	11	dbSNP_134	83	2,8590	2.2+/-6.3	0,2,4294	yes	missense	IL10RA	NM_001558.3	43	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	263/579	117866403	2,12990	2200	4296	6496	SO:0001583	missense	3587	exon6			GGCGCCGAAAGAA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.788G>A	chr11.hg19:g.117866403G>A	ENSP00000227752:p.Arg263Gln	43.0	0.0	.		42.0	20.0	.	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066789	0.55539	0.0	2.33E-4	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.56941	0.43;0.43;1.15	5.16	-1.2	0.09554	.	0.427526	0.16007	N	0.233988	T	0.52757	0.1754	M	0.63428	1.95	0.09310	N	1	D;D	0.69078	0.997;0.995	P;P	0.51945	0.685;0.639	T	0.47420	-0.9119	10	0.45353	T	0.12	-4.5989	7.1947	0.25845	0.1825:0.5157:0.3019:0.0	.	243;263	F5GYV8;Q13651	.;I10R1_HUMAN	Q	263;243;114;243	ENSP00000227752:R263Q;ENSP00000441397:R243Q;ENSP00000443019:R114Q	ENSP00000227752:R263Q	R	+	2	0	IL10RA	117371613	0.000000	0.05858	0.024000	0.17045	0.667000	0.39255	-0.002000	0.12924	0.003000	0.14656	0.563000	0.77884	CGA	.	G|1.000;A|0.000	0.000	weak		0.602	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
ARHGAP9	64333	hgsc.bcm.edu	37	12	57869643	57869643	+	Silent	SNP	G	G	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr12:57869643G>T	ENST00000356411.2	-	10	1422	c.1284C>A	c.(1282-1284)cgC>cgA	p.R428R	ARHGAP9_ENST00000393797.2_Silent_p.R499R|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000550288.1_Silent_p.R507R|ARHGAP9_ENST00000393791.3_Silent_p.R428R|ARHGAP9_ENST00000424809.2_Silent_p.R428R|ARHGAP9_ENST00000430041.2_Silent_p.R244R			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	428	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TCCGCAGCGCGCGGTGCCAGG	0.672																																					p.R428R		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1284A						PASS	.						26.0	29.0	28.0					12																	57869643		2202	4297	6499	SO:0001819	synonymous_variant	64333	exon9			CAGCGCGCGGTGC	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1284C>A	chr12.hg19:g.57869643G>T		31.0	0.0	.		65.0	4.0	.	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Silent	SNP	ENST00000356411.2	hg19																																																																																				.	.	.	none		0.672	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
MICU2	221154	hgsc.bcm.edu	37	13	22088516	22088516	+	Silent	SNP	C	C	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:22088516C>T	ENST00000382374.4	-	7	704	c.639G>A	c.(637-639)gtG>gtA	p.V213V		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	213					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										CATTAGTTTTCACTGTCATCA	0.318																																					p.V213V		Atlas-SNP	.											.	EFHA1	33	.	0			c.G639A						PASS	.						184.0	177.0	179.0					13																	22088516		2202	4300	6502	SO:0001819	synonymous_variant	221154	exon7			AGTTTTCACTGTC	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"""EF-hand domain containing"""	31830	protein-coding gene	gene with protein product		610632	"""EF hand domain family A1"", ""EF-hand domain family, member A1"""	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.639G>A	chr13.hg19:g.22088516C>T		98.0	0.0	.		93.0	9.0	.	NM_152726	Q8N0T6|Q8NAX8	Silent	SNP	ENST00000382374.4	hg19	CCDS9297.1																																																																																			.	.	.	none		0.318	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726	
KL	9365	hgsc.bcm.edu	37	13	33591076	33591076	+	Silent	SNP	C	C	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:33591076C>T	ENST00000380099.3	+	1	506	c.498C>T	c.(496-498)aaC>aaT	p.N166N	KL_ENST00000426690.2_Intron|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	166	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GCGTCCCCAACCGCGAGGGGC	0.726																																					p.N166N		Atlas-SNP	.											.	KL	106	.	0			c.C498T						PASS	.						11.0	11.0	11.0					13																	33591076		2131	4184	6315	SO:0001819	synonymous_variant	9365	exon1			CCCCAACCGCGAG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.498C>T	chr13.hg19:g.33591076C>T		23.0	0.0	.		18.0	6.0	.	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.	.	none		0.726	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
