#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
COL16A1	1307	hgsc.bcm.edu	37	1	32157042	32157042	+	Silent	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:32157042A>G	ENST00000373672.3	-	19	1890	c.1374T>C	c.(1372-1374)ccT>ccC	p.P458P	COL16A1_ENST00000373668.3_Silent_p.P458P|COL16A1_ENST00000271069.6_Silent_p.P458P	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	458	Triple-helical region 9 (COL9) with 3 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GTCCTATCCCAGGGGGTCCAG	0.657																																					p.P458P	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.T1374C						.						35.0	43.0	40.0					1																	32157042		1877	4093	5970	SO:0001819	synonymous_variant	1307	exon19			TATCCCAGGGGGT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1374T>C	chr1.hg19:g.32157042A>G		191.0	0.0		138.0	48.0	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.657	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
IFI44L	10964	hgsc.bcm.edu	37	1	79107135	79107135	+	Missense_Mutation	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:79107135A>G	ENST00000370751.5	+	8	1344	c.1165A>G	c.(1165-1167)Aaa>Gaa	p.K389E	IFI44L_ENST00000476521.1_3'UTR|IFI44L_ENST00000342282.3_Missense_Mutation_p.K131E	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	389					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GAATGTCCATAAAATGCTAGG	0.318																																					p.K389E		Atlas-SNP	.											.	IFI44L	93	.	0			c.A1165G						.																																			SO:0001583	missense	10964	exon8			GTCCATAAAATGC	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"""chromosome 1 open reading frame 29"""	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.1165A>G	chr1.hg19:g.79107135A>G	ENSP00000359787:p.Lys389Glu	98.0	0.0		111.0	6.0	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	hg19	CCDS687.2	.	.	.	.	.	.	.	.	.	.	A	6.120	0.390370	0.11581	.	.	ENSG00000137959	ENST00000370751;ENST00000342282	T;T	0.28895	3.16;1.59	4.11	-3.89	0.04193	.	2.356070	0.01429	N	0.014659	T	0.07369	0.0186	L	0.60455	1.87	0.09310	N	1	B	0.20550	0.046	B	0.15870	0.014	T	0.13791	-1.0496	10	0.11182	T	0.66	-0.0955	0.8403	0.01149	0.3049:0.3283:0.2061:0.1606	.	389	Q53G44	IF44L_HUMAN	E	389;131	ENSP00000359787:K389E;ENSP00000342833:K131E	ENSP00000342833:K131E	K	+	1	0	IFI44L	78879723	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.338000	0.07842	-0.408000	0.07565	0.456000	0.33151	AAA	.	.		0.318	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820	
COL11A1	1301	hgsc.bcm.edu	37	1	103455118	103455118	+	Missense_Mutation	SNP	C	C	A	rs387906611		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:103455118C>A	ENST00000370096.3	-	29	2662	c.2350G>T	c.(2350-2352)Ggt>Tgt	p.G784C	COL11A1_ENST00000358392.2_Missense_Mutation_p.G796C|COL11A1_ENST00000353414.4_Missense_Mutation_p.G745C|COL11A1_ENST00000512756.1_Missense_Mutation_p.G668C	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	784	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTGGAAAACCATCTTCACCC	0.294																																					p.G796C		Atlas-SNP	.											.	COL11A1	972	.	0			c.G2386T						.						59.0	63.0	62.0					1																	103455118		2203	4295	6498	SO:0001583	missense	1301	exon29			GAAAACCATCTTC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2350G>T	chr1.hg19:g.103455118C>A	ENSP00000359114:p.Gly784Cys	576.0	1.0		596.0	176.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.638621	0.87760	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.99637	-6.29;-6.29;-5.89;-5.89	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.99862	0.9935	H	0.98370	4.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96794	0.9584	10	0.87932	D	0	.	19.2483	0.93912	0.0:1.0:0.0:0.0	.	668;745;796;784	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	C	784;796;745;668	ENSP00000359114:G784C;ENSP00000351163:G796C;ENSP00000302551:G745C;ENSP00000426533:G668C	ENSP00000302551:G745C	G	-	1	0	COL11A1	103227706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.695000	0.74593	2.882000	0.98803	0.655000	0.94253	GGT	.	.		0.294	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
