#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_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
ZC3H18	124245	hgsc.bcm.edu	37	16	88675458	88675461	+	Splice_Site	DEL	GAGT	GAGT	-			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	GAGT	GAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr16:88675458_88675461delGAGT	ENST00000301011.5	+	7	1405_1406	c.1205_1206delGAGT	c.(1204-1206)cga>c	p.R402fs	ZC3H18_ENST00000452588.2_Splice_Site_p.R426fs	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	402						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CATAATTACCGAGTAAGTATGACT	0.363																																					p.402_402del	Ovarian(121;375 2276 20373 38669)	Atlas-Indel	.											.	ZC3H18	90	.	0			c.1204_1206del						PASS	.																																			SO:0001630	splice_region_variant	124245	exon7			.	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1206+1GAGT>-	16.37:g.88675458_88675461delGAGT		167.0	0.0	0		131.0	13.0	0.0992366	NM_144604	Q96DG4|Q96MP7	In_Frame_Del	DEL	ENST00000301011.5	37	CCDS10967.1																																																																																			.	.	none		0.363	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	Frame_Shift_Del
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234939	26234939	+	Missense_Mutation	SNP	C	C	T	rs2050949	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:26234939C>T	ENST00000244534.5	-	1	277	c.223G>A	c.(223-225)Gaa>Aaa	p.E75K		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	75	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.		E -> K (in dbSNP:rs2050949).		nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				TTGTTTTTTTCTACATCGTAG	0.532													C|||	439	0.0876597	0.0348	0.1037	5008	,	,		15763	0.2113		0.1004	False		,,,				2504	0.0072				p.E75K		Atlas-SNP	.											HIST1H1D,colon,carcinoma,+2,1	HIST1H1D	40	1	0			c.G223A						scavenged	.						71.0	80.0	77.0					6																	26234939		2203	4300	6503	SO:0001583	missense	3007	exon1			TTTTTTCTACATC	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.223G>A	6.37:g.26234939C>T	ENSP00000244534:p.Glu75Lys	201.0	1.0	0.00497512		195.0	10.0	0.0512821	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	22.3	4.269948	0.80469	.	.	ENSG00000124575	ENST00000244534	T	0.09255	3.0	5.23	5.23	0.72850	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.262738	0.43110	D	0.000603	T	0.17066	0.0410	L	0.54908	1.71	0.80722	D	1	B	0.29188	0.236	P	0.48304	0.573	T	0.02966	-1.1088	10	0.59425	D	0.04	-77.8298	18.1633	0.89717	0.0:1.0:0.0:0.0	rs2050949;rs2050949	75	P16402	H13_HUMAN	K	75	ENSP00000244534:E75K	ENSP00000244534:E75K	E	-	1	0	HIST1H1D	26342918	1.000000	0.71417	1.000000	0.80357	0.153000	0.21895	4.012000	0.57131	2.623000	0.88846	0.655000	0.94253	GAA	C|0.998;T|0.002	0.002	strong		0.532	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766417	27766417	+	Missense_Mutation	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:27766417A>G	ENST00000451261.2	+	5	1804	c.1405A>G	c.(1405-1407)Aat>Gat	p.N469D		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	469										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						ACACAGAAATAATACCACAGT	0.443																																					p.N469D		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A1405G						PASS	.						84.0	56.0	65.0					X																	27766417		692	1591	2283	SO:0001583	missense	347442	exon1			AGAAATAATACCA		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1405A>G	X.37:g.27766417A>G	ENSP00000462745:p.Asn469Asp	265.0	0.0	0		227.0	14.0	0.061674	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	none		0.443	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
AMER1	139285	hgsc.bcm.edu	37	X	63412763	63412763	+	Missense_Mutation	SNP	C	C	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:63412763C>A	ENST00000330258.3	-	2	676	c.404G>T	c.(403-405)gGg>gTg	p.G135V	AMER1_ENST00000374869.3_Missense_Mutation_p.G135V|AMER1_ENST00000403336.1_Missense_Mutation_p.G135V	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	135					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CTCCAAAGCCCCATGGGCACT	0.547																																					p.G135V		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.G404T						PASS	.						52.0	48.0	49.0					X																	63412763		2203	4300	6503	SO:0001583	missense	139285	exon2			AAAGCCCCATGGG	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.404G>T	X.37:g.63412763C>A	ENSP00000329117:p.Gly135Val	146.0	0.0	0		125.0	10.0	0.08	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181715	0.21787	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.18338	2.22;2.22;2.22	4.59	2.79	0.32731	.	0.360426	0.27807	N	0.017766	T	0.10637	0.0260	L	0.43152	1.355	0.20703	N	0.999866	B	0.23854	0.092	B	0.23574	0.047	T	0.26467	-1.0102	10	0.17369	T	0.5	-4.6723	1.1464	0.01776	0.1844:0.4399:0.1755:0.2003	.	135	Q5JTC6	F123B_HUMAN	V	135	ENSP00000364003:G135V;ENSP00000329117:G135V;ENSP00000384722:G135V	ENSP00000329117:G135V	G	-	2	0	FAM123B	63329488	0.000000	0.05858	0.010000	0.14722	0.766000	0.43426	0.351000	0.20096	0.641000	0.30601	0.600000	0.82982	GGG	.	.	none		0.547	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
TBC1D8B	54885	hgsc.bcm.edu	37	X	106116883	106116883	+	Silent	SNP	T	T	A	rs140391999	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:106116883T>A	ENST00000357242.5	+	21	3225	c.3051T>A	c.(3049-3051)gcT>gcA	p.A1017A	TBC1D8B_ENST00000276175.3_Silent_p.A1011A	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	1017							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AAGCCATTGCTGTTGTAACCA	0.403																																					p.A1017A		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.T3051A						PASS	.						126.0	122.0	123.0					X																	106116883		2203	4300	6503	SO:0001819	synonymous_variant	54885	exon21			CATTGCTGTTGTA	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.3051T>A	X.37:g.106116883T>A		232.0	0.0	0		236.0	20.0	0.0847458	NM_017752	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Silent	SNP	ENST00000357242.5	37	CCDS14522.1																																																																																			T|0.999;C|0.001	.	alt		0.403	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752	
ADRM1	11047	hgsc.bcm.edu	37	20	60878686	60878686	+	Missense_Mutation	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:60878686A>G	ENST00000253003.2	+	2	108	c.62A>G	c.(61-63)aAg>aGg	p.K21R	RP11-157P1.4_ENST00000414042.1_RNA|ADRM1_ENST00000462554.1_3'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	21	Interaction with PSMD1.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GCCTCCAACAAGTACTTGGTG	0.622																																					p.K21R		Atlas-SNP	.											.	ADRM1	28	.	0			c.A62G						PASS	.						78.0	86.0	83.0					20																	60878686		2203	4299	6502	SO:0001583	missense	11047	exon2			CCAACAAGTACTT	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.62A>G	20.37:g.60878686A>G	ENSP00000253003:p.Lys21Arg	30.0	0.0	0		35.0	6.0	0.171429	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.834980	0.71373	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.65637	0.2710	L	0.41632	1.29	0.80722	D	1	B;P	0.48350	0.018;0.909	B;D	0.63957	0.046;0.92	T	0.64622	-0.6364	9	0.39692	T	0.17	-25.6551	13.6872	0.62524	1.0:0.0:0.0:0.0	.	21;21	B4DMP7;Q16186	.;ADRM1_HUMAN	R	21	.	ENSP00000253003:K21R	K	+	2	0	ADRM1	60312081	1.000000	0.71417	0.998000	0.56505	0.767000	0.43475	7.101000	0.76997	1.707000	0.51288	0.459000	0.35465	AAG	.	.	none		0.622	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
GNPTAB	79158	hgsc.bcm.edu	37	12	102158979	102158979	+	Silent	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr12:102158979G>A	ENST00000299314.7	-	13	1978	c.1716C>T	c.(1714-1716)gcC>gcT	p.A572A	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	572					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						CTCCTCTTTTGGCTACTTCTG	0.393																																					p.A572A		Atlas-SNP	.											GNPTAB,NS,carcinoma,-1,1	GNPTAB	120	1	0			c.C1716T						PASS	.						186.0	174.0	178.0					12																	102158979		2203	4300	6503	SO:0001819	synonymous_variant	79158	exon13			TCTTTTGGCTACT	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.1716C>T	12.37:g.102158979G>A		147.0	0.0	0		158.0	11.0	0.0696203	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Silent	SNP	ENST00000299314.7	37	CCDS9088.1																																																																																			.	.	none		0.393	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
GPR82	27197	hgsc.bcm.edu	37	X	41586775	41586775	+	Missense_Mutation	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:41586775A>G	ENST00000302548.4	+	3	736	c.496A>G	c.(496-498)Ata>Gta	p.I166V	CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	10						TGTACTGGGCATAATCATTCC	0.408																																					p.I166V		Atlas-SNP	.											.	GPR82	52	.	0			c.A496G						PASS	.						69.0	67.0	67.0					X																	41586775		2203	4300	6503	SO:0001583	missense	27197	exon3			CTGGGCATAATCA	AF411111	CCDS14259.1	Xp11.4	2012-08-21			ENSG00000171657	ENSG00000171657		"""GPCR / Class A : Orphans"""	4533	protein-coding gene	gene with protein product		300748				11574155	Standard	NM_080817		Approved		uc004dft.3	Q96P67	OTTHUMG00000021373	ENST00000302548.4:c.496A>G	X.37:g.41586775A>G	ENSP00000303549:p.Ile166Val	216.0	0.0	0		192.0	16.0	0.0833333	NM_080817	Q5VT13	Missense_Mutation	SNP	ENST00000302548.4	37	CCDS14259.1	.	.	.	.	.	.	.	.	.	.	A	0.372	-0.933289	0.02359	.	.	ENSG00000171657	ENST00000302548	T	0.72051	-0.62	5.62	-6.3	0.02007	GPCR, rhodopsin-like superfamily (1);	0.298098	0.25604	N	0.029527	T	0.35770	0.0943	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46965	-0.9153	10	0.02654	T	1	-6.7524	9.1887	0.37187	0.2148:0.3218:0.4634:0.0	.	166	Q96P67	GPR82_HUMAN	V	166	ENSP00000303549:I166V	ENSP00000303549:I166V	I	+	1	0	GPR82	41471719	0.000000	0.05858	0.015000	0.15790	0.245000	0.25701	-2.276000	0.01161	-1.138000	0.02884	-0.314000	0.08810	ATA	.	.	none		0.408	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817	
ERGIC2	51290	hgsc.bcm.edu	37	12	29514613	29514613	+	Silent	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr12:29514613T>C	ENST00000360150.4	-	6	414	c.339A>G	c.(337-339)gtA>gtG	p.V113V		NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2	113					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)				endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)					AAAGATCAAATACTGTCTGAA	0.308																																					p.V113V		Atlas-SNP	.											ERGIC2,NS,carcinoma,-2,1	ERGIC2	29	1	0			c.A339G						PASS	.						146.0	146.0	146.0					12																	29514613		1833	4083	5916	SO:0001819	synonymous_variant	51290	exon6			ATCAAATACTGTC	AF216751	CCDS41765.1	12p11.22	2006-02-08							30208	protein-coding gene	gene with protein product		612236				11445006, 12932305	Standard	NM_016570		Approved	PTX1, Erv41	uc001riv.3	Q96RQ1		ENST00000360150.4:c.339A>G	12.37:g.29514613T>C		131.0	0.0	0		143.0	8.0	0.0559441	NM_016570	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	Silent	SNP	ENST00000360150.4	37	CCDS41765.1																																																																																			.	.	none		0.308	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403489.1	NM_016570	
SIM2	6493	hgsc.bcm.edu	37	21	38072069	38072069	+	Missense_Mutation	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr21:38072069C>T	ENST00000290399.6	+	1	636	c.23C>T	c.(22-24)gCg>gTg	p.A8V	SIM2_ENST00000430056.3_Missense_Mutation_p.A8V|SIM2_ENST00000460783.1_3'UTR|AP000697.6_ENST00000430607.1_RNA	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	8	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						TCCAAGAATGCGGCCAAGACC	0.657																																					p.A8V		Atlas-SNP	.											.	SIM2	55	.	0			c.C23T						PASS	.						120.0	94.0	103.0					21																	38072069		2202	4300	6502	SO:0001583	missense	6493	exon1			AGAATGCGGCCAA		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.23C>T	21.37:g.38072069C>T	ENSP00000290399:p.Ala8Val	105.0	0.0	0		92.0	5.0	0.0543478	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	37	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244806	0.95272	.	.	ENSG00000159263	ENST00000290399;ENST00000430056	T;D	0.97850	2.88;-4.57	4.41	3.52	0.40303	Helix-loop-helix DNA-binding (4);	0.056007	0.64402	N	0.000001	D	0.98836	0.9607	M	0.92367	3.3	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.99449	1.0940	10	0.87932	D	0	.	12.3321	0.55046	0.0:0.9181:0.0:0.0819	.	8;8	Q14190;Q14190-2	SIM2_HUMAN;.	V	8	ENSP00000290399:A8V;ENSP00000404176:A8V	ENSP00000290399:A8V	A	+	2	0	SIM2	36993939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.443000	0.80521	1.084000	0.41184	0.563000	0.77884	GCG	.	.	none		0.657	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362350	105362350	+	Silent	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr10:105362350G>A	ENST00000369774.4	-	15	2901	c.2625C>T	c.(2623-2625)agC>agT	p.S875S	SH3PXD2A_ENST00000540321.1_Silent_p.S742S|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000538130.1_Silent_p.S710S|SH3PXD2A_ENST00000355946.2_Silent_p.S847S			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	875	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.				superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		ACCACCACCCGCTCTCCTGCT	0.617																																					p.S847S		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.C2541T						PASS	.						50.0	51.0	51.0					10																	105362350		2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			CCACCCGCTCTCC	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.2625C>T	10.37:g.105362350G>A		113.0	0.0	0		104.0	5.0	0.0480769	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		.	.	.	.	.	.	.	.	.	.	G	0.409	-0.914168	0.02415	.	.	ENSG00000107957	ENST00000420222	.	.	.	4.59	-2.81	0.05805	.	.	.	.	.	T	0.57169	0.2035	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55976	-0.8055	4	.	.	.	-16.5179	11.8174	0.52218	0.728:0.0:0.272:0.0	.	.	.	.	W	802	.	.	R	-	1	2	SH3PXD2A	105352340	0.038000	0.19896	0.854000	0.33618	0.429000	0.31625	-0.502000	0.06390	-0.468000	0.06922	-0.258000	0.10820	CGG	.	.	none		0.617	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