RANBP10	57610	hgsc.bcm.edu	37	16	67840335	67840335	+	Silent	SNP	C	C	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr16:67840335C>T	ENST00000317506.3	-	1	220	c.105G>A	c.(103-105)ctG>ctA	p.L35L	RANBP10_ENST00000602677.1_Silent_p.L35L|RANBP10_ENST00000602887.1_5'UTR|RANBP10_ENST00000425512.2_5'UTR|RANBP10_ENST00000448631.2_Silent_p.L35L|TSNAXIP1_ENST00000561639.1_5'Flank|TSNAXIP1_ENST00000415766.3_5'Flank|TSNAXIP1_ENST00000388833.3_5'Flank|RANBP10_ENST00000536251.1_5'UTR|RANBP10_ENST00000411657.2_5'UTR	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	35	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		AGCGCCGGCTCAGCTCCTGCT	0.701																																					p.L35L		Atlas-SNP	.											.	RANBP10	56	.	0			c.G105A						PASS	.						14.0	15.0	15.0					16																	67840335		2183	4253	6436	SO:0001819	synonymous_variant	57610	exon1			CCGGCTCAGCTCC	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.105G>A	chr16.hg19:g.67840335C>T		14.0	0.0	.		18.0	6.0	.	NM_020850	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Silent	SNP	ENST00000317506.3	hg19	CCDS32469.1																																																																																			.	.	.	none		0.701	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850	
AKAP10	11216	hgsc.bcm.edu	37	17	19861611	19861611	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr17:19861611A>G	ENST00000225737.6	-	4	750	c.593T>C	c.(592-594)tTt>tCt	p.F198S	AKAP10_ENST00000572155.1_5'Flank|AKAP10_ENST00000395536.3_Missense_Mutation_p.F198S	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	198	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					ATCAGTTAAAAAAGACGCTGT	0.418																																					p.F198S		Atlas-SNP	.											.	AKAP10	47	.	0			c.T593C						PASS	.						65.0	65.0	65.0					17																	19861611		2203	4300	6503	SO:0001583	missense	11216	exon4			GTTAAAAAAGACG	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"""A-kinase anchor proteins"""	368	protein-coding gene	gene with protein product	"""dual-specificity A-kinase anchoring protein 2"", ""protein kinase A anchoring protein 10"", ""mitochondrial A kinase PPKA anchor protein 10"""	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.593T>C	chr17.hg19:g.19861611A>G	ENSP00000225737:p.Phe198Ser	73.0	0.0	.		99.0	49.0	.	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	hg19	CCDS11214.1	.	.	.	.	.	.	.	.	.	.	A	5.074	0.199347	0.09652	.	.	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.17054	2.3	5.98	3.72	0.42706	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.607188	0.19356	N	0.116264	T	0.05914	0.0154	N	0.03115	-0.41	0.24009	N	0.996183	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.42068	-0.9473	10	0.06236	T	0.91	-3.1154	7.7403	0.28837	0.6869:0.0:0.3131:0.0	.	198;198;198	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	S	198	ENSP00000225737:F198S	ENSP00000225737:F198S	F	-	2	0	AKAP10	19802203	1.000000	0.71417	0.995000	0.50966	0.345000	0.29048	1.891000	0.39738	0.471000	0.27319	0.482000	0.46254	TTT	.	.	.	none		0.418	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202	
MUC16	94025	hgsc.bcm.edu	37	19	9065718	9065718	+	Missense_Mutation	SNP	G	G	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:9065718G>T	ENST00000397910.4	-	3	21931	c.21728C>A	c.(21727-21729)tCc>tAc	p.S7243Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7245	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGCTCAGGGAGGAAATTGA	0.468																																					p.S7243Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C21728A						PASS	.						169.0	161.0	164.0					19																	9065718		1979	4157	6136	SO:0001583	missense	94025	exon3			CTCAGGGAGGAAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21728C>A	chr19.hg19:g.9065718G>T	ENSP00000381008:p.Ser7243Tyr	198.0	0.0	.		220.0	16.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.932	-0.016036	0.07681	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	2.75	-0.661	0.11417	.	