VAV3	10451	hgsc.bcm.edu	37	1	108138911	108138911	+	Missense_Mutation	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:108138911A>G	ENST00000370056.4	-	25	2547	c.2273T>C	c.(2272-2274)tTa>tCa	p.L758S	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Missense_Mutation_p.L162S|VAV3_ENST00000527011.1_Missense_Mutation_p.L758S|VAV3_ENST00000415432.2_Missense_Mutation_p.L198S	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	758	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.|Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.L758*(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AGTTGTATCTAAGGTTCTGAA	0.393																																					p.L758S		Atlas-SNP	.											VAV3,NS,carcinoma,0,1	VAV3	176	.	1	Substitution - Nonsense(1)	breast(1)	c.T2273C						.						161.0	152.0	155.0					1																	108138911		2203	4300	6503	SO:0001583	missense	10451	exon25			GTATCTAAGGTTC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.2273T>C	chr1.hg19:g.108138911A>G	ENSP00000359073:p.Leu758Ser	103.0	0.0		109.0	42.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534895	0.85812	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432	T;D;T;T	0.94687	1.43;-3.49;1.43;1.43	5.22	5.22	0.72569	SH2 motif (2);	0.000000	0.64402	D	0.000001	D	0.97717	0.9251	M	0.93328	3.405	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.992;0.997;1.0	D	0.98977	1.0803	10	0.87932	D	0	.	15.1068	0.72326	1.0:0.0:0.0:0.0	.	758;162;758;198	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3	.;.;VAV3_HUMAN;.	S	758;758;162;198	ENSP00000359073:L758S;ENSP00000432540:L758S;ENSP00000446404:L162S;ENSP00000394897:L198S	ENSP00000359073:L758S	L	-	2	0	VAV3	107940434	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.914000	0.75764	1.980000	0.57719	0.477000	0.44152	TTA	.	.		0.393	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
BCAN	63827	hgsc.bcm.edu	37	1	156616814	156616814	+	Missense_Mutation	SNP	C	C	T	rs115373136	byFrequency	TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:156616814C>T	ENST00000329117.5	+	3	649	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.R105W	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	105	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CGAGGCCTACCGGTTCCGCGT	0.682																																					p.R105W		Atlas-SNP	.											.	BCAN	174	.	0			c.C313T						.						47.0	35.0	39.0					1																	156616814		2203	4298	6501	SO:0001583	missense	63827	exon3			GCCTACCGGTTCC	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.313C>T	chr1.hg19:g.156616814C>T	ENSP00000331210:p.Arg105Trp	192.0	0.0		153.0	45.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.143221	0.57044	.	.	ENSG00000132692	ENST00000441358;ENST00000255029;ENST00000329117;ENST00000457777;ENST00000361588	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	4.61	2.47	0.30058	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000061	T	0.75042	0.3796	M	0.77616	2.38	0.38665	D	0.952163	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.972	T	0.79876	-0.1618	10	0.87932	D	0	-20.2388	12.8011	0.57586	0.3062:0.6938:0.0:0.0	.	105;105	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	W	105	ENSP00000392731:R105W;ENSP00000331210:R105W;ENSP00000389898:R105W;ENSP00000354925:R105W	ENSP00000255029:R105W	R	+	1	2	BCAN	154883438	0.000000	0.05858	1.000000	0.80357	0.530000	0.34684	-0.350000	0.07721	1.088000	0.41272	0.455000	0.32223	CGG	.	C|0.989;G|0.011		0.682	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