CCDC88C	440193	hgsc.bcm.edu	37	14	91883122	91883122	+	Missense_Mutation	SNP	A	A	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr14:91883122A>C	ENST00000389857.6	-	2	207	c.121T>G	c.(121-123)Tta>Gta	p.L41V	CCDC88C_ENST00000553403.1_Missense_Mutation_p.L41V|CCDC88C_ENST00000389856.5_Missense_Mutation_p.L33V|RP11-895M11.3_ENST00000557524.1_lincRNA|CCDC88C_ENST00000554165.1_5'UTR	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	41					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CCGTCCACTAAATCCATGTAC	0.473																																					p.L41V		Atlas-SNP	.											.	CCDC88C	192	.	0			c.T121G						PASS	.						56.0	54.0	54.0					14																	91883122		1952	4139	6091	SO:0001583	missense	440193	exon2			CCACTAAATCCAT		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.121T>G	14.37:g.91883122A>C	ENSP00000374507:p.Leu41Val	87.0	0.0	0		88.0	6.0	0.0681818	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	A	19.24	3.789352	0.70337	.	.	ENSG00000015133	ENST00000389857;ENST00000541408;ENST00000389856;ENST00000553403	T;T;T	0.65732	-0.17;-0.17;-0.17	5.18	1.39	0.22231	.	0.000000	0.30329	U	0.009879	T	0.73845	0.3639	M	0.86864	2.845	0.80722	D	1	D;D	0.65815	0.971;0.995	D;P	0.64506	0.926;0.894	T	0.70781	-0.4779	10	0.87932	D	0	-4.4737	2.9797	0.05949	0.4867:0.0:0.3289:0.1844	.	41;41	Q9P219;G3V3S0	DAPLE_HUMAN;.	V	41;5;33;41	ENSP00000374507:L41V;ENSP00000374506:L33V;ENSP00000451392:L41V	ENSP00000374506:L33V	L	-	1	2	CCDC88C	90952875	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	1.407000	0.34657	0.333000	0.23563	0.379000	0.24179	TTA	.	.	none		0.473	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
ZNF217	7764	hgsc.bcm.edu	37	20	52198348	52198348	+	Missense_Mutation	SNP	T	T	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:52198348T>A	ENST00000371471.2	-	2	1443	c.1018A>T	c.(1018-1020)Agt>Tgt	p.S340C	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Missense_Mutation_p.S340C			O75362	ZN217_HUMAN	zinc finger protein 217	340					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CCTGCACAACTGCCCTTATTT	0.542																																					p.S340C		Atlas-SNP	.											.	ZNF217	227	.	0			c.A1018T						PASS	.						126.0	128.0	128.0					20																	52198348		2203	4300	6503	SO:0001583	missense	7764	exon1			CACAACTGCCCTT	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1018A>T	20.37:g.52198348T>A	ENSP00000360526:p.Ser340Cys	221.0	0.0	0		259.0	24.0	0.0926641	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	T	8.872	0.949551	0.18356	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.10099	2.91;2.91	5.7	0.987	0.19790	.	0.778438	0.12010	N	0.507981	T	0.09686	0.0238	L	0.40543	1.245	0.09310	N	1	P	0.47106	0.89	B	0.40101	0.319	T	0.18935	-1.0321	10	0.66056	D	0.02	-9.5155	9.5173	0.39113	0.0:0.5469:0.0:0.4531	.	340	O75362	ZN217_HUMAN	C	340	ENSP00000360526:S340C;ENSP00000304308:S340C	ENSP00000304308:S340C	S	-	1	0	ZNF217	51631755	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	0.015000	0.13355	-0.056000	0.13221	-0.376000	0.06991	AGT	.	.	none		0.542	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
UACA	55075	hgsc.bcm.edu	37	15	70976724	70976724	+	Missense_Mutation	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr15:70976724T>C	ENST00000322954.6	-	8	849	c.664A>G	c.(664-666)Aat>Gat	p.N222D	UACA_ENST00000560441.1_Missense_Mutation_p.N209D|UACA_ENST00000559183.1_5'Flank|UACA_ENST00000539319.1_Intron|UACA_ENST00000379983.2_Missense_Mutation_p.N209D	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	222					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TCAGCACCATTTTTAATTAAG	0.403																																					p.N222D		Atlas-SNP	.											UACA_ENST00000322954,colon,carcinoma,+1,2	UACA	235	2	0			c.A664G						PASS	.						180.0	172.0	175.0					15																	70976724		2199	4297	6496	SO:0001583	missense	55075	exon8			CACCATTTTTAAT	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.664A>G	15.37:g.70976724T>C	ENSP00000314556:p.Asn222Asp	182.0	0.0	0		140.0	7.0	0.05	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	T	19.67	3.870855	0.72065	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362	T;T	0.64618	-0.11;-0.11	5.4	5.4	0.78164	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000015	T	0.68604	0.3019	L	0.42744	1.35	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.976;0.976;0.997	T	0.65356	-0.6188	10	0.25751	T	0.34	-31.1748	9.4231	0.38563	0.0:0.0794:0.0:0.9206	.	222;222;209	B7ZKM6;Q9BZF9;G3XAG2	.;UACA_HUMAN;.	D	222;209;209	ENSP00000314556:N222D;ENSP00000369319:N209D	ENSP00000314556:N222D	N	-	1	0	UACA	68763778	1.000000	0.71417	0.973000	0.42090	0.995000	0.86356	3.516000	0.53436	2.176000	0.68965	0.379000	0.24179	AAT	.	.	none		0.403	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
UNC13B	10497	hgsc.bcm.edu	37	9	35399645	35399645	+	Splice_Site	SNP	G	G	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:35399645G>T	ENST00000378495.3	+	35	4230		c.e35-1		UNC13B_ENST00000396787.1_Splice_Site|UNC13B_ENST00000378496.4_Splice_Site	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)						apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TCTCTGAACAGGATCACATGG	0.532																																					.		Atlas-SNP	.											.	UNC13B	153	.	0			c.4009-1G>T						PASS	.						249.0	228.0	235.0					9																	35399645		2203	4300	6503	SO:0001630	splice_region_variant	10497	exon35			TGAACAGGATCAC	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4009-1G>T	9.37:g.35399645G>T		59.0	0.0	0		61.0	6.0	0.0983607	NM_006377	Q5VYM8	Splice_Site	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611073	0.87258	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4471	0.94852	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13B	35389645	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.267000	0.95665	2.824000	0.97209	0.655000	0.94253	.	.	.	none		0.532	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	Intron
FLG	2312	hgsc.bcm.edu	37	1	152280084	152280084	+	Silent	SNP	G	G	A	rs200015722		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:152280084G>A	ENST00000368799.1	-	3	7313	c.7278C>T	c.(7276-7278)tcC>tcT	p.S2426S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2426	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCATGGGCGGACTCAGACT	0.602									Ichthyosis																												p.S2426S		Atlas-SNP	.											.	FLG	900	.	0			c.C7278T						PASS	.	A		3,4403	825.6+/-416.5	0,3,2200	245.0	231.0	236.0		7278	-9.1	0.0	1		236	3,8597	819.0+/-406.8	0,3,4297	no	coding-synonymous	FLG	NM_002016.1		0,6,6497	AA,AG,GG		0.0349,0.0681,0.0461		2426/4062	152280084	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATGGGCGGACTCA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7278C>T	1.37:g.152280084G>A		225.0	0.0	0		199.0	15.0	0.0753769	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			G|0.999;A|0.001	0.001	weak		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
EIF2B5	8893	hgsc.bcm.edu	37	3	183853228	183853228	+	Missense_Mutation	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:183853228C>T	ENST00000273783.3	+	1	177	c.55C>T	c.(55-57)Cgc>Tgc	p.R19C	EIF2B5_ENST00000432569.1_Missense_Mutation_p.R19C|RP11-778D9.12_ENST00000608232.1_RNA|RP11-778D9.13_ENST00000609288.1_lincRNA|EIF2B5_ENST00000444495.1_Missense_Mutation_p.R19C|RP11-778D9.12_ENST00000608135.1_RNA	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	19					astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			GGCTAACAAGCGCAGCGGCGC	0.687											OREG0015363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R19C		Atlas-SNP	.											.	EIF2B5	62	.	0			c.C55T						PASS	.						6.0	8.0	7.0					3																	183853228		2147	4220	6367	SO:0001583	missense	8893	exon1			AACAAGCGCAGCG	U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"""eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"""			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.55C>T	3.37:g.183853228C>T	ENSP00000273783:p.Arg19Cys	171.0	0.0	0	1987	151.0	7.0	0.0463576	NM_003907	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	37	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	c	15.18	2.756467	0.49362	.	.	ENSG00000145191	ENST00000273783;ENST00000432569;ENST00000444495	D;D;D	0.98150	-4.74;-4.08;-4.75	4.93	4.93	0.64822	.	0.270105	0.30959	N	0.008529	D	0.94666	0.8280	N	0.08118	0	0.54753	D	0.999983	D	0.76494	0.999	P	0.50754	0.649	D	0.95051	0.8187	10	0.66056	D	0.02	-12.6109	13.4835	0.61351	0.0:0.8436:0.1564:0.0	.	19	Q13144	EI2BE_HUMAN	C	19	ENSP00000273783:R19C;ENSP00000414775:R19C;ENSP00000409142:R19C	ENSP00000273783:R19C	R	+	1	0	EIF2B5	185335922	1.000000	0.71417	0.995000	0.50966	0.168000	0.22595	2.282000	0.43461	2.719000	0.93026	0.650000	0.86243	CGC	.	.	none		0.687	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1		
GPR55	9290	hgsc.bcm.edu	37	2	231774792	231774792	+	Missense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:231774792G>A	ENST00000392040.1	-	2	1078	c.886C>T	c.(886-888)Cgc>Tgc	p.R296C	AC012507.4_ENST00000454890.1_RNA|GPR55_ENST00000392039.2_Missense_Mutation_p.R296C	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	296					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		ATGTTCATGCGGAATTCTTTG	0.532																																					p.R296C		Atlas-SNP	.											GPR55,colon,carcinoma,+1,1	GPR55	46	1	0			c.C886T						PASS	.						83.0	85.0	84.0					2																	231774792		2203	4300	6503	SO:0001583	missense	9290	exon2			TCATGCGGAATTC	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"""GPCR / Class A : Orphans"""	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.886C>T	2.37:g.231774792G>A	ENSP00000375894:p.Arg296Cys	80.0	0.0	0		80.0	4.0	0.05	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650184	0.67472	.	.	ENSG00000135898	ENST00000392040;ENST00000392039	T;T	0.58358	0.34;0.34	4.6	3.65	0.41850	.	0.057515	0.64402	D	0.000002	T	0.49029	0.1533	N	0.08118	0	0.48975	D	0.999738	D	0.89917	1.0	D	0.65874	0.939	T	0.57516	-0.7798	10	0.87932	D	0	-42.499	11.8792	0.52564	0.0:0.0:0.8252:0.1748	.	296	Q9Y2T6	GPR55_HUMAN	C	296	ENSP00000375894:R296C;ENSP00000375893:R296C	ENSP00000375893:R296C	R	-	1	0	GPR55	231483036	0.999000	0.42202	0.980000	0.43619	0.953000	0.61014	2.382000	0.44345	2.522000	0.85027	0.561000	0.74099	CGC	.	.	none		0.532	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
F8	2157	hgsc.bcm.edu	37	X	154221377	154221377	+	Missense_Mutation	SNP	A	A	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:154221377A>T	ENST00000360256.4	-	4	635	c.435T>A	c.(433-435)gaT>gaA	p.D145E		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	145	F5/8 type A 1.|Plastocyanin-like 1.		D -> H (in HEMA; moderate). {ECO:0000269|PubMed:9886318}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)	p.D145D(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GGAAGACTTTATCATCTTCTT	0.423																																					p.D145E		Atlas-SNP	.											.	F8	646	.	2	Substitution - coding silent(2)	endometrium(2)	c.T435A						PASS	.						228.0	210.0	217.0					X																	154221377		2203	4300	6503	SO:0001583	missense	2157	exon4			GACTTTATCATCT	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.435T>A	X.37:g.154221377A>T	ENSP00000353393:p.Asp145Glu	320.0	0.0	0		231.0	16.0	0.0692641	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513344	0.64522	.	.	ENSG00000185010	ENST00000360256;ENST00000423959;ENST00000453950	D;D;D	0.99462	-5.43;-5.43;-5.94	5.35	-1.68	0.08212	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.145374	0.64402	D	0.000012	D	0.99290	0.9752	M	0.82433	2.59	0.23550	N	0.997433	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99628	1.0985	10	0.87932	D	0	-6.3892	9.7796	0.40640	0.4251:0.0:0.5749:0.0	.	110;145	B1B0G8;P00451	.;FA8_HUMAN	E	145;110;139	ENSP00000353393:D145E;ENSP00000409446:D110E;ENSP00000389153:D139E	ENSP00000353393:D145E	D	-	3	2	F8	153874571	0.337000	0.24766	0.482000	0.27366	0.727000	0.41649	0.869000	0.27996	-0.449000	0.07117	-0.520000	0.04383	GAT	.	.	none		0.423	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
OR4D10	390197	hgsc.bcm.edu	37	11	59244978	59244978	+	Missense_Mutation	SNP	G	G	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr11:59244978G>C	ENST00000530162.1	+	1	133	c.76G>C	c.(76-78)Gtc>Ctc	p.V26L		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGTGAGCTTAGTCTTATTTCT	0.433																																					p.V26L		Atlas-SNP	.											.	OR4D10	120	.	0			c.G76C						PASS	.						107.0	110.0	109.0					11																	59244978		2053	4220	6273	SO:0001583	missense	390197	exon1			AGCTTAGTCTTAT	AB065808	CCDS53636.1	11q12.1	2012-10-03		2004-03-10	ENSG00000254466	ENSG00000254466		"""GPCR / Class A : Olfactory receptors"""	15173	protein-coding gene	gene with protein product				OR4D10P			Standard	NM_001004705		Approved	OST711	uc001nnz.1	Q8NGI6	OTTHUMG00000167341	ENST00000530162.1:c.76G>C	11.37:g.59244978G>C	ENSP00000436424:p.Val26Leu	147.0	0.0	0		175.0	17.0	0.0971429	NM_001004705	B2RNH6	Missense_Mutation	SNP	ENST00000530162.1	37	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	G	2.795	-0.250377	0.05867	.	.	ENSG00000254466	ENST00000530162	T	0.00063	8.78	4.2	-8.41	0.00961	.	.	.	.	.	T	0.00073	0.0002	N	0.02286	-0.61	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.18967	-1.0320	9	0.33940	T	0.23	.	8.643	0.33989	0.0831:0.1004:0.6209:0.1956	.	26	Q8NGI6	OR4DA_HUMAN	L	26	ENSP00000436424:V26L	ENSP00000436424:V26L	V	+	1	0	OR4D10	59001554	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.203000	0.00076	-1.731000	0.01360	-1.107000	0.02091	GTC	.	.	none		0.433	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705	