.	.	.	.	T	0.06962	0.0177	L	0.42245	1.32	.	.	.	D	0.65815	0.995	D	0.68943	0.961	T	0.29274	-1.0017	8	0.87932	D	0	.	5.0419	0.14463	0.4634:0.0:0.5366:0.0	.	7243	B5ME49	.	Y	7243	ENSP00000381008:S7243Y	ENSP00000381008:S7243Y	S	-	2	0	MUC16	8926718	0.015000	0.18098	0.000000	0.03702	0.007000	0.05969	2.004000	0.40854	-0.046000	0.13446	0.195000	0.17529	TCC	.	.	.	none		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NFKBIB	4793	hgsc.bcm.edu	37	19	39401467	39401467	+	IGR	SNP	C	C	G	rs535236978	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:39401467C>G	ENST00000313582.5	+	0	1159				CTC-360G5.1_ENST00000571838.1_Missense_Mutation_p.E149D	NM_002503.4	NP_002494.2	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta						innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|signal transduction (GO:0007165)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	8	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCTCAAAGGTCTCCATGGGcc	0.617													C|||	2	0.000399361	0.0015	0.0	5008	,	,		16415	0.0		0.0	False		,,,				2504	0.0				p.E149D	Pancreas(165;1492 2005 6979 7739 34483)	Atlas-SNP	.											.	.	.	.	0			c.G447C						PASS	.																																			SO:0001628	intergenic_variant	0	exon4			AAAGGTCTCCATG	L40407	CCDS12524.1, CCDS74362.1	19q13.1	2013-01-10				ENSG00000104825		"""Ankyrin repeat domain containing"""	7798	protein-coding gene	gene with protein product		604495				9763672	Standard	NM_002503		Approved	IKBB, TRIP9	uc002ojw.3	Q15653			chr19.hg19:g.39401467C>G		4.0	0.0	.		5.0	5.0	.	NM_001243212	A8K3F4|Q96BJ7	Missense_Mutation	SNP	ENST00000313582.5	hg19	CCDS12524.1																																																																																			.	.	.	none		0.617	NFKBIB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438155.1	NM_002503	
ZNF761	388561	hgsc.bcm.edu	37	19	53958709	53958709	+	RNA	SNP	T	T	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:53958709T>A	ENST00000454407.1	+	0	1401							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TTGAAAGACATAGGATAATTC	0.383																																					p.H316Q		Atlas-SNP	.											.	ZNF761	104	.	0			c.T948A						PASS	.						83.0	85.0	85.0					19																	53958709		2203	4300	6503			388561	exon7			AAGACATAGGATA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53958709T>A		114.0	0.0	.		114.0	97.0	.	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	.	.	none		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
ZNF761	388561	hgsc.bcm.edu	37	19	53958711	53958711	+	RNA	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:53958711G>A	ENST00000454407.1	+	0	1403							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GAAAGACATAGGATAATTCAT	0.383																																					p.R317K		Atlas-SNP	.											.	ZNF761	104	.	0			c.G950A						PASS	.						84.0	85.0	85.0					19																	53958711		2203	4300	6503			388561	exon7			GACATAGGATAAT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53958711G>A		115.0	0.0	.		114.0	98.0	.	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	.	.	none		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
GGTLC1	92086	hgsc.bcm.edu	37	20	23967129	23967129	+	Silent	SNP	C	C	T			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr20:23967129C>T	ENST00000335694.4	-	2	324	c.120G>A	c.(118-120)ctG>ctA	p.L40L	GGTLC1_ENST00000286890.4_Silent_p.L40L|GGTLC1_ENST00000278765.4_Silent_p.L40L	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	40					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						CGACCACAGACAGGTGAGCAG	0.647																																					p.L40L		Atlas-SNP	.											.	GGTLC1	37	.	0			c.G120A						PASS	.						51.0	45.0	47.0					20																	23967129		2203	4300	6503	SO:0001819	synonymous_variant	92086	exon2			CACAGACAGGTGA	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.120G>A	chr20.hg19:g.23967129C>T		56.0	0.0	.		101.0	56.0	.	NM_178311	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	hg19	CCDS13163.1																																																																																			.	.	.	