CNTN2	6900	hgsc.bcm.edu	37	1	205036323	205036323	+	Missense_Mutation	SNP	T	T	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:205036323T>G	ENST00000331830.4	+	16	2354	c.2070T>G	c.(2068-2070)atT>atG	p.I690M		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	690	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCAGCAACATTCTGGGCACTG	0.577																																					p.I690M	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.T2070G						.						84.0	85.0	85.0					1																	205036323		2203	4300	6503	SO:0001583	missense	6900	exon16			CAACATTCTGGGC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.2070T>G	chr1.hg19:g.205036323T>G	ENSP00000330633:p.Ile690Met	231.0	0.0		234.0	17.0	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395047	0.62066	.	.	ENSG00000184144	ENST00000331830	T	0.56941	0.43	5.61	3.72	0.42706	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000088	T	0.64294	0.2585	L	0.58669	1.825	0.44352	D	0.997242	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.984	T	0.62586	-0.6823	10	0.52906	T	0.07	.	8.6501	0.34029	0.0:0.7603:0.0:0.2397	.	690;581	Q02246;Q68DA2	CNTN2_HUMAN;.	M	690	ENSP00000330633:I690M	ENSP00000330633:I690M	I	+	3	3	CNTN2	203302946	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.021000	0.30040	0.704000	0.31869	-0.456000	0.05471	ATT	.	.		0.577	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
TTN	7273	hgsc.bcm.edu	37	2	179433556	179433556	+	Missense_Mutation	SNP	A	A	C	rs572569285		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr2:179433556A>C	ENST00000591111.1	-	276	72604	c.72380T>G	c.(72379-72381)cTt>cGt	p.L24127R	TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L16828R|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L23200R|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L16895R|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L16703R|TTN_ENST00000589042.1_Missense_Mutation_p.L25768R|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24127	Fibronectin type-III 75. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTCTAAAAAGATATTCTTC	0.418																																					p.L25768R		Atlas-SNP	.											.	TTN	18412	.	0			c.T77303G						.						94.0	93.0	93.0					2																	179433556		1881	4109	5990	SO:0001583	missense	7273	exon326			CTAAAAAGATATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72380T>G	chr2.hg19:g.179433556A>C	ENSP00000465570:p.Leu24127Arg	71.0	0.0		98.0	10.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.978	1.227375	0.22542	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.83	5.83	0.93111	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46249	0.1383	N	0.05608	-0.01	0.47698	D	0.999491	D;D;D;D	0.56521	0.976;0.976;0.976;0.976	P;P;P;P	0.52109	0.69;0.69;0.69;0.69	T	0.57423	-0.7814	9	0.87932	D	0	.	16.1893	0.81975	1.0:0.0:0.0:0.0	.	16703;16828;16895;24127	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	23200;16703;16895;16828;16701	ENSP00000343764:L23200R;ENSP00000434586:L16703R;ENSP00000340554:L16895R;ENSP00000352154:L16828R	ENSP00000340554:L16895R	L	-	2	0	TTN	179141802	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.887000	0.56197	2.217000	0.71921	0.528000	0.53228	CTT	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ALPPL2	251	hgsc.bcm.edu	37	2	233274402	233274402	+	Missense_Mutation	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr2:233274402G>T	ENST00000295453.3	+	11	1471	c.1419G>T	c.(1417-1419)gaG>gaT	p.E473D		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	473					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	GCGTGCAGGAGCAGACCTTCA	0.731																																					p.E473D		Atlas-SNP	.											.	ALPPL2	36	.	0			c.G1419T						.						