NUMBL	9253	hgsc.bcm.edu	37	19	41173904	41173904	+	Silent	SNP	T	T	C	rs79658769		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr19:41173904T>C	ENST00000252891.4	-	10	1466	c.1299A>G	c.(1297-1299)caA>caG	p.Q433Q	NUMBL_ENST00000540131.1_Silent_p.Q392Q|NUMBL_ENST00000598779.1_Silent_p.Q392Q	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	433	Poly-Gln.				adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			gctgttgctgttgctgctgct	0.662																																					p.Q433Q		Atlas-SNP	.											NUMBL,colon,carcinoma,0,2	NUMBL	49	2	0			c.A1299G						scavenged	.						8.0	8.0	8.0					19																	41173904		2119	4125	6244	SO:0001819	synonymous_variant	9253	exon10			TTGCTGTTGCTGC	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"""numb (Drosophila) homolog-like"""			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.1299A>G	19.37:g.41173904T>C		45.0	1.0	0.0222222		29.0	8.0	0.275862	NM_004756	Q7Z4J9	Silent	SNP	ENST00000252891.4	37	CCDS12561.1																																																																																			C|1.000;|0.000	1.000	weak		0.662	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756	
ATRX	546	hgsc.bcm.edu	37	X	76907651	76907651	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:76907651G>A	ENST00000373344.5	-	15	4724	c.4510C>T	c.(4510-4512)Cga>Tga	p.R1504*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1466*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1504					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ATACGTTTTCGTCTCTCTTCC	0.388			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.R1504X		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.C4510T						PASS	.						346.0	308.0	321.0					X																	76907651		2203	4300	6503	SO:0001587	stop_gained	546	exon15			GTTTTCGTCTCTC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4510C>T	X.37:g.76907651G>A	ENSP00000362441:p.Arg1504*	303.0	0.0	0		255.0	15.0	0.0588235	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	G	46	12.165867	0.99642	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	4.9	2.85	0.33270	.	0.066609	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0156	10.5199	0.44912	0.0:0.0:0.3258:0.6742	.	.	.	.	X	1504;1466	.	ENSP00000362441:R1504X	R	-	1	2	ATRX	76794307	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	2.678000	0.46900	0.817000	0.34445	0.594000	0.82650	CGA	.	.	none		0.388	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
LTB	4050	hgsc.bcm.edu	37	6	31548738	31548738	+	Silent	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:31548738G>A	ENST00000429299.2	-	4	490	c.483C>T	c.(481-483)agC>agT	p.S161S	LTB_ENST00000446745.2_3'UTR|LTB_ENST00000483972.1_5'UTR	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	161					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGTACAGAGAGCTGCGCAGCG	0.746																																					p.S161S		Atlas-SNP	.											.	LTB	19	.	0			c.C483T						PASS	.						4.0	4.0	4.0					6																	31548738		1367	2501	3868	SO:0001819	synonymous_variant	4050	exon4			CAGAGAGCTGCGC	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.483C>T	6.37:g.31548738G>A		58.0	0.0	0		51.0	4.0	0.0784314	NM_002341	P78370|Q52LU8|Q99761	Silent	SNP	ENST00000429299.2	37	CCDS4703.1																																																																																			.	.	none		0.746	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
ASXL3	80816	hgsc.bcm.edu	37	18	31326209	31326209	+	Missense_Mutation	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr18:31326209C>T	ENST00000269197.5	+	12	6397	c.6397C>T	c.(6397-6399)Cct>Tct	p.P2133S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2133					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GCCACAAAAGCCTTTTACCCA	0.398																																					p.P2133S		Atlas-SNP	.											.	ASXL3	405	.	0			c.C6397T						PASS	.						82.0	87.0	85.0					18																	31326209		1892	4117	6009	SO:0001583	missense	80816	exon12			CAAAAGCCTTTTA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6397C>T	18.37:g.31326209C>T	ENSP00000269197:p.Pro2133Ser	164.0	0.0	0		110.0	7.0	0.0636364	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.938029	0.73557	.	.	ENSG00000141431	ENST00000269197	T	0.15718	2.4	6.17	6.17	0.99709	.	.	.	.	.	T	0.23965	0.0580	N	0.24115	0.695	0.52501	D	0.999954	D	0.59767	0.986	P	0.55615	0.78	T	0.01363	-1.1374	9	0.17369	T	0.5	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	2133	Q9C0F0	ASXL3_HUMAN	S	2133	ENSP00000269197:P2133S	ENSP00000269197:P2133S	P	+	1	0	ASXL3	29580207	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.078000	0.57606	2.941000	0.99782	0.655000	0.94253	CCT	.	.	none		0.398	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
USH2A	7399	hgsc.bcm.edu	37	1	216424362	216424362	+	Missense_Mutation	SNP	G	G	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:216424362G>T	ENST00000307340.3	-	12	2436	c.2050C>A	c.(2050-2052)Caa>Aaa	p.Q684K	USH2A_ENST00000366943.2_Missense_Mutation_p.Q684K|USH2A_ENST00000366942.3_Missense_Mutation_p.Q684K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	684	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCCAACTCTTGTAGATTGTAG	0.458										HNSCC(13;0.011)																											p.Q684K		Atlas-SNP	.											.	USH2A	1168	.	0			c.C2050A						PASS	.						152.0	127.0	136.0					1																	216424362		2203	4300	6503	SO:0001583	missense	7399	exon12			ACTCTTGTAGATT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2050C>A	1.37:g.216424362G>T	ENSP00000305941:p.Gln684Lys	124.0	0.0	0		103.0	7.0	0.0679612	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	2.472	-0.321570	0.05386	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.60548	0.18;0.18;0.18	5.26	4.34	0.51931	EGF-like, laminin (4);	0.000000	0.42172	D	0.000754	T	0.53222	0.1783	M	0.69248	2.105	0.09310	N	1	B;B	0.30146	0.061;0.27	B;B	0.34931	0.041;0.192	T	0.42565	-0.9444	10	0.18710	T	0.47	.	8.7337	0.34514	0.0764:0.0:0.7737:0.1499	.	684;684	O75445-2;O75445	.;USH2A_HUMAN	K	684	ENSP00000305941:Q684K;ENSP00000355910:Q684K;ENSP00000355909:Q684K	ENSP00000305941:Q684K	Q	-	1	0	USH2A	214490985	0.947000	0.32204	0.009000	0.14445	0.997000	0.91878	3.904000	0.56325	1.209000	0.43321	0.655000	0.94253	CAA	.	.	none		0.458	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
MAGI1	9223	hgsc.bcm.edu	37	3	65425603	65425603	+	Silent	SNP	T	T	C	rs113562374|rs62642828	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:65425603T>C	ENST00000497477.2	-	9	1220	c.1221A>G	c.(1219-1221)caA>caG	p.Q407Q	MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000483466.1_Silent_p.Q407Q|MAGI1_ENST00000402939.2_Silent_p.Q407Q|MAGI1_ENST00000330909.8_Silent_p.Q407Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	407	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		gctgctgctgttgctgctgct	0.532											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q407Q		Atlas-SNP	.											.	MAGI1	481	.	0			c.A1221G						PASS	.						77.0	69.0	72.0					3																	65425603		2202	4299	6501	SO:0001819	synonymous_variant	9223	exon9			CTGCTGTTGCTGC	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1221A>G	3.37:g.65425603T>C		122.0	0.0	0	1084	123.0	6.0	0.0487805	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	2.459	-0.324601	0.05350	.	.	ENSG00000151276	ENST00000460329	.	.	.	3.74	-1.34	0.09143	.	.	.	.	.	T	0.30665	0.0772	.	.	.	0.28889	N	0.893947	.	.	.	.	.	.	T	0.31668	-0.9935	4	.	.	.	2.613	7.1494	0.25601	0.123:0.2818:0.0:0.5952	.	.	.	.	S	288	.	.	N	-	2	0	MAGI1	65400643	0.949000	0.32298	0.008000	0.14137	0.009000	0.06853	-0.343000	0.07791	-1.060000	0.03189	-1.632000	0.00781	AAC	T|0.742;C|0.258	0.258	strong		0.532	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
PLCB1	23236	hgsc.bcm.edu	37	20	8352096	8352096	+	Splice_Site	SNP	A	A	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:8352096A>C	ENST00000338037.6	+	3	272	c.245A>C	c.(244-246)aAg>aCg	p.K82T	PLCB1_ENST00000378641.3_Splice_Site_p.K82T|PLCB1_ENST00000378637.2_Splice_Site_p.K82T	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	82					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.K82T(2)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						AAAGCTCCCAAGGTAGGAGGT	0.448																																					p.E82A		Atlas-SNP	.											PLCB1_ENST00000378641,caecum,carcinoma,0,2	PLCB1	394	2	2	Substitution - Missense(2)	large_intestine(2)	c.A245C						PASS	.						157.0	127.0	137.0					20																	8352096		2203	4300	6503	SO:0001630	splice_region_variant	23236	exon3			CTCCCAAGGTAGG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.246+1A>C	20.37:g.8352096A>C		82.0	0.0	0		86.0	5.0	0.0581395	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337731	0.81911	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000404098	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.52	5.52	0.82312	.	0.058303	0.64402	D	0.000004	T	0.75774	0.3895	M	0.88979	2.995	0.80722	D	1	B;D;D	0.63880	0.048;0.993;0.993	B;P;D	0.74023	0.034;0.849;0.982	T	0.80830	-0.1207	10	0.87932	D	0	.	13.4657	0.61251	1.0:0.0:0.0:0.0	.	82;82;81	Q9NQ66;Q9NQ66-2;B1AK73	PLCB1_HUMAN;.;.	T	82;82;82;81	ENSP00000367908:K82T;ENSP00000338185:K82T;ENSP00000367904:K82T;ENSP00000384001:K81T	ENSP00000338185:K82T	K	+	2	0	PLCB1	8300096	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.240000	0.65378	2.216000	0.71823	0.533000	0.62120	AAG	.	.	none		0.448	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Missense_Mutation
PROKR1	10887	hgsc.bcm.edu	37	2	68882188	68882188	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:68882188G>A	ENST00000303786.3	+	3	1082	c.662G>A	c.(661-663)tGg>tAg	p.W221*	PROKR1_ENST00000394342.2_Nonsense_Mutation_p.W221*			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	221					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GGCCAGATCTGGCCTGTGGAC	0.552																																					p.W221X		Atlas-SNP	.											.	PROKR1	69	.	0			c.G662A						PASS	.						152.0	140.0	144.0					2																	68882188		2203	4300	6503	SO:0001587	stop_gained	10887	exon2			AGATCTGGCCTGT	AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"""GPCR / Class A : Prokineticin receptors"""	4524	protein-coding gene	gene with protein product		607122	"""G protein-coupled receptor 73"""	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.662G>A	2.37:g.68882188G>A	ENSP00000303775:p.Trp221*	88.0	0.0	0		88.0	6.0	0.0681818	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Nonsense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765035	0.90020	.	.	ENSG00000169618	ENST00000303786;ENST00000394342	.	.	.	4.55	4.55	0.56014	.	0.050126	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6333	0.76929	0.0:0.0:1.0:0.0	.	.	.	.	X	221	.	ENSP00000303775:W221X	W	+	2	0	PROKR1	68735692	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.297000	0.96120	2.816000	0.96949	0.563000	0.77884	TGG	.	.	none		0.552	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2		
KAT2B	8850	hgsc.bcm.edu	37	3	20178459	20178459	+	Missense_Mutation	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:20178459A>G	ENST00000263754.4	+	12	2230	c.1775A>G	c.(1774-1776)cAt>cGt	p.H592R	MIR3135A_ENST00000578460.1_RNA	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	592	N-acetyltransferase. {ECO:0000250|UniProtKB:Q92830, ECO:0000255|PROSITE-ProRule:PRU00532}.				cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CTGATGAATCATTTGAAAGAA	0.353																																					p.H592R		Atlas-SNP	.											KAT2B,trunk,malignant_melanoma,+1,1	KAT2B	73	1	0			c.A1775G						PASS	.						129.0	112.0	118.0					3																	20178459		2203	4300	6503	SO:0001583	missense	8850	exon12			TGAATCATTTGAA	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"""Chromatin-modifying enzymes / K-acetyltransferases"""	8638	protein-coding gene	gene with protein product		602303	"""p300/CBP-associated factor"""	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.1775A>G	3.37:g.20178459A>G	ENSP00000263754:p.His592Arg	141.0	0.0	0		100.0	7.0	0.07	NM_003884	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	37	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.709027	0.89018	.	.	ENSG00000114166	ENST00000263754	T	0.24908	1.83	5.66	5.66	0.87406	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.55194	0.1905	M	0.83852	2.665	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.61657	-0.7018	10	0.87932	D	0	-21.8842	16.2026	0.82095	1.0:0.0:0.0:0.0	.	592	Q92831	KAT2B_HUMAN	R	592	ENSP00000263754:H592R	ENSP00000263754:H592R	H	+	2	0	KAT2B	20153463	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.285000	0.76669	0.533000	0.62120	CAT	.	.	none		0.353	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884	
TET1	80312	hgsc.bcm.edu	37	10	70405864	70405864	+	Silent	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr10:70405864A>G	ENST00000373644.4	+	4	3587	c.3378A>G	c.(3376-3378)aaA>aaG	p.K1126K		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1126					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TACAACAGAAACCACCTTCAA	0.388																																					p.K1126K		Atlas-SNP	.											.	TET1	255	.	0			c.A3378G						PASS	.						89.0	77.0	81.0					10																	70405864		2203	4300	6503	SO:0001819	synonymous_variant	80312	exon4			ACAGAAACCACCT	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.3378A>G	10.37:g.70405864A>G		115.0	0.0	0		121.0	14.0	0.115702	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Silent	SNP	ENST00000373644.4	37	CCDS7281.1																																																																																			.	.	none		0.388	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
COPS3	8533	hgsc.bcm.edu	37	17	17163724	17163724	+	Missense_Mutation	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr17:17163724C>T	ENST00000268717.5	-	8	933	c.827G>A	c.(826-828)cGa>cAa	p.R276Q	COPS3_ENST00000539941.2_Missense_Mutation_p.R256Q|COPS3_ENST00000439936.2_Intron	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	276	PCI.				cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						CACCAGGTTTCGGAGTTCTGA	0.418																																					p.R276Q		Atlas-SNP	.											.	COPS3	41	.	0			c.G827A						PASS	.						223.0	186.0	198.0					17																	17163724		2203	4300	6503	SO:0001583	missense	8533	exon8			AGGTTTCGGAGTT	AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3"", ""COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"""			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.827G>A	17.37:g.17163724C>T	ENSP00000268717:p.Arg276Gln	173.0	0.0	0		173.0	19.0	0.109827	NM_003653	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	37	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527788	0.64860	.	.	ENSG00000141030	ENST00000268717;ENST00000539941;ENST00000417352	T;T	0.29917	1.55;1.55	5.47	4.5	0.54988	Proteasome component (PCI) domain (1);	0.000000	0.85682	D	0.000000	T	0.22589	0.0545	L	0.35723	1.085	0.80722	D	1	B	0.27853	0.191	B	0.26416	0.069	T	0.03212	-1.1060	10	0.10377	T	0.69	-10.3403	13.1739	0.59615	0.0:0.9235:0.0:0.0765	.	276	Q9UNS2	CSN3_HUMAN	Q	276;256;307	ENSP00000268717:R276Q;ENSP00000437606:R256Q	ENSP00000268717:R276Q	R	-	2	0	COPS3	17104449	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	7.481000	0.81124	1.306000	0.44926	0.655000	0.94253	CGA	.	.	none		0.418	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2		