none		0.647	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19685347	19685347	+	Silent	SNP	T	T	G	rs111276490		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr21:19685347T>G	ENST00000284885.3	-	18	2113	c.2080A>C	c.(2080-2082)Aga>Cga	p.R694R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	694	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTCTGGATTCTGAACCGCACT	0.443																																					p.R694R		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A2080C						PASS	.						149.0	133.0	138.0					21																	19685347		2203	4300	6503	SO:0001819	synonymous_variant	5651	exon18			GGATTCTGAACCG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2080A>C	chr21.hg19:g.19685347T>G		119.0	0.0	.		114.0	107.0	.	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	T|0.500;C|0.500	.	alt		0.443	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
CCDC116	164592	hgsc.bcm.edu	37	22	21989095	21989095	+	Nonsense_Mutation	SNP	C	C	G			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr22:21989095C>G	ENST00000292779.3	+	4	904	c.743C>G	c.(742-744)tCa>tGa	p.S248*	CCDC116_ENST00000607942.1_Nonsense_Mutation_p.S248*	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	248										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					CTGCTGGGCTCAAGCTCTGGC	0.577																																					p.S248X		Atlas-SNP	.											.	CCDC116	56	.	0			c.C743G						PASS	.						85.0	90.0	88.0					22																	21989095		2203	4300	6503	SO:0001587	stop_gained	164592	exon4			TGGGCTCAAGCTC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.743C>G	chr22.hg19:g.21989095C>G	ENSP00000292779:p.Ser248*	171.0	0.0	.		181.0	8.0	.	NM_152612	Q8N9Y9	Nonsense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.687235	0.68157	.	.	ENSG00000161180	ENST00000292779	.	.	.	4.56	4.56	0.56223	.	0.269330	0.27035	N	0.021260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-55.3163	13.0826	0.59121	0.0:1.0:0.0:0.0	.	.	.	.	X	248	.	ENSP00000292779:S248X	S	+	2	0	CCDC116	20319095	0.644000	0.27277	0.178000	0.23040	0.062000	0.15995	3.279000	0.51670	2.554000	0.86153	0.485000	0.47835	TCA	.	.	.	none		0.577	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
MT-ATP8	4509	hgsc.bcm.edu	37	M	8368	8368	+	Start_Codon_SNP	SNP	G	G	A			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chrM:8368G>A	ENST00000361851.1	+	1	3	c.3G>A	c.(1-3)atG>atA	p.M1I	MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TA_ENST00000387392.1_RNA			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	1					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										TACAGTGAAATGCCCCAACTA	0.408																																					p.M1M		Atlas-SNP	.											.	.	.	.	0			c.G3A						PASS	.																																			SO:0001582	initiator_codon_variant	0	exon1			TGAAATGCCCCAA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.3G>A	chrM.hg19:g.8368G>A	ENSP00000355265:p.Met1Ile	18.0	0.0	.		14.0	9.0	.	ENST00000361851	Q34771	Silent	SNP	ENST00000361851.1	hg19																																																																																				.	.	.	none		0.408	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	Missense_Mutation
SETD2	29072	hgsc.bcm.edu	37	3	47162849	47162850	+	Frame_Shift_Del	DEL	TT	TT	-	rs114327122		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:47162849_47162850delTT	ENST00000409792.3	-	3	3318_3319	c.3276_3277delAA	c.(3274-3279)caaagtfs	p.S1093fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1093					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)	p.S1093R(1)|p.S590R(1)		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)		TGTCTATAACTTTGACTGCTCC	0.416			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.1093_1093del		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	2	Substitution - Missense(2)	large_intestine(2)	c.3277_3278del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon3			.	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.3276_3277delAA	chr3.hg19:g.47162849_47162850delTT	ENSP00000386759:p.Ser1093fs	167.0	0.0	0		141.0	121.0	0.858156	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.416	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