16.0	19.0	18.0					2																	233274402		2186	4261	6447	SO:0001583	missense	251	exon11			GCAGGAGCAGACC	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.1419G>T	chr2.hg19:g.233274402G>T	ENSP00000295453:p.Glu473Asp	184.0	0.0		146.0	8.0	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	hg19	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	g	15.73	2.921168	0.52653	.	.	ENSG00000163286	ENST00000295453	D	0.96913	-4.17	2.54	1.61	0.23674	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.95918	0.8671	M	0.62209	1.925	0.48087	D	0.999588	P	0.47762	0.9	P	0.53649	0.731	D	0.94222	0.7468	10	0.87932	D	0	.	8.8221	0.35032	0.1214:0.0:0.8786:0.0	.	473	P10696	PPBN_HUMAN	D	473	ENSP00000295453:E473D	ENSP00000295453:E473D	E	+	3	2	ALPPL2	232982646	1.000000	0.71417	0.996000	0.52242	0.166000	0.22503	1.512000	0.35812	0.352000	0.24053	0.205000	0.17691	GAG	.	.		0.731	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
BRPF1	7862	hgsc.bcm.edu	37	3	9781391	9781391	+	Missense_Mutation	SNP	C	C	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr3:9781391C>G	ENST00000457855.1	+	2	1319	c.1308C>G	c.(1306-1308)ttC>ttG	p.F436L	BRPF1_ENST00000424362.1_Missense_Mutation_p.F436L|BRPF1_ENST00000302054.3_Missense_Mutation_p.F436L|BRPF1_ENST00000433861.2_Missense_Mutation_p.F436L|BRPF1_ENST00000383829.2_Missense_Mutation_p.F436L			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	436					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GCACCTCTTTCAGTGTCCGCA	0.597																																					p.F436L		Atlas-SNP	.											.	BRPF1	104	.	0			c.C1308G						.						51.0	48.0	49.0					3																	9781391		2203	4300	6503	SO:0001583	missense	7862	exon3			CTCTTTCAGTGTC	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.1308C>G	chr3.hg19:g.9781391C>G	ENSP00000410210:p.Phe436Leu	173.0	0.0		173.0	10.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240670	0.58995	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.16897	2.32;2.31;3.7;2.31;2.31	6.04	5.16	0.70880	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.19005	0.0456	L	0.32530	0.975	0.80722	D	1	P;B;B;P	0.44260	0.83;0.198;0.198;0.597	P;B;B;P	0.51582	0.674;0.155;0.108;0.656	T	0.06320	-1.0833	10	0.11794	T	0.64	.	10.5988	0.45354	0.0:0.853:0.0:0.147	.	436;436;436;436	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	L	436	ENSP00000402485:F436L;ENSP00000398863:F436L;ENSP00000373340:F436L;ENSP00000306297:F436L;ENSP00000410210:F436L	ENSP00000306297:F436L	F	+	3	2	BRPF1	9756391	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.811000	0.55620	1.539000	0.49286	0.561000	0.74099	TTC	.	.		0.597	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694	
TRA2B	6434	hgsc.bcm.edu	37	3	185644397	185644397	+	Silent	SNP	A	A	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr3:185644397A>T	ENST00000453386.2	-	2	437	c.162T>A	c.(160-162)tcT>tcA	p.S54S	TRA2B_ENST00000382191.4_Intron|TRA2B_ENST00000471134.1_5'Flank	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	54	Arg/Ser-rich (RS1 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						ACCTAGATTCAGATCGGGACC	0.478																																					p.S54S		Atlas-SNP	.											.	TRA2B	36	.	0			c.T162A						.						119.0	117.0	118.0					3																	185644397		2203	4300	6503	SO:0001819	synonymous_variant	6434	exon2			AGATTCAGATCGG	AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"""RNA binding motif (RRM) containing"""	10781	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 156"""	602719	"""splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"""	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.162T>A	chr3.hg19:g.185644397A>T		91.0	0.0		92.0	9.0	NM_004593	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Silent	SNP	ENST00000453386.2	hg19	CCDS33905.1																																																																																			.	