TECPR2	9895	hgsc.bcm.edu	37	14	102894692	102894692	+	Missense_Mutation	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr14:102894692A>G	ENST00000359520.7	+	7	1283	c.1057A>G	c.(1057-1059)Agc>Ggc	p.S353G	TECPR2_ENST00000558678.1_Missense_Mutation_p.S353G	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	353					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						AAGAATTTCAAGCAGGCCTGA	0.338																																					p.S353G		Atlas-SNP	.											.	TECPR2	114	.	0			c.A1057G						PASS	.						69.0	75.0	73.0					14																	102894692		2203	4300	6503	SO:0001583	missense	9895	exon7			ATTTCAAGCAGGC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.1057A>G	14.37:g.102894692A>G	ENSP00000352510:p.Ser353Gly	305.0	0.0	0		297.0	14.0	0.047138	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	a	19.19	3.779964	0.70222	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	T	0.15487	2.42	5.31	5.31	0.75309	.	0.087074	0.85682	D	0.000000	T	0.22475	0.0542	L	0.51422	1.61	0.38609	D	0.950842	P;P	0.49447	0.86;0.924	B;P	0.45167	0.243;0.472	T	0.03933	-1.0991	10	0.56958	D	0.05	.	15.3084	0.74011	1.0:0.0:0.0:0.0	.	353;353	A5PKY3;O15040	.;TCPR2_HUMAN	G	353	ENSP00000352510:S353G	ENSP00000352510:S353G	S	+	1	0	TECPR2	101964445	1.000000	0.71417	0.940000	0.37924	0.997000	0.91878	8.560000	0.90712	2.029000	0.59856	0.472000	0.43445	AGC	.	.	none		0.338	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
ATG4A	115201	hgsc.bcm.edu	37	X	107396261	107396261	+	Missense_Mutation	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:107396261C>T	ENST00000372232.3	+	12	1229	c.1070C>T	c.(1069-1071)tCa>tTa	p.S357L	ATG4A_ENST00000545696.1_Missense_Mutation_p.S218L|ATG4A_ENST00000489247.1_3'UTR|COL4A6_ENST00000418180.1_Intron|ATG4A_ENST00000372254.3_Missense_Mutation_p.S333L|ATG4A_ENST00000345734.3_Missense_Mutation_p.S295L	NM_052936.3	NP_443168.2	Q8WYN0	ATG4A_HUMAN	autophagy related 4A, cysteine peptidase	357					autophagy (GO:0006914)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)			endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)	11						AAACATCCATCACACTGGCCT	0.428																																					p.S357L		Atlas-SNP	.											.	ATG4A	68	.	0			c.C1070T						PASS	.						72.0	58.0	63.0					X																	107396261		2203	4300	6503	SO:0001583	missense	115201	exon12			ATCCATCACACTG	AJ320508	CCDS14538.1, CCDS14539.1	Xq22.1-q22.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000101844	ENSG00000101844			16489	protein-coding gene	gene with protein product		300663	"""AUT-like 2, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog A (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog A (S. cerevisiae)"""	AUTL2, APG4A		12446702, 12473658	Standard	NM_052936		Approved		uc004enr.3	Q8WYN0	OTTHUMG00000022176	ENST00000372232.3:c.1070C>T	X.37:g.107396261C>T	ENSP00000361306:p.Ser357Leu	565.0	0.0	0		469.0	33.0	0.0703625	NM_052936	A6NCH2|B2RAZ7|D3DUY0|O95534|Q5JYY9|Q5JYZ0|Q86VE5|Q96KQ0|Q96KQ1	Missense_Mutation	SNP	ENST00000372232.3	37	CCDS14538.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323638	0.60634	.	.	ENSG00000101844	ENST00000372232;ENST00000345734;ENST00000372254;ENST00000545696	T;T;T;T	0.46819	0.86;0.88;0.87;0.89	5.88	5.88	0.94601	.	0.358447	0.29080	N	0.013207	T	0.42517	0.1206	L	0.41824	1.3	0.80722	D	1	B;B;B	0.25169	0.119;0.001;0.002	B;B;B	0.19666	0.026;0.002;0.002	T	0.17776	-1.0358	10	0.25751	T	0.34	-2.0371	19.2176	0.93783	0.0:1.0:0.0:0.0	.	218;295;357	F5H3G3;Q8WYN0-2;Q8WYN0	.;.;ATG4A_HUMAN	L	357;295;333;218	ENSP00000361306:S357L;ENSP00000298131:S295L;ENSP00000361328:S333L;ENSP00000438936:S218L	ENSP00000298131:S295L	S	+	2	0	ATG4A	107282917	0.998000	0.40836	0.986000	0.45419	0.985000	0.73830	6.135000	0.71696	2.489000	0.83994	0.600000	0.82982	TCA	.	.	none		0.428	ATG4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057860.1	NM_052936	
ZNF217	7764	hgsc.bcm.edu	37	20	52193210	52193210	+	Missense_Mutation	SNP	G	G	A	rs369074794		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:52193210G>A	ENST00000371471.2	-	4	2518	c.2093C>T	c.(2092-2094)cCg>cTg	p.P698L	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.P698L			O75362	ZN217_HUMAN	zinc finger protein 217	698					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.P698Q(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			AGAAATTGCCGGGCAATTGTG	0.428																																					p.P698L		Atlas-SNP	.											.	ZNF217	227	.	2	Substitution - Missense(2)	lung(2)	c.C2093T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	74.0	83.0	80.0		2093	4.2	0.0	20		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF217	NM_006526.2	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	698/1049	52193210	1,13005	2203	4300	6503	SO:0001583	missense	7764	exon3			ATTGCCGGGCAAT	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2093C>T	20.37:g.52193210G>A	ENSP00000360526:p.Pro698Leu	174.0	0.0	0		160.0	18.0	0.1125	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.366604	0.24771	0.0	1.16E-4	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.08984	3.03;3.03	5.18	4.22	0.49857	.	0.790776	0.11324	N	0.575710	T	0.06735	0.0172	L	0.34521	1.04	0.20196	N	0.999922	B	0.18166	0.026	B	0.08055	0.003	T	0.34378	-0.9831	10	0.10636	T	0.68	-6.4731	10.3081	0.43693	0.1521:0.0:0.8479:0.0	.	698	O75362	ZN217_HUMAN	L	698	ENSP00000360526:P698L;ENSP00000304308:P698L	ENSP00000304308:P698L	P	-	2	0	ZNF217	51626617	0.963000	0.33076	0.029000	0.17559	0.089000	0.18198	3.870000	0.56070	2.411000	0.81874	0.555000	0.69702	CCG	.	.	weak		0.428	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C	rs553572799|rs199957151	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr17:39240796G>C	ENST00000391417.4	+	1	338	c.338G>C	c.(337-339)aGc>aCc	p.S113T		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						tgccgccccagctgctgccgc	0.667																																					p.S113T		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,+1,1	KRTAP4-7	49	1	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						scavenged	.																																			SO:0001583	missense	100132476	exon1			GCCCCAGCTGCTG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.338G>C	17.37:g.39240796G>C	ENSP00000375236:p.Ser113Thr	11.0	0.0	0		33.0	4.0	0.121212	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.047	-1.263726	0.01433	.	.	ENSG00000240871	ENST00000391417	T	0.00627	6.12	2.73	1.66	0.24008	.	2.038930	0.02697	N	0.111300	T	0.00552	0.0018	.	.	.	0.21290	N	0.999731	B	0.13145	0.007	B	0.12837	0.008	T	0.47222	-0.9134	9	0.17832	T	0.49	.	5.1702	0.15107	0.0:0.2319:0.5315:0.2367	.	168	Q9BYR0	KRA47_HUMAN	T	113	ENSP00000375236:S113T	ENSP00000375236:S113T	S	+	2	0	KRTAP4-7	36494322	0.010000	0.17322	0.067000	0.19924	0.024000	0.10985	-0.517000	0.06275	0.191000	0.20236	0.289000	0.19496	AGC	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
ANKRD30B	374860	hgsc.bcm.edu	37	18	14797834	14797834	+	Silent	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr18:14797834C>T	ENST00000358984.4	+	20	2190	c.2010C>T	c.(2008-2010)gaC>gaT	p.D670D	ANKRD30B_ENST00000579292.1_3'UTR	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	670										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AATTAAAGGACAGAGAAACAC	0.308																																					p.D670D		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.C2010T						PASS	.						60.0	47.0	51.0					18																	14797834		692	1587	2279	SO:0001819	synonymous_variant	374860	exon20			AAAGGACAGAGAA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.2010C>T	18.37:g.14797834C>T		281.0	0.0	0		258.0	19.0	0.0736434	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			.	.	none		0.308	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
FBXO38	81545	hgsc.bcm.edu	37	5	147813265	147813265	+	Missense_Mutation	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr5:147813265T>C	ENST00000340253.5	+	17	2990	c.2822T>C	c.(2821-2823)gTg>gCg	p.V941A	CTD-2283N19.1_ENST00000520980.2_RNA|FBXO38_ENST00000296701.6_Missense_Mutation_p.V696A|FBXO38_ENST00000394370.3_Missense_Mutation_p.V866A|FBXO38_ENST00000513826.1_Missense_Mutation_p.V696A			Q6PIJ6	FBX38_HUMAN	F-box protein 38	941					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAGATCTAGTGCTAAAAGAC	0.328																																					p.V866A		Atlas-SNP	.											.	FBXO38	115	.	0			c.T2597C						PASS	.						147.0	150.0	149.0					5																	147813265		2203	4300	6503	SO:0001583	missense	81545	exon17			ATCTAGTGCTAAA	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"""F-boxes /  ""other"""""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.2822T>C	5.37:g.147813265T>C	ENSP00000342023:p.Val941Ala	275.0	0.0	0		226.0	10.0	0.0442478	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	37		.	.	.	.	.	.	.	.	.	.	T	23.5	4.426516	0.83667	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.38240	1.15;1.24;1.21;1.24	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.48874	0.1524	L	0.34521	1.04	0.35153	D	0.769977	P;D;D	0.71674	0.954;0.998;0.998	D;D;D	0.77557	0.932;0.979;0.99	T	0.62431	-0.6856	10	0.87932	D	0	-14.1344	14.1172	0.65161	0.0:0.0:0.0:1.0	.	696;866;941	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	A	941;696;866;696	ENSP00000342023:V941A;ENSP00000296701:V696A;ENSP00000377895:V866A;ENSP00000426410:V696A	ENSP00000296701:V696A	V	+	2	0	FBXO38	147793458	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	7.679000	0.84048	2.069000	0.61940	0.460000	0.39030	GTG	.	.	none		0.328	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793	
OGG1	4968	hgsc.bcm.edu	37	3	9792009	9792009	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:9792009T>G	ENST00000344629.7	+	1	382	c.39T>G	c.(37-39)caT>caG	p.H13Q	OGG1_ENST00000349503.5_Missense_Mutation_p.H13Q|OGG1_ENST00000302003.7_Missense_Mutation_p.H13Q|OGG1_ENST00000449570.2_Missense_Mutation_p.H13Q|OGG1_ENST00000302008.8_Missense_Mutation_p.H13Q|OGG1_ENST00000436092.1_3'UTR|OGG1_ENST00000339511.5_Missense_Mutation_p.H13Q|OGG1_ENST00000383826.5_Missense_Mutation_p.H13Q|OGG1_ENST00000302036.7_Missense_Mutation_p.H13Q			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	13					acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					GCATGGGGCATCGTACTCTAG	0.667								Base excision repair (BER), DNA glycosylases																													p.H13Q		Atlas-SNP	.											.	OGG1	57	.	0			c.T39G						PASS	.						51.0	46.0	48.0					3																	9792009		2203	4300	6503	SO:0001583	missense	4968	exon1			GGGGCATCGTACT	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"""8-hydroxyguanine DNA glycosylase"", ""OGG1 type 1e"", ""OGG1 type 1d"", ""OGG1 type 1g"", ""OGG1 type 1h"""	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.39T>G	3.37:g.9792009T>G	ENSP00000342851:p.His13Gln	110.0	0.0	0		119.0	12.0	0.10084	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.645755	0.87958	.	.	ENSG00000114026	ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000383826	T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.85	-2.38	0.06622	Transcription factor TFIID, C-terminal/DNA glycosylase, N-terminal (1);	0.044063	0.85682	D	0.000000	T	0.62441	0.2428	M	0.61703	1.905	0.36706	D	0.88038	D;D;D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.993;0.996;0.994;0.996	D;D;P;P;P;P;P;P	0.65573	0.915;0.936;0.892;0.765;0.701;0.764;0.832;0.843	T	0.67776	-0.5583	10	0.72032	D	0.01	-25.825	12.1556	0.54074	0.0:0.6561:0.1289:0.215	.	13;13;13;13;13;13;13;13	E5KPM8;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.;.;.;.;.;.;OGG1_HUMAN;.	Q	13	ENSP00000305584:H13Q;ENSP00000342851:H13Q;ENSP00000306561:H13Q;ENSP00000303132:H13Q;ENSP00000345520:H13Q;ENSP00000403598:H13Q;ENSP00000305527:H13Q;ENSP00000373337:H13Q	ENSP00000305584:H13Q	H	+	3	2	OGG1	9767009	0.905000	0.30787	0.598000	0.28837	0.920000	0.55202	-0.374000	0.07484	-0.414000	0.07495	0.533000	0.62120	CAT	.	.	none		0.667	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821	
ZNF217	7764	hgsc.bcm.edu	37	20	52198483	52198483	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:52198483T>G	ENST00000371471.2	-	2	1308	c.883A>C	c.(883-885)Acc>Ccc	p.T295P	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Missense_Mutation_p.T295P			O75362	ZN217_HUMAN	zinc finger protein 217	295					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GCCTGGAAGGTGGTGAACGGA	0.532																																					p.T295P		Atlas-SNP	.											.	ZNF217	227	.	0			c.A883C						PASS	.						122.0	114.0	117.0					20																	52198483		2203	4300	6503	SO:0001583	missense	7764	exon1			GGAAGGTGGTGAA	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.883A>C	20.37:g.52198483T>G	ENSP00000360526:p.Thr295Pro	172.0	0.0	0		155.0	10.0	0.0645161	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.386055	0.82902	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.10382	2.88;2.88	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.35008	0.0917	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.06092	-1.0846	10	0.49607	T	0.09	-39.6624	15.6258	0.76855	0.0:0.0:0.0:1.0	.	295	O75362	ZN217_HUMAN	P	295	ENSP00000360526:T295P;ENSP00000304308:T295P	ENSP00000304308:T295P	T	-	1	0	ZNF217	51631890	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.585000	0.82584	2.170000	0.68504	0.482000	0.46254	ACC	.	.	none		0.532	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
GRIN3A	116443	hgsc.bcm.edu	37	9	104449271	104449271	+	Missense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:104449271G>A	ENST00000361820.3	-	2	1511	c.911C>T	c.(910-912)aCc>aTc	p.T304I		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	304					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	GAGGTCCTGGGTGGAGGGGAG	0.507																																					p.T304I		Atlas-SNP	.											.	GRIN3A	186	.	0			c.C911T						PASS	.						125.0	114.0	118.0					9																	104449271		2203	4300	6503	SO:0001583	missense	116443	exon2			TCCTGGGTGGAGG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.911C>T	9.37:g.104449271G>A	ENSP00000355155:p.Thr304Ile	169.0	0.0	0		172.0	12.0	0.0697674	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	G	9.953	1.220762	0.22457	.	.	ENSG00000198785	ENST00000361820	D	0.86562	-2.14	5.82	3.79	0.43588	.	0.741427	0.13472	N	0.385327	T	0.81158	0.4764	L	0.36672	1.1	0.37462	D	0.915272	B	0.14012	0.009	B	0.10450	0.005	T	0.76830	-0.2814	10	0.34782	T	0.22	.	12.3574	0.55184	0.0:0.242:0.6501:0.108	.	304	Q8TCU5	NMD3A_HUMAN	I	304	ENSP00000355155:T304I	ENSP00000355155:T304I	T	-	2	0	GRIN3A	103489092	0.033000	0.19621	0.999000	0.59377	0.882000	0.50991	0.538000	0.23160	2.759000	0.94783	0.557000	0.71058	ACC	.	.	none		0.507	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
MYC	4609	hgsc.bcm.edu	37	8	128751013	128751013	+	Missense_Mutation	SNP	A	A	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr8:128751013A>T	ENST00000259523.6	+	2	1710	c.505A>T	c.(505-507)Agc>Tgc	p.S169C	MYC_ENST00000377970.2_Missense_Mutation_p.S184C|MYC_ENST00000524013.1_Missense_Mutation_p.S183C			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	169					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular iron ion homeostasis (GO:0006879)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|chromosome organization (GO:0051276)|energy reserve metabolic process (GO:0006112)|fibroblast apoptotic process (GO:0044346)|gene expression (GO:0010467)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell division (GO:0051782)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|oxygen transport (GO:0015671)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric cap mesenchymal cell proliferation (GO:0090096)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of telomere maintenance (GO:0032204)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to growth factor (GO:0070848)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein complex binding (GO:0032403)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185)	Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22)	Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151)	KIRC - Kidney renal clear cell carcinoma(542;0.248)	Nadroparin(DB08813)	CCGCGGCCACAGCGTCTGCTC	0.677		3	"""A, T"""	"""IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"""	"""Burkitt lymphoma,  amplified in other cancers, B-CLL"""						OREG0018982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S184C		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"""L, E"""	.	MYC	168	.	0			c.A550T						PASS	.						20.0	22.0	21.0					8																	128751013		2203	4298	6501	SO:0001583	missense	4609	exon2			GGCCACAGCGTCT		CCDS6359.2	8q24	2013-07-09	2013-07-09		ENSG00000136997	ENSG00000136997		"""Basic helix-loop-helix proteins"""	7553	protein-coding gene	gene with protein product		190080					Standard	NM_002467		Approved	c-Myc, bHLHe39, MYCC	uc003ysi.3	P01106	OTTHUMG00000128475	ENST00000259523.6:c.505A>T	8.37:g.128751013A>T	ENSP00000259523:p.Ser169Cys	56.0	0.0	0	1567	53.0	4.0	0.0754717	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		.	.	.	.	.	.	.	.	.	.	A	15.75	2.926604	0.52759	.	.	ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617	T;T;T;T	0.25749	2.14;1.78;2.14;2.14	4.78	-3.13	0.05266	Transcription regulator Myc, N-terminal (1);	0.630931	0.16999	N	0.190997	T	0.28234	0.0697	L	0.52573	1.65	0.21020	N	0.99981	P	0.50156	0.932	P	0.55455	0.776	T	0.12863	-1.0531	10	0.62326	D	0.03	-9.1089	3.8255	0.08852	0.5346:0.1046:0.2554:0.1053	.	169	P01106	MYC_HUMAN	C	169;183;184;183;150	ENSP00000259523:S169C;ENSP00000429441:S183C;ENSP00000367207:S184C;ENSP00000430235:S183C	ENSP00000259523:S169C	S	+	1	0	MYC	128820195	0.000000	0.05858	0.819000	0.32651	0.693000	0.40251	-0.773000	0.04689	-0.571000	0.06014	0.459000	0.35465	AGC	.	.	none		0.677	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1		
RANBP2	5903	hgsc.bcm.edu	37	2	109392255	109392255	+	Missense_Mutation	SNP	T	T	G	rs367864778		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:109392255T>G	ENST00000283195.6	+	24	8486	c.8360T>G	c.(8359-8361)gTa>gGa	p.V2787G		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2787					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GAAGTGATGGTACCTTCTTTC	0.383																																					p.V2787G		Atlas-SNP	.											.	RANBP2	488	.	0			c.T8360G						PASS	.	T	GLY/VAL	0,4406		0,0,2203	172.0	170.0	171.0		8360	-3.3	0.0	2		171	1,8599	1.2+/-3.3	0,1,4299	no	missense	RANBP2	NM_006267.4	109	0,1,6502	GG,GT,TT		0.0116,0.0,0.0077	benign	2787/3225	109392255	1,13005	2203	4300	6503	SO:0001583	missense	5903	exon24			TGATGGTACCTTC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.8360T>G	2.37:g.109392255T>G	ENSP00000283195:p.Val2787Gly	138.0	0.0	0		100.0	5.0	0.05	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.904645	0.33628	0.0	1.16E-4	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.27720	1.65	5.58	-3.34	0.04943	.	.	.	.	.	T	0.21590	0.0520	L	0.47716	1.5	0.09310	N	1	B	0.20887	0.049	B	0.14023	0.01	T	0.33929	-0.9849	9	0.17369	T	0.5	2.9813	9.2618	0.37616	0.1243:0.6276:0.0:0.248	.	2787	P49792	RBP2_HUMAN	G	1811;2787	ENSP00000283195:V2787G	ENSP00000283195:V2787G	V	+	2	0	RANBP2	108758687	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.045000	0.01410	-0.487000	0.06735	-0.250000	0.11733	GTA	.	.	weak		0.383	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
GPD2	2820	hgsc.bcm.edu	37	2	157369859	157369859	+	Missense_Mutation	SNP	C	C	T	rs143467322		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:157369859C>T	ENST00000310454.6	+	6	884	c.512C>T	c.(511-513)cCt>cTt	p.P171L	GPD2_ENST00000409674.1_Missense_Mutation_p.P171L|GPD2_ENST00000540309.1_Missense_Mutation_p.P171L|GPD2_ENST00000438166.2_Missense_Mutation_p.P171L|GPD2_ENST00000409125.4_Intron	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	171					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGGCAGTTACCTTACTACTGG	0.393																																					p.P171L		Atlas-SNP	.											.	GPD2	59	.	0			c.C512T						PASS	.	C	LEU/PRO,LEU/PRO	0,4406		0,0,2203	153.0	142.0	146.0		512,512	5.0	1.0	2	dbSNP_134	146	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPD2	NM_000408.4,NM_001083112.2	98,98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	171/728,171/728	157369859	1,13005	2203	4300	6503	SO:0001583	missense	2820	exon6			AGTTACCTTACTA		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"""EF-hand domain containing"""	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.512C>T	2.37:g.157369859C>T	ENSP00000308610:p.Pro171Leu	170.0	0.0	0		166.0	7.0	0.0421687	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.385374	0.82792	0.0	1.16E-4	ENSG00000115159	ENST00000310454;ENST00000438166;ENST00000540309;ENST00000409674	D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51	4.99	4.99	0.66335	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.87680	0.6238	M	0.71036	2.16	0.80722	D	1	B	0.27140	0.169	P	0.46885	0.53	D	0.87211	0.2247	10	0.66056	D	0.02	.	18.6714	0.91513	0.0:1.0:0.0:0.0	.	171	P43304	GPDM_HUMAN	L	171	ENSP00000308610:P171L;ENSP00000409708:P171L;ENSP00000440892:P171L;ENSP00000386425:P171L	ENSP00000308610:P171L	P	+	2	0	GPD2	157078105	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.489000	0.83994	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	weak		0.393	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3		
ABCA12	26154	hgsc.bcm.edu	37	2	215855677	215855677	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:215855677T>G	ENST00000272895.7	-	24	3592	c.3373A>C	c.(3373-3375)Acc>Ccc	p.T1125P	ABCA12_ENST00000389661.4_Missense_Mutation_p.T807P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1125					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATCACGATGGTAACCAGTAAA	0.388																																					p.T1125P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A3373C						PASS	.						100.0	102.0	101.0					2																	215855677		2203	4300	6503	SO:0001583	missense	26154	exon24			CGATGGTAACCAG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3373A>C	2.37:g.215855677T>G	ENSP00000272895:p.Thr1125Pro	92.0	0.0	0		87.0	4.0	0.045977	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.767808	0.69878	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.85773	-2.03;-2.03	5.39	5.39	0.77823	.	0.158061	0.45361	D	0.000373	D	0.92172	0.7518	M	0.80746	2.51	0.80722	D	1	D;D	0.76494	0.999;0.976	D;D	0.70487	0.969;0.937	D	0.93226	0.6613	10	0.87932	D	0	.	15.5646	0.76281	0.0:0.0:0.0:1.0	.	1125;807	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	1125;807	ENSP00000272895:T1125P;ENSP00000374312:T807P	ENSP00000272895:T1125P	T	-	1	0	ABCA12	215563922	1.000000	0.71417	0.998000	0.56505	0.655000	0.38815	7.832000	0.86757	2.263000	0.75096	0.528000	0.53228	ACC	.	.	none		0.388	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
FAM120A	23196	hgsc.bcm.edu	37	9	96318697	96318697	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:96318697T>G	ENST00000277165.6	+	13	2502	c.2308T>G	c.(2308-2310)Tca>Gca	p.S770A	FAM120A_ENST00000333936.5_Missense_Mutation_p.S798A|FAM120A_ENST00000340893.4_Missense_Mutation_p.S770A	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	770						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AATTCAGCTATCAGCTCTCTT	0.393																																					p.S770A		Atlas-SNP	.											.	FAM120A	105	.	0			c.T2308G						PASS	.						135.0	138.0	137.0					9																	96318697		2203	4300	6503	SO:0001583	missense	23196	exon13			CAGCTATCAGCTC	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.2308T>G	9.37:g.96318697T>G	ENSP00000277165:p.Ser770Ala	155.0	0.0	0		171.0	15.0	0.0877193	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643701	0.29246	.	.	ENSG00000048828	ENST00000277165;ENST00000333936;ENST00000340893;ENST00000427765	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000010	T	0.12860	0.0312	N	0.00661	-1.28	0.40403	D	0.979668	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.13407	0.004;0.007;0.009	T	0.27971	-1.0058	10	0.02654	T	1	-11.3047	11.8715	0.52523	0.0:0.0:0.1456:0.8543	.	770;798;770	Q9NZB2-4;Q9NZB2-6;Q9NZB2	.;.;F120A_HUMAN	A	770;798;770;192	ENSP00000277165:S770A;ENSP00000334918:S798A;ENSP00000344698:S770A;ENSP00000412440:S192A	ENSP00000277165:S770A	S	+	1	0	FAM120A	95358518	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.176000	0.65026	2.172000	0.68678	0.533000	0.62120	TCA	.	.	none		0.393	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612	
BCAP29	55973	hgsc.bcm.edu	37	7	107236323	107236323	+	Missense_Mutation	SNP	G	G	A	rs115169101		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr7:107236323G>A	ENST00000005259.4	+	5	695	c.356G>A	c.(355-357)cGt>cAt	p.R119H	BCAP29_ENST00000494086.1_3'UTR|BCAP29_ENST00000379121.2_Missense_Mutation_p.R25H|BCAP29_ENST00000465919.1_Missense_Mutation_p.R25H|BCAP29_ENST00000445771.2_Missense_Mutation_p.R119H|BCAP29_ENST00000379119.2_Missense_Mutation_p.R119H|BCAP29_ENST00000379117.2_Missense_Mutation_p.R119H	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	119					apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						GTTTTGAGACGTCTGGTTACG	0.338													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15250	0.0		0.0	False		,,,				2504	0.0				p.R119H		Atlas-SNP	.											BCAP29,colon,carcinoma,+1,1	BCAP29	46	1	0			c.G356A						PASS	.	G	HIS/ARG,HIS/ARG	1,4403	2.1+/-5.4	0,1,2201	112.0	108.0	109.0		356,356	4.6	1.0	7	dbSNP_132	109	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BCAP29	NM_001008405.2,NM_018844.3	29,29	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	119/349,119/242	107236323	2,13002	2202	4300	6502	SO:0001583	missense	55973	exon5			TGAGACGTCTGGT		CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.356G>A	7.37:g.107236323G>A	ENSP00000005259:p.Arg119His	220.0	0.0	0		202.0	10.0	0.049505	NM_018844	G5E9L4|O95003	Missense_Mutation	SNP	ENST00000005259.4	37	CCDS34731.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323123	0.81580	2.27E-4	1.16E-4	ENSG00000075790	ENST00000005259;ENST00000465919;ENST00000445771;ENST00000479917;ENST00000421217;ENST00000457837;ENST00000379117;ENST00000379119;ENST00000491150;ENST00000379121	.	.	.	5.45	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.84061	0.5389	M	0.90369	3.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87335	0.2327	9	0.87932	D	0	0.1468	13.3198	0.60426	0.0778:0.0:0.9222:0.0	.	119;119;119	G5E9L4;C9JTE9;Q9UHQ4	.;.;BAP29_HUMAN	H	119;25;119;119;119;119;119;119;76;25	.	ENSP00000005259:R119H	R	+	2	0	BCAP29	107023559	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.256000	0.72473	1.444000	0.47605	0.650000	0.86243	CGT	G|1.000;A|0.000	0.000	strong		0.338	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844	
DOPEY1	23033	hgsc.bcm.edu	37	6	83849764	83849764	+	Silent	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:83849764T>C	ENST00000349129.2	+	22	5426	c.5166T>C	c.(5164-5166)acT>acC	p.T1722T	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Silent_p.T1713T|DOPEY1_ENST00000237163.5_Silent_p.T1703T	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1722					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)		TGATTCTTACTCTTTTGGAAG	0.338																																					p.T1722T		Atlas-SNP	.											.	DOPEY1	190	.	0			c.T5166C						PASS	.						141.0	130.0	134.0					6																	83849764		2203	4300	6503	SO:0001819	synonymous_variant	23033	exon22			TCTTACTCTTTTG	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.5166T>C	6.37:g.83849764T>C		208.0	0.0	0		169.0	8.0	0.0473373	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																			.	.	none		0.338	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