.		0.478	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180592	57180592	+	Silent	SNP	T	T	G	rs386674634		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr4:57180592T>G	ENST00000504228.1	+	6	1029	c.924T>G	c.(922-924)cgT>cgG	p.R308R	KIAA1211_ENST00000264229.6_Silent_p.R308R|KIAA1211_ENST00000541073.1_Silent_p.R301R			Q6ZU35	K1211_HUMAN	KIAA1211	308	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GGAGGGAGCGTGAGGAGCGCG	0.736																																					p.R308R		Atlas-SNP	.											KIAA1211,NS,carcinoma,+2,2	KIAA1211	178	.	0			c.T924G						.						5.0	7.0	6.0					4																	57180592		1903	3760	5663	SO:0001819	synonymous_variant	57482	exon8			GGAGCGTGAGGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.924T>G	chr4.hg19:g.57180592T>G		136.0	0.0		130.0	31.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.		0.736	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
AMBN	258	hgsc.bcm.edu	37	4	71467282	71467282	+	Missense_Mutation	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr4:71467282A>G	ENST00000322937.6	+	6	545	c.442A>G	c.(442-444)Att>Gtt	p.I148V	AMBN_ENST00000449493.2_Missense_Mutation_p.I133V	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	148					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			TCAGCCTCCAATTCACCTGGG	0.532											OREG0016218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I148V		Atlas-SNP	.											.	AMBN	73	.	0			c.A442G						.						129.0	123.0	125.0					4																	71467282		2203	4300	6503	SO:0001583	missense	258	exon6			CCTCCAATTCACC	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.442A>G	chr4.hg19:g.71467282A>G	ENSP00000313809:p.Ile148Val	111.0	0.0	1130	104.0	6.0	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	hg19	CCDS3543.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.905229	0.00512	.	.	ENSG00000178522	ENST00000322937;ENST00000538728;ENST00000449493	T;T	0.32753	1.44;1.44	5.95	-3.55	0.04639	.	0.916713	0.09309	N	0.819802	T	0.09512	0.0234	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.33954	-0.9848	10	0.12103	T	0.63	-0.0492	1.8736	0.03214	0.4452:0.2415:0.2025:0.1107	.	148	Q9NP70	AMBN_HUMAN	V	148;148;133	ENSP00000313809:I148V;ENSP00000391234:I133V	ENSP00000313809:I148V	I	+	1	0	AMBN	71501871	0.000000	0.05858	0.057000	0.19452	0.040000	0.13550	-0.059000	0.11731	-0.325000	0.08577	-0.376000	0.06991	ATT	.	.		0.532	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
ABLIM3	22885	hgsc.bcm.edu	37	5	148617156	148617156	+	Missense_Mutation	SNP	G	G	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr5:148617156G>A	ENST00000506113.1	+	10	1516	c.1034G>A	c.(1033-1035)gGc>gAc	p.G345D	RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000356541.3_Intron|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.G345D|ABLIM3_ENST00000519549.1_3'UTR|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000309868.7_Missense_Mutation_p.G345D|ABLIM3_ENST00000326685.7_Intron|AC012613.2_ENST00000523176.1_RNA			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	345					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGAGATGTGGCTATGGAGAG	0.532																																					p.G345D		Atlas-SNP	.											.	ABLIM3	91	.	0			c.G1034A						.						134.0	133.0	134.0					5																	148617156		2203	4300	6503	SO:0001583	missense	22885	exon11			GATGTGGCTATGG	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1034G>A	chr5.hg19:g.148617156G>A	ENSP00000425394:p.Gly345Asp	113.0	0.0		105.0	11.0	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	hg19	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247128	0.59103	.	.	ENSG00000173210	ENST00000309868;ENST00000506113;ENST00000508983	T;T;T	0.52754	0.65;0.65;0.67	5.79	5.79	0.91817	.	0.153166	0.53938	D	0.000042	T	0.33876	0.0878	N	0.08118	0	0.80722	D	1	B	0.15930	0.015	B	0.15484	0.013	T	0.12243	-1.0555	10	0.54805	T	0.06	.	20.0313	0.97540	0.0:0.0:1.0:0.0	.	345	O94929	ABLM3_HUMAN	D	345	ENSP00000310309:G345D;ENSP00000425394:G345D;ENSP00000420855:G345D	ENSP00000310309:G345D	G	+	2	0	ABLIM3	148597349	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.889000	0.56212	2.746000	0.94184	0.655000	0.94253	GGC	.	.		0.532	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