NUBPL	80224	hgsc.bcm.edu	37	14	32142594	32142594	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr14:32142594T>G	ENST00000281081.7	+	5	461	c.416T>G	c.(415-417)aTt>aGt	p.I139S	NUBPL_ENST00000536705.1_Missense_Mutation_p.I43S	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like	139					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		AATTATGGTATTGCTTGGTGA	0.279																																					p.I139S		Atlas-SNP	.											.	NUBPL	21	.	0			c.T416G						PASS	.						46.0	42.0	43.0					14																	32142594		1788	4062	5850	SO:0001583	missense	80224	exon5			ATGGTATTGCTTG	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"""Mitochondrial respiratory chain complex assembly factors"""	20278	protein-coding gene	gene with protein product	"""iron-sulfur protein required for NADH dehydrogenase"""	613621	"""chromosome 14 open reading frame 127"""	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.416T>G	14.37:g.32142594T>G	ENSP00000281081:p.Ile139Ser	382.0	0.0	0		353.0	17.0	0.0481586	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Missense_Mutation	SNP	ENST00000281081.7	37	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132126	0.77662	.	.	ENSG00000151413	ENST00000281081;ENST00000551314;ENST00000536705	T;T;T	0.49432	0.78;0.87;0.78	5.53	5.53	0.82687	.	0.096119	0.64402	D	0.000001	T	0.67144	0.2862	H	0.96015	3.755	0.48135	D	0.99959	P;P	0.40578	0.586;0.722	B;B	0.43809	0.375;0.432	T	0.77395	-0.2604	10	0.87932	D	0	0.811	13.3964	0.60856	0.0:0.0:0.0:1.0	.	43;139	B4DWB0;Q8TB37	.;NUBPL_HUMAN	S	139;87;43	ENSP00000281081:I139S;ENSP00000447234:I87S;ENSP00000439286:I43S	ENSP00000281081:I139S	I	+	2	0	NUBPL	31212345	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.612000	0.74187	2.097000	0.63578	0.455000	0.32223	ATT	.	.	none		0.279	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152	
RNF19A	25897	hgsc.bcm.edu	37	8	101276899	101276899	+	Splice_Site	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr8:101276899C>T	ENST00000519449.1	-	7	1622	c.1306G>A	c.(1306-1308)Ggt>Agt	p.G436S	RNF19A_ENST00000523255.1_5'UTR|RNF19A_ENST00000341084.2_Splice_Site_p.G436S	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	436					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			ATTTTCTTACCTACAGTCACT	0.353																																					p.G436S		Atlas-SNP	.											.	RNF19A	67	.	0			c.G1306A						PASS	.						175.0	155.0	162.0					8																	101276899		2203	4300	6503	SO:0001630	splice_region_variant	25897	exon7			TCTTACCTACAGT	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"""RING-type (C3HC4) zinc fingers"""	13432	protein-coding gene	gene with protein product		607119	"""ring finger protein 19"", ""ring finger protein 19A"", ""ring finger protein 19A, E3 ubiquitin protein ligase"""	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1306+1G>A	8.37:g.101276899C>T		114.0	0.0	0		108.0	8.0	0.0740741	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	35	5.552861	0.96501	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.86097	-2.07;-2.07	5.41	5.41	0.78517	.	0.046563	0.85682	D	0.000000	D	0.91112	0.7202	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89895	0.4040	9	.	.	.	.	19.229	0.93829	0.0:1.0:0.0:0.0	.	436	Q9NV58	RN19A_HUMAN	S	436	ENSP00000428968:G436S;ENSP00000342667:G436S	.	G	-	1	0	RNF19A	101346075	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.776000	0.85560	2.699000	0.92147	0.650000	0.86243	GGT	.	.	none		0.353	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435	Missense_Mutation
SMPDL3A	10924	hgsc.bcm.edu	37	6	123116916	123116916	+	Silent	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:123116916T>C	ENST00000368440.4	+	2	384	c.207T>C	c.(205-207)aaT>aaC	p.N69N	SMPDL3A_ENST00000539041.1_Intron|SMPDL3A_ENST00000487215.1_3'UTR	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	69					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|cervix(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(226;0.236)		AAGGTGCAAATGCCTCCAACC	0.403																																					p.N69N		Atlas-SNP	.											.	SMPDL3A	31	.	0			c.T207C						PASS	.						167.0	149.0	155.0					6																	123116916		2203	4300	6503	SO:0001819	synonymous_variant	10924	exon2			TGCAAATGCCTCC	AK000184	CCDS5128.1, CCDS69190.1	6q22.32	2006-04-12			ENSG00000172594	ENSG00000172594			17389	protein-coding gene	gene with protein product	"""acid sphingomyelinase-like phosphodiesterase 3a"""	610728				12442002	Standard	XM_005266798		Approved	FLJ20177, ASM3A, ASML3a, yR36GH4.1	uc003pzg.3	Q92484	OTTHUMG00000015490	ENST00000368440.4:c.207T>C	6.37:g.123116916T>C		265.0	0.0	0		242.0	10.0	0.0413223	NM_006714	B7Z729|Q8WV13	Silent	SNP	ENST00000368440.4	37	CCDS5128.1																																																																																			.	.	none		0.403	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714	
B2M	567	hgsc.bcm.edu	37	15	45003779	45003779	+	Missense_Mutation	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr15:45003779T>C	ENST00000558401.1	+	1	105	c.35T>C	c.(34-36)cTa>cCa	p.L12P	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Missense_Mutation_p.L12P|B2M_ENST00000544417.1_Missense_Mutation_p.L12P	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	12					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.A11fs*42(1)|p.L12Q(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GTGCTCGCGCTACTCTCTCTT	0.617																																					p.L12P		Atlas-SNP	.											B2M,colon,carcinoma,0,2	B2M	99	2	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	c.T35C						PASS	.						132.0	94.0	107.0					15																	45003779		2198	4298	6496	SO:0001583	missense	567	exon1			TCGCGCTACTCTC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.35T>C	15.37:g.45003779T>C	ENSP00000452780:p.Leu12Pro	81.0	0.0	0		95.0	7.0	0.0736842	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.443926	0.63067	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01388	4.95	5.35	5.35	0.76521	.	9.011740	0.00721	U	0.000881	T	0.10809	0.0264	M	0.74647	2.275	0.29321	N	0.867335	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.17107	-1.0380	10	0.87932	D	0	.	11.9001	0.52678	0.0:0.0:0.0:1.0	.	12;12;12	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	P	12	ENSP00000437604:L12P	ENSP00000340858:L12P	L	+	2	0	B2M	42791071	0.253000	0.23982	0.051000	0.19133	0.007000	0.05969	3.556000	0.53734	2.371000	0.80710	0.533000	0.62120	CTA	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
ELF4	2000	hgsc.bcm.edu	37	X	129201410	129201410	+	Silent	SNP	C	C	T	rs369363653		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:129201410C>T	ENST00000308167.5	-	9	1657	c.1278G>A	c.(1276-1278)acG>acA	p.T426T	ELF4_ENST00000335997.7_Silent_p.T426T	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TGGTCAGCACCGTGGTCAGTG	0.597			T	ERG	AML																																p.T426T		Atlas-SNP	.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4	67	.	0			c.G1278A						PASS	.		,	1,3834		0,0,1,1632,570	66.0	62.0	63.0		1278,1278	-0.1	1.0	X		63	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous	ELF4	NM_001127197.1,NM_001421.3	,	0,0,1,4060,2442	TT,TC,T,CC,C		0.0,0.0261,0.0095	,	426/664,426/664	129201410	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	2000	exon9			CAGCACCGTGGTC	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1278G>A	X.37:g.129201410C>T		139.0	0.0	0		146.0	9.0	0.0616438	NM_001421		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																			.	.	weak		0.597	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421	
TBC1D1	23216	hgsc.bcm.edu	37	4	38053568	38053568	+	Intron	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr4:38053568T>C	ENST00000261439.4	+	11	2265				TBC1D1_ENST00000508802.1_Silent_p.S653S	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1						membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CAGGTCAGTCTTCAGCTCCTG	0.537																																					p.S653S		Atlas-SNP	.											.	TBC1D1	94	.	0			c.T1959C						PASS	.																																			SO:0001627	intron_variant	23216	exon12			TCAGTCTTCAGCT	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.1910+2049T>C	4.37:g.38053568T>C		147.0	0.0	0		144.0	27.0	0.1875	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	37	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	T	3.720	-0.057741	0.07317	.	.	ENSG00000065882	ENST00000443855	.	.	.	5.56	0.202	0.15190	.	.	.	.	.	T	0.29556	0.0737	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.27157	-1.0082	4	.	.	.	.	6.0231	0.19640	0.0:0.2056:0.1269:0.6675	.	.	.	.	P	145	.	.	L	+	2	0	TBC1D1	37729963	0.305000	0.24481	0.494000	0.27515	0.397000	0.30659	0.907000	0.28531	0.048000	0.15891	0.482000	0.46254	CTT	.	.	none		0.537	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
FBP2	8789	hgsc.bcm.edu	37	9	97346890	97346890	+	Missense_Mutation	SNP	G	G	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:97346890G>C	ENST00000375337.3	-	3	461	c.395C>G	c.(394-396)tCc>tGc	p.S132C		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	132					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				GGTTCCGATGGAGGCCAGGCA	0.483																																					p.S132C		Atlas-SNP	.											.	FBP2	26	.	0			c.C395G						PASS	.						150.0	122.0	132.0					9																	97346890		2203	4300	6503	SO:0001583	missense	8789	exon3			CCGATGGAGGCCA	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.395C>G	9.37:g.97346890G>C	ENSP00000364486:p.Ser132Cys	64.0	0.0	0		78.0	8.0	0.102564	NM_003837	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	37	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555699	0.86231	.	.	ENSG00000130957	ENST00000375337	T	0.79454	-1.27	4.87	4.87	0.63330	.	0.169189	0.53938	D	0.000045	D	0.89543	0.6745	M	0.88640	2.97	0.80722	D	1	D	0.71674	0.998	D	0.66196	0.942	D	0.91770	0.5427	10	0.87932	D	0	-19.1055	18.3657	0.90390	0.0:0.0:1.0:0.0	.	132	O00757	F16P2_HUMAN	C	132	ENSP00000364486:S132C	ENSP00000364486:S132C	S	-	2	0	FBP2	96386711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.542000	0.98086	2.397000	0.81536	0.655000	0.94253	TCC	.	.	none		0.483	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837	
TMSB4X	7114	hgsc.bcm.edu	37	X	12994394	12994394	+	Missense_Mutation	SNP	C	C	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:12994394C>G	ENST00000380635.1	+	2	230	c.14C>G	c.(13-15)cCc>cGc	p.P5R	TMSB4X_ENST00000380633.1_Missense_Mutation_p.P5R|TMSB4X_ENST00000380636.1_Missense_Mutation_p.P5R|TMSB4X_ENST00000451311.2_Missense_Mutation_p.P5R			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	5					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						TCTGACAAACCCGATATGGCT	0.542																																					p.P5R		Atlas-SNP	.											.	TMSB4X	3	.	0			c.C14G						PASS	.						66.0	64.0	65.0					X																	12994394		2203	4300	6503	SO:0001583	missense	7114	exon2			ACAAACCCGATAT		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"""thymosin, beta 4, X chromosome"""	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.14C>G	X.37:g.12994394C>G	ENSP00000370009:p.Pro5Arg	348.0	0.0	0		323.0	20.0	0.0619195	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Missense_Mutation	SNP	ENST00000380635.1	37	CCDS35202.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023167	0.75275	.	.	ENSG00000205542	ENST00000451311;ENST00000380636;ENST00000380635;ENST00000380633	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	4.66	4.66	0.58398	.	0.000000	0.64402	U	0.000010	T	0.68476	0.3005	.	.	.	0.58432	D	0.99999	P	0.49307	0.922	P	0.51895	0.683	T	0.74685	-0.3582	9	0.87932	D	0	-6.1801	16.7451	0.85470	0.0:1.0:0.0:0.0	.	5	P62328	TYB4_HUMAN	R	5	ENSP00000414376:P5R;ENSP00000370010:P5R;ENSP00000370009:P5R;ENSP00000370007:P5R	ENSP00000370007:P5R	P	+	2	0	TMSB4X	12904315	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.929000	0.75852	2.064000	0.61679	0.600000	0.82982	CCC	.	.	none		0.542	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109	
IL13RA1	3597	hgsc.bcm.edu	37	X	117907928	117907928	+	Missense_Mutation	SNP	T	T	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:117907928T>A	ENST00000371666.3	+	9	1163	c.1096T>A	c.(1096-1098)Tac>Aac	p.Y366N	IL13RA1_ENST00000371637.3_Missense_Mutation_p.Y165N	NM_001560.2	NP_001551.1	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1	366					cell surface receptor signaling pathway (GO:0007166)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin production (GO:0002639)	interleukin-13 receptor complex (GO:0005898)|plasma membrane (GO:0005886)	interleukin-13 receptor activity (GO:0016515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)	12						ACTCCTGCTTTACCTAAAAAG	0.428																																					p.Y366N		Atlas-SNP	.											.	IL13RA1	41	.	0			c.T1096A						PASS	.						178.0	150.0	160.0					X																	117907928		2203	4300	6503	SO:0001583	missense	3597	exon9			CTGCTTTACCTAA	U62858	CCDS14573.1	Xq24	2008-02-05			ENSG00000131724	ENSG00000131724		"""Interleukins and interleukin receptors"", ""CD molecules"""	5974	protein-coding gene	gene with protein product	"""IL13 receptor alpha-1 chain"", ""CD213a1 antigen"""	300119				8910586, 9013879	Standard	NM_001560		Approved	IL-13Ra, NR4, CD213a1	uc004eqs.3	P78552	OTTHUMG00000022258	ENST00000371666.3:c.1096T>A	X.37:g.117907928T>A	ENSP00000360730:p.Tyr366Asn	89.0	0.0	0		92.0	6.0	0.0652174	NM_001560	O95646|Q5JSL4|Q99656|Q9UDY5	Missense_Mutation	SNP	ENST00000371666.3	37	CCDS14573.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.143297	0.57044	.	.	ENSG00000131724	ENST00000371666;ENST00000371637	D	0.90732	-2.72	5.54	4.37	0.52481	.	0.089367	0.49305	D	0.000160	D	0.93504	0.7927	M	0.72894	2.215	0.40981	D	0.984779	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.981	D	0.92830	0.6279	10	0.87932	D	0	-17.3933	7.6269	0.28218	0.0:0.0979:0.0:0.9021	.	366;366	Q5JSL4;P78552	.;I13R1_HUMAN	N	366;165	ENSP00000360730:Y366N	ENSP00000360700:Y165N	Y	+	1	0	IL13RA1	117791956	1.000000	0.71417	0.856000	0.33681	0.596000	0.36781	4.240000	0.58701	0.834000	0.34852	0.439000	0.28862	TAC	.	.	none		0.428	IL13RA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058009.1	NM_001560	
HTATSF1	27336	hgsc.bcm.edu	37	X	135593333	135593333	+	Missense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:135593333G>A	ENST00000218364.4	+	9	1603	c.1429G>A	c.(1429-1431)Gaa>Aaa	p.E477K	HTATSF1_ENST00000535601.1_Missense_Mutation_p.E477K	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	477	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					AAGAGGGTTTGAAGGCAGCTG	0.443																																					p.E477K		Atlas-SNP	.											.	HTATSF1	66	.	0			c.G1429A						PASS	.						46.0	50.0	49.0					X																	135593333		2193	4279	6472	SO:0001583	missense	27336	exon10			GGGTTTGAAGGCA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1429G>A	X.37:g.135593333G>A	ENSP00000218364:p.Glu477Lys	124.0	0.0	0		139.0	10.0	0.0719424	NM_001163280	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	37	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	G	5.369	0.253360	0.10185	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.04360	3.64;3.64	4.38	2.61	0.31194	.	0.642678	0.16646	N	0.205430	T	0.03477	0.0100	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.40440	-0.9563	10	0.41790	T	0.15	-2.2713	5.8919	0.18917	0.3322:0.0:0.6678:0.0	.	477	O43719	HTSF1_HUMAN	K	477	ENSP00000442699:E477K;ENSP00000218364:E477K	ENSP00000218364:E477K	E	+	1	0	HTATSF1	135420999	0.007000	0.16637	0.001000	0.08648	0.006000	0.05464	1.430000	0.34914	0.607000	0.29982	0.523000	0.50628	GAA	.	.	none		0.443	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209218719	209218719	+	Missense_Mutation	SNP	A	A	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:209218719A>G	ENST00000264380.4	+	40	6100	c.5942A>G	c.(5941-5943)aAg>aGg	p.K1981R		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1981	Catalytic.|PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						AATCTCCTAAAGATGGTTCGA	0.418																																					p.K1981R		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.A5942G						PASS	.						142.0	145.0	144.0					2																	209218719		2203	4300	6503	SO:0001583	missense	200576	exon40			TCCTAAAGATGGT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5942A>G	2.37:g.209218719A>G	ENSP00000264380:p.Lys1981Arg	150.0	0.0	0		128.0	7.0	0.0546875	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.651372	0.88056	.	.	ENSG00000115020	ENST00000264380	T	0.30182	1.54	6.17	6.17	0.99709	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.45617	0.1351	L	0.28458	0.855	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.39860	-0.9593	10	0.59425	D	0.04	-24.4674	16.8222	0.85835	1.0:0.0:0.0:0.0	.	1981	Q9Y2I7	FYV1_HUMAN	R	1981	ENSP00000264380:K1981R	ENSP00000264380:K1981R	K	+	2	0	PIKFYVE	208926964	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.401000	0.79962	2.371000	0.80710	0.533000	0.62120	AAG	.	.	none		0.418	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
PDLIM4	8572	hgsc.bcm.edu	37	5	131607911	131607911	+	Missense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr5:131607911G>A	ENST00000253754.3	+	7	1046	c.982G>A	c.(982-984)Gaa>Aaa	p.E328K	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000379018.3_3'UTR	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	328							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGCCAAGGTGGAACTCGTCTG	0.607																																					p.E328K		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G982A						PASS	.						44.0	45.0	45.0					5																	131607911		2203	4300	6503	SO:0001583	missense	8572	exon7			AAGGTGGAACTCG	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.982G>A	5.37:g.131607911G>A	ENSP00000253754:p.Glu328Lys	44.0	0.0	0		52.0	6.0	0.115385	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	37	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	G	32	5.192528	0.94960	.	.	ENSG00000131435	ENST00000253754	T	0.14516	2.5	5.05	4.16	0.48862	.	0.276256	0.34435	N	0.003965	T	0.28001	0.0690	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.02526	-1.1146	10	0.87932	D	0	-8.9848	15.2133	0.73244	0.0:0.1416:0.8584:0.0	.	328	P50479	PDLI4_HUMAN	K	328	ENSP00000253754:E328K	ENSP00000253754:E328K	E	+	1	0	PDLIM4	131635810	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	9.617000	0.98361	1.068000	0.40764	0.655000	0.94253	GAA	.	.	none		0.607	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
FSIP2	401024	hgsc.bcm.edu	37	2	186671112	186671112	+	Silent	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:186671112T>G	ENST00000424728.1	+	17	17079	c.17079T>G	c.(17077-17079)tcT>tcG	p.S5693S	FSIP2_ENST00000343098.5_Silent_p.S5782S			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5693										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AACTATCTTCTTCTCCAGAAC	0.373																																					p.S5782S		Atlas-SNP	.											.	FSIP2	251	.	0			c.T17346G						PASS	.						91.0	85.0	87.0					2																	186671112		1827	4088	5915	SO:0001819	synonymous_variant	401024	exon17			ATCTTCTTCTCCA	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17079T>G	2.37:g.186671112T>G		206.0	0.0	0		195.0	8.0	0.0410256	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				.	.	none		0.373	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
GPR82	27197	hgsc.bcm.edu	37	X	41586752	41586752	+	Missense_Mutation	SNP	A	A	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:41586752A>C	ENST00000302548.4	+	3	713	c.473A>C	c.(472-474)tAc>tCc	p.Y158S	CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	10						CTATGCATTTACATATGGGGA	0.408																																					p.Y158S		Atlas-SNP	.											.	GPR82	52	.	0			c.A473C						PASS	.						59.0	58.0	58.0					X																	41586752		2202	4299	6501	SO:0001583	missense	27197	exon3			GCATTTACATATG	AF411111	CCDS14259.1	Xp11.4	2012-08-21			ENSG00000171657	ENSG00000171657		"""GPCR / Class A : Orphans"""	4533	protein-coding gene	gene with protein product		300748				11574155	Standard	NM_080817		Approved		uc004dft.3	Q96P67	OTTHUMG00000021373	ENST00000302548.4:c.473A>C	X.37:g.41586752A>C	ENSP00000303549:p.Tyr158Ser	228.0	0.0	0		208.0	18.0	0.0865385	NM_080817	Q5VT13	Missense_Mutation	SNP	ENST00000302548.4	37	CCDS14259.1	.	.	.	.	.	.	.	.	.	.	A	4.819	0.152221	0.09185	.	.	ENSG00000171657	ENST00000302548	T	0.36340	1.26	5.73	2.98	0.34508	GPCR, rhodopsin-like superfamily (1);	0.469762	0.19219	N	0.119739	T	0.33411	0.0862	L	0.34521	1.04	0.09310	N	1	P	0.51933	0.949	P	0.54815	0.761	T	0.08289	-1.0729	10	0.22706	T	0.39	-4.4926	4.8507	0.13535	0.5399:0.0:0.0899:0.3702	.	158	Q96P67	GPR82_HUMAN	S	158	ENSP00000303549:Y158S	ENSP00000303549:Y158S	Y	+	2	0	GPR82	41471696	0.014000	0.17966	0.138000	0.22173	0.818000	0.46254	0.717000	0.25851	0.766000	0.33244	0.486000	0.48141	TAC	.	.	none		0.408	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817	
RBM10	8241	hgsc.bcm.edu	37	X	47045745	47045745	+	Missense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:47045745G>A	ENST00000377604.3	+	23	3368	c.2626G>A	c.(2626-2628)Ggc>Agc	p.G876S	RBM10_ENST00000329236.7_Missense_Mutation_p.G798S|RBM10_ENST00000345781.6_Missense_Mutation_p.G799S	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	876	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						AGAGGGCAGCGGCCTGGGCCG	0.647																																					p.G941S	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G2821A						PASS	.						56.0	53.0	54.0					X																	47045745		2199	4292	6491	SO:0001583	missense	8241	exon23			GGCAGCGGCCTGG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.2626G>A	X.37:g.47045745G>A	ENSP00000366829:p.Gly876Ser	167.0	0.0	0		204.0	16.0	0.0784314	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.006668	0.93287	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.80994	-1.44;-1.44;-1.44	5.53	5.53	0.82687	D111/G-patch (3);	0.000000	0.56097	D	0.000033	D	0.91442	0.7299	M	0.90425	3.115	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;0.998	D	0.93001	0.6423	10	0.87932	D	0	-22.4447	16.0209	0.80493	0.0:0.0:1.0:0.0	.	799;941;875;798;876	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	S	876;798;799	ENSP00000366829:G876S;ENSP00000328848:G798S;ENSP00000329659:G799S	ENSP00000328848:G798S	G	+	1	0	RBM10	46930689	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.359000	0.97115	2.471000	0.83476	0.600000	0.82982	GGC	.	.	none		0.647	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
PLCZ1	89869	hgsc.bcm.edu	37	12	18841114	18841114	+	Silent	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr12:18841114T>C	ENST00000538330.1	-	9	1227	c.846A>G	c.(844-846)tcA>tcG	p.S282S	PLCZ1_ENST00000435379.1_Silent_p.S305S|PLCZ1_ENST00000534932.1_5'UTR|PLCZ1_ENST00000541695.1_Silent_p.S363S|PLCZ1_ENST00000539875.1_Silent_p.S307S|PLCZ1_ENST00000447925.2_Silent_p.S498S|PLCZ1_ENST00000266505.7_Silent_p.S500S					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					CTTTGTTAGATGATGAATGAG	0.318																																					p.S500S		Atlas-SNP	.											.	PLCZ1	107	.	0			c.A1500G						PASS	.						94.0	103.0	100.0					12																	18841114		2203	4298	6501	SO:0001819	synonymous_variant	89869	exon13			GTTAGATGATGAA	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"""EF-hand domain containing"""	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.846A>G	12.37:g.18841114T>C		94.0	0.0	0		93.0	7.0	0.0752688	NM_033123		Silent	SNP	ENST00000538330.1	37		.	.	.	.	.	.	.	.	.	.	T	1.226	-0.625562	0.03610	.	.	ENSG00000139151	ENST00000536023	.	.	.	5.39	0.37	0.16160	.	.	.	.	.	T	0.21718	0.0523	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22977	-1.0201	4	.	.	.	.	2.5671	0.04785	0.1216:0.0984:0.3429:0.4371	.	.	.	.	V	70	.	.	I	-	1	0	PLCZ1	18732381	0.003000	0.15002	0.004000	0.12327	0.331000	0.28603	-0.103000	0.10940	0.407000	0.25591	0.260000	0.18958	ATC	.	.	none		0.318	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123	
ADRM1	11047	hgsc.bcm.edu	37	20	60878716	60878716	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:60878716T>G	ENST00000253003.2	+	2	138	c.92T>G	c.(91-93)aTg>aGg	p.M31R	RP11-157P1.4_ENST00000414042.1_RNA|ADRM1_ENST00000462554.1_3'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	31	Interaction with PSMD1.|PH.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GCGGGAAAGATGTCCCTGAAG	0.587																																					p.M31R		Atlas-SNP	.											.	ADRM1	28	.	0			c.T92G						PASS	.						79.0	84.0	82.0					20																	60878716		2203	4300	6503	SO:0001583	missense	11047	exon2			GAAAGATGTCCCT	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.92T>G	20.37:g.60878716T>G	ENSP00000253003:p.Met31Arg	36.0	0.0	0		37.0	7.0	0.189189	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.849175	0.71603	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.84051	0.5387	M	0.90145	3.09	0.80722	D	1	D;P	0.65815	0.995;0.935	D;D	0.76575	0.988;0.971	D	0.87579	0.2483	9	0.87932	D	0	-22.7347	13.6872	0.62524	0.0:0.0:0.0:1.0	.	31;31	B4DMP7;Q16186	.;ADRM1_HUMAN	R	31	.	ENSP00000253003:M31R	M	+	2	0	ADRM1	60312111	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	7.676000	0.84012	1.707000	0.51288	0.459000	0.35465	ATG	.	.	none		0.587	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
OR4C13	283092	hgsc.bcm.edu	37	11	49974680	49974680	+	Missense_Mutation	SNP	T	T	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr11:49974680T>A	ENST00000555099.1	+	1	738	c.706T>A	c.(706-708)Tct>Act	p.S236T		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						CGAAGCCCTCTCTACCTGTGT	0.463																																					p.S236T		Atlas-SNP	.											.	OR4C13	96	.	0			c.T706A						PASS	.						181.0	155.0	164.0					11																	49974680		2201	4296	6497	SO:0001583	missense	283092	exon1			GCCCTCTCTACCT	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"""GPCR / Class A : Olfactory receptors"""	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.706T>A	11.37:g.49974680T>A	ENSP00000452277:p.Ser236Thr	227.0	0.0	0		185.0	9.0	0.0486486	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	9.238	1.037466	0.19669	.	.	ENSG00000258817	ENST00000555099	T	0.00295	8.25	2.91	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000319	T	0.00695	0.0023	M	0.88031	2.925	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.25222	-1.0138	9	.	.	.	.	9.2733	0.37684	0.0:0.0:0.0:1.0	.	236	Q8NGP0	OR4CD_HUMAN	T	236	ENSP00000452277:S236T	.	S	+	1	0	OR4C13	49931256	0.000000	0.05858	0.955000	0.39395	0.029000	0.11900	0.475000	0.22164	1.342000	0.45619	0.156000	0.16432	TCT	.	.	none		0.463	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955	
C4orf48	401115	hgsc.bcm.edu	37	4	2044128	2044128	+	Missense_Mutation	SNP	C	C	T	rs570712	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr4:2044128C>T	ENST00000409860.1	+	2	201	c.50C>T	c.(49-51)cCg>cTg	p.P17L	C4orf48_ENST00000409248.4_Missense_Mutation_p.P50L|C4orf48_ENST00000382878.3_Missense_Mutation_p.P61L	NM_001141936.2	NP_001135408	Q5BLP8	CD048_HUMAN	chromosome 4 open reading frame 48	17				P -> L (in Ref. 4; AI929674). {ECO:0000305}.		extracellular region (GO:0005576)				kidney(1)|skin(2)	3						ccgccgccgccgctgctgctg	0.806													C|||	4972	0.992812	0.9728	1.0	5008	,	,		4692	1.0		1.0	False		,,,				2504	1.0				p.P50L		Atlas-SNP	.											.	C4orf48	4	.	0			c.C149T						PASS	.						1.0	1.0	1.0					4																	2044128		37	208	245	SO:0001583	missense	401115	exon2			CGCCGCCGCTGCT		CCDS47000.1, CCDS47000.2, CCDS54707.1	4p16.3	2012-09-03			ENSG00000243449	ENSG00000243449			34437	protein-coding gene	gene with protein product		614690				21287218	Standard	NM_001141936		Approved		uc021xkn.1	Q5BLP8	OTTHUMG00000154503	ENST00000409860.1:c.50C>T	4.37:g.2044128C>T	ENSP00000386528:p.Pro17Leu	0.0	0.0	.		7.0	7.0	1	NM_001168243	B6ZDN0|B7ZBI7|B7ZBI8	Missense_Mutation	SNP	ENST00000409860.1	37	CCDS47000.2	1880	0.8608058608058609	416	0.8455284552845529	285	0.787292817679558	530	0.9265734265734266	649	0.8562005277044855	C	0.045	-1.270959	0.01421	.	.	ENSG00000243449	ENST00000382878;ENST00000409248;ENST00000409860	.	.	.	2.86	-3.27	0.05048	.	0.685323	0.13031	U	0.419306	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.35151	-0.9800	7	0.02654	T	1	-1.1219	8.057	0.30610	0.0:0.3609:0.0:0.6391	rs570712	17;61	Q5BLP8;Q5BLP8-2	CD048_HUMAN;.	L	61;50;17	.	ENSP00000372331:P61L	P	+	2	0	C4orf48	2013926	0.197000	0.23362	0.016000	0.15963	0.431000	0.31685	1.890000	0.39728	-0.746000	0.04766	-0.450000	0.05554	CCG	C|0.139;T|0.861	0.861	strong		0.806	C4orf48-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335537.1	NM_001141936	
KPRP	448834	hgsc.bcm.edu	37	1	152733644	152733644	+	Missense_Mutation	SNP	C	C	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:152733644C>G	ENST00000606109.1	+	1	1608	c.1580C>G	c.(1579-1581)gCt>gGt	p.A527G	KPRP_ENST00000368773.1_Missense_Mutation_p.A527G			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	527						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACACCGAAGCTCCCTACTGT	0.602																																					p.A527G		Atlas-SNP	.											.	KPRP	152	.	0			c.C1580G						PASS	.						74.0	70.0	71.0					1																	152733644		2203	4300	6503	SO:0001583	missense	448834	exon2			CCGAAGCTCCCTA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1580C>G	1.37:g.152733644C>G	ENSP00000475216:p.Ala527Gly	93.0	0.0	0		83.0	6.0	0.0722892	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348734	0.24426	.	.	ENSG00000203786	ENST00000368773	T	0.12984	2.63	4.61	1.46	0.22682	.	0.519669	0.16240	N	0.223183	T	0.02083	0.0065	N	0.21194	0.64	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.46925	-0.9156	10	0.22706	T	0.39	-2.3812	4.8838	0.13692	0.0:0.5548:0.2368:0.2084	.	527	Q5T749	KPRP_HUMAN	G	527	ENSP00000357762:A527G	ENSP00000357762:A527G	A	+	2	0	KPRP	151000268	0.848000	0.29623	0.007000	0.13788	0.317000	0.28152	1.056000	0.30480	0.224000	0.20940	0.462000	0.41574	GCT	.	.	none		0.602	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
WDR53	348793	hgsc.bcm.edu	37	3	196281315	196281315	+	Missense_Mutation	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:196281315T>C	ENST00000332629.5	-	4	1411	c.844A>G	c.(844-846)Aca>Gca	p.T282A	WDR53_ENST00000433160.1_Missense_Mutation_p.T123A|WDR53_ENST00000429115.1_Missense_Mutation_p.T121A	NM_182627.1	NP_872433.1	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	282										breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		GTACGTTTTGTGGGACTCTTC	0.443																																					p.T282A		Atlas-SNP	.											.	WDR53	26	.	0			c.A844G						PASS	.						244.0	210.0	221.0					3																	196281315		2203	4300	6503	SO:0001583	missense	348793	exon4			GTTTTGTGGGACT	BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798		"""WD repeat domain containing"""	28786	protein-coding gene	gene with protein product		615110				12477932	Standard	NM_182627		Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000332629.5:c.844A>G	3.37:g.196281315T>C	ENSP00000328079:p.Thr282Ala	669.0	0.0	0		619.0	28.0	0.0452342	NM_182627	A0MNP1	Missense_Mutation	SNP	ENST00000332629.5	37	CCDS3318.1	.	.	.	.	.	.	.	.	.	.	T	0.841	-0.742019	0.03088	.	.	ENSG00000185798	ENST00000332629;ENST00000429115;ENST00000433160	T;T;T	0.72505	-0.66;1.24;1.24	5.67	1.29	0.21616	.	0.959404	0.08745	N	0.899979	T	0.47154	0.1430	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	10	0.14656	T	0.56	-7.5464	8.8373	0.35119	0.0:0.6094:0.0:0.3906	.	282	Q7Z5U6	WDR53_HUMAN	A	282;121;123	ENSP00000328079:T282A;ENSP00000396668:T121A;ENSP00000410677:T123A	ENSP00000328079:T282A	T	-	1	0	WDR53	197765712	0.000000	0.05858	0.008000	0.14137	0.027000	0.11550	0.693000	0.25497	0.229000	0.21039	0.528000	0.53228	ACA	.	.	none		0.443	WDR53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340689.1	NM_182627	
INTS3	65123	hgsc.bcm.edu	37	1	153741377	153741377	+	Missense_Mutation	SNP	T	T	G	rs372522734		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:153741377T>G	ENST00000318967.2	+	22	2821	c.2253T>G	c.(2251-2253)gaT>gaG	p.D751E	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Missense_Mutation_p.D545E|INTS3_ENST00000456435.1_Missense_Mutation_p.D545E|INTS3_ENST00000435409.2_Missense_Mutation_p.D751E	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	752					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGTTTCCAGATGAAACCTTGA	0.488																																					p.D751E		Atlas-SNP	.											.	INTS3	83	.	0			c.T2253G						PASS	.						93.0	89.0	90.0					1																	153741377		2203	4300	6503	SO:0001583	missense	65123	exon22			TCCAGATGAAACC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2253T>G	1.37:g.153741377T>G	ENSP00000318641:p.Asp751Glu	70.0	0.0	0		84.0	4.0	0.047619	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.979299	0.34942	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.46	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.34019	0.0883	N	0.10874	0.06	0.44085	D	0.996848	D;D;D	0.61697	0.99;0.984;0.99	D;D;D	0.75484	0.986;0.935;0.971	T	0.24728	-1.0152	9	0.19590	T	0.45	.	9.4306	0.38608	0.0:0.0845:0.0:0.9155	.	545;752;751	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	E	751;545;751;545	.	ENSP00000318641:D751E	D	+	3	2	INTS3	152008001	0.997000	0.39634	1.000000	0.80357	0.968000	0.65278	0.276000	0.18716	0.920000	0.36970	0.482000	0.46254	GAT	.	.	none		0.488	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
VMA21	203547	hgsc.bcm.edu	37	X	150573449	150573449	+	Silent	SNP	C	C	G	rs139323488	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:150573449C>G	ENST00000330374.6	+	3	330	c.225C>G	c.(223-225)gcC>gcG	p.A75A	VMA21_ENST00000370361.1_Silent_p.A130A|VMA21_ENST00000477649.1_3'UTR	NM_001017980.3	NP_001017980.1			VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	7						CAGTGGTCGCCGTCCATGTGG	0.458																																					p.A75A		Atlas-SNP	.											.	VMA21	17	.	0			c.C225G						PASS	.						137.0	108.0	118.0					X																	150573449		2203	4300	6503	SO:0001819	synonymous_variant	203547	exon3			GGTCGCCGTCCAT	AK096835	CCDS35430.1	Xq28	2014-09-17			ENSG00000160131	ENSG00000160131			22082	protein-coding gene	gene with protein product		300913	"""myopathy with excessive autophagy"""	MEAX		2892402, 10757644, 19379691	Standard	NM_001017980		Approved	XMEA	uc004feu.3	Q3ZAQ7	OTTHUMG00000024168	ENST00000330374.6:c.225C>G	X.37:g.150573449C>G		145.0	0.0	0		179.0	11.0	0.0614525	NM_001017980		Silent	SNP	ENST00000330374.6	37	CCDS35430.1																																																																																			C|0.996;T|0.004	.	alt		0.458	VMA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060876.1	NM_001017980	
FAM13C	220965	hgsc.bcm.edu	37	10	61022354	61022354	+	Missense_Mutation	SNP	G	G	A			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr10:61022354G>A	ENST00000373868.2	-	10	1163	c.1076C>T	c.(1075-1077)cCt>cTt	p.P359L	FAM13C_ENST00000419214.2_Intron|FAM13C_ENST00000442566.3_Missense_Mutation_p.P380L|FAM13C_ENST00000422313.2_Missense_Mutation_p.P359L|FAM13C_ENST00000277705.6_Missense_Mutation_p.P380L|FAM13C_ENST00000373867.3_Missense_Mutation_p.P276L|FAM13C_ENST00000435852.2_Missense_Mutation_p.P359L|FAM13C_ENST00000468840.2_Missense_Mutation_p.P276L	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	359								p.P359R(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CAGGTTTCTAGGTGGACCTTT	0.493																																					p.P359L		Atlas-SNP	.											FAM13C_ENST00000422313,NS,carcinoma,0,2	FAM13C	124	2	1	Substitution - Missense(1)	lung(1)	c.C1076T						PASS	.						89.0	89.0	89.0					10																	61022354		2203	4300	6503	SO:0001583	missense	220965	exon10			TTTCTAGGTGGAC	U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"""family with sequence similarity 13, member C1"""	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.1076C>T	10.37:g.61022354G>A	ENSP00000362975:p.Pro359Leu	190.0	0.0	0		159.0	10.0	0.0628931	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	G	8.792	0.930800	0.18131	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000468840;ENST00000435852;ENST00000422313	T;T;T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89;-0.89;-0.89	5.72	1.65	0.23941	.	0.704485	0.13552	N	0.379439	T	0.61035	0.2315	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.11235	0.003;0.001;0.004;0.001	B;B;B;B	0.14023	0.004;0.006;0.01;0.003	T	0.52719	-0.8538	10	0.48119	T	0.1	-0.0153	1.2001	0.01883	0.162:0.2361:0.3334:0.2684	.	359;276;359;359	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31	.;.;.;FA13C_HUMAN	L	276;359;380;380;276;359;359	ENSP00000362974:P276L;ENSP00000362975:P359L;ENSP00000395661:P380L;ENSP00000277705:P380L;ENSP00000423896:P276L;ENSP00000392302:P359L;ENSP00000400241:P359L	ENSP00000277705:P380L	P	-	2	0	FAM13C	60692360	0.287000	0.24315	0.110000	0.21437	0.648000	0.38561	0.848000	0.27710	0.306000	0.22856	0.563000	0.77884	CCT	.	.	none		0.493	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2		
ZNF607	84775	hgsc.bcm.edu	37	19	38189064	38189064	+	Missense_Mutation	SNP	A	A	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr19:38189064A>C	ENST00000355202.4	-	5	2563	c.1968T>G	c.(1966-1968)agT>agG	p.S656R	ZNF607_ENST00000395835.3_Missense_Mutation_p.S655R|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	656					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			GTTCATGGCTACTATTAAAAG	0.393																																					p.S656R		Atlas-SNP	.											.	ZNF607	82	.	0			c.T1968G						PASS	.						106.0	103.0	104.0					19																	38189064		2203	4300	6503	SO:0001583	missense	84775	exon5			ATGGCTACTATTA	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1968T>G	19.37:g.38189064A>C	ENSP00000347338:p.Ser656Arg	206.0	0.0	0		188.0	8.0	0.0425532	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	A	7.766	0.706483	0.15239	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.28069	1.63;1.63	1.83	-3.66	0.04489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11623	0.0283	N	0.11698	0.16	0.09310	N	1	B;B	0.26081	0.141;0.068	B;B	0.29077	0.098;0.062	T	0.26395	-1.0104	9	0.12430	T	0.62	.	0.6026	0.00747	0.2396:0.2281:0.3116:0.2206	.	656;655	Q96SK3;F5H141	ZN607_HUMAN;.	R	656;655	ENSP00000347338:S656R;ENSP00000438015:S655R	ENSP00000347338:S656R	S	-	3	2	ZNF607	42880904	0.000000	0.05858	0.000000	0.03702	0.929000	0.56500	-1.367000	0.02583	-2.253000	0.00698	0.260000	0.18958	AGT	.	.	none		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
RFC4	5984	hgsc.bcm.edu	37	3	186507948	186507948	+	Missense_Mutation	SNP	T	T	C			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:186507948T>C	ENST00000392481.2	-	10	1260	c.979A>G	c.(979-981)Atc>Gtc	p.I327V	RFC4_ENST00000296273.2_Missense_Mutation_p.I327V|RFC4_ENST00000433496.1_Missense_Mutation_p.I300V|SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	327					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		TTTTCTGTGATAATAGACTTC	0.353																																					p.I327V		Atlas-SNP	.											.	RFC4	54	.	0			c.A979G						PASS	.						107.0	103.0	105.0					3																	186507948		2203	4300	6503	SO:0001583	missense	5984	exon10			CTGTGATAATAGA		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.979A>G	3.37:g.186507948T>C	ENSP00000376272:p.Ile327Val	224.0	0.0	0		241.0	20.0	0.0829876	NM_181573	B4DM41|D3DNV2|Q6FHX7	Missense_Mutation	SNP	ENST00000392481.2	37	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.966155	0.53507	.	.	ENSG00000163918	ENST00000433496;ENST00000392481;ENST00000296273;ENST00000417876	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.85	5.85	0.93711	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56292	0.1975	M	0.81802	2.56	0.80722	D	1	B	0.16802	0.019	B	0.31614	0.133	T	0.57516	-0.7798	10	0.59425	D	0.04	-17.5765	14.1937	0.65656	0.0:0.0:0.0:1.0	.	327	P35249	RFC4_HUMAN	V	300;327;327;102	ENSP00000399769:I300V;ENSP00000376272:I327V;ENSP00000296273:I327V;ENSP00000401429:I102V	ENSP00000296273:I327V	I	-	1	0	RFC4	187990642	1.000000	0.71417	0.268000	0.24571	0.954000	0.61252	5.725000	0.68507	2.229000	0.72834	0.533000	0.62120	ATC	.	.	none		0.353	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
DSP	1832	hgsc.bcm.edu	37	6	7584037	7584037	+	Missense_Mutation	SNP	T	T	G			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:7584037T>G	ENST00000379802.3	+	24	6883	c.6542T>G	c.(6541-6543)gTc>gGc	p.V2181G	DSP_ENST00000418664.2_Missense_Mutation_p.V1582G	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2181	4.5 X 38 AA tandem repeats (Domain A).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AAAAAGAAGGTCAGTTACGTG	0.478																																					p.V2181G		Atlas-SNP	.											.	DSP	306	.	0			c.T6542G						PASS	.						103.0	101.0	102.0					6																	7584037		2203	4300	6503	SO:0001583	missense	1832	exon24			AGAAGGTCAGTTA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.6542T>G	6.37:g.7584037T>G	ENSP00000369129:p.Val2181Gly	69.0	0.0	0		57.0	6.0	0.105263	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.275748	0.40294	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.70749	-0.51;-0.51	5.37	5.37	0.77165	.	0.000000	0.53938	D	0.000058	T	0.62950	0.2470	L	0.55990	1.75	0.41567	D	0.988661	P;D	0.56521	0.925;0.976	P;B	0.46758	0.526;0.335	T	0.67078	-0.5761	10	0.46703	T	0.11	.	15.6695	0.77262	0.0:0.0:0.0:1.0	.	1629;2181	Q4LE79;P15924	.;DESP_HUMAN	G	2181;1582	ENSP00000369129:V2181G;ENSP00000396591:V1582G	ENSP00000369129:V2181G	V	+	2	0	DSP	7529036	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.250000	0.72435	2.178000	0.69098	0.533000	0.62120	GTC	.	.	none		0.478	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
VIT	5212	hgsc.bcm.edu	37	2	37035632	37035632	+	Silent	SNP	C	C	T			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:37035632C>T	ENST00000389975.3	+	14	1664	c.1362C>T	c.(1360-1362)aaC>aaT	p.N454N	VIT_ENST00000497382.1_Silent_p.N123N|VIT_ENST00000401530.1_Silent_p.N433N|VIT_ENST00000404084.1_Silent_p.N406N|VIT_ENST00000379241.3_Silent_p.N432N|VIT_ENST00000379242.3_Silent_p.N469N	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	454	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				GCAGAACAAACGGCTTCTACT	0.622																																					p.N469N		Atlas-SNP	.											.	VIT	138	.	0			c.C1407T						PASS	.						33.0	29.0	30.0					2																	37035632		2203	4300	6503	SO:0001819	synonymous_variant	5212	exon15			AACAAACGGCTTC	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1362C>T	2.37:g.37035632C>T		94.0	0.0	0		95.0	8.0	0.0842105	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			.	.	none		0.622	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