TXNDC5	81567	hgsc.bcm.edu	37	6	7899894	7899894	+	Missense_Mutation	SNP	C	C	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:7899894C>A	ENST00000379757.4	-	3	471	c.434G>T	c.(433-435)gGc>gTc	p.G145V	TXNDC5_ENST00000473453.1_Missense_Mutation_p.G37V|TXNDC5_ENST00000539054.1_Missense_Mutation_p.G73V|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	145	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					AGCTTCTTGGCCTGGCTTGAA	0.448																																					p.G145V	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.G434T						.						87.0	84.0	85.0					6																	7899894		2203	4300	6503	SO:0001583	missense	81567	exon3			TCTTGGCCTGGCT	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"""Protein disulfide isomerases"""	21073	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 15"""		"""thioredoxin domain containing 5"""				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.434G>T	chr6.hg19:g.7899894C>A	ENSP00000369081:p.Gly145Val	68.0	0.0		78.0	17.0	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	hg19	CCDS4505.1	.	.	.	.	.	.	.	.	.	.	.	17.58	3.424782	0.62733	.	.	ENSG00000239264	ENST00000539054;ENST00000379757;ENST00000473453	T;T;T	0.56611	0.45;0.45;0.45	5.5	5.5	0.81552	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.144069	0.64402	D	0.000007	T	0.74854	0.3771	H	0.94183	3.505	0.80722	D	1	B;D	0.69078	0.218;0.997	B;D	0.70716	0.196;0.97	T	0.79897	-0.1609	10	0.51188	T	0.08	.	13.9999	0.64427	0.0:0.9276:0.0:0.0724	.	73;145	Q86UY0;Q8NBS9	.;TXND5_HUMAN	V	73;145;37	ENSP00000442453:G73V;ENSP00000369081:G145V;ENSP00000420784:G37V	ENSP00000442453:G73V	G	-	2	0	TXNDC5	7844893	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.763000	0.55257	2.735000	0.93741	0.655000	0.94253	GGC	.	.		0.448	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810	
ZNF318	24149	hgsc.bcm.edu	37	6	43305119	43305119	+	Missense_Mutation	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:43305119C>T	ENST00000361428.2	-	10	6694	c.6617G>A	c.(6616-6618)gGg>gAg	p.G2206E	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2206					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CTGTAATGGCCCCAACTCCAG	0.468																																					p.G2206E		Atlas-SNP	.											.	ZNF318	175	.	0			c.G6617A						.						83.0	73.0	76.0					6																	43305119		2203	4300	6503	SO:0001583	missense	24149	exon10			AATGGCCCCAACT	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.6617G>A	chr6.hg19:g.43305119C>T	ENSP00000354964:p.Gly2206Glu	100.0	0.0		91.0	8.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	C	11.80	1.745686	0.30955	.	.	ENSG00000171467	ENST00000361428	T	0.13901	2.55	5.66	3.89	0.44902	.	0.253773	0.28971	N	0.013545	T	0.10937	0.0267	L	0.32530	0.975	0.09310	N	0.999999	D	0.76494	0.999	D	0.72075	0.976	T	0.11518	-1.0584	10	0.37606	T	0.19	-7.2305	8.9849	0.35988	0.0:0.7649:0.0:0.2351	.	2206	Q5VUA4	ZN318_HUMAN	E	2206	ENSP00000354964:G2206E	ENSP00000354964:G2206E	G	-	2	0	ZNF318	43413097	0.036000	0.19791	0.891000	0.34965	0.511000	0.34104	0.340000	0.19892	0.750000	0.32877	0.655000	0.94253	GGG	.	.		0.468	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
AMD1	262	hgsc.bcm.edu	37	6	111196314	111196314	+	Silent	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:111196314A>G	ENST00000368885.3	+	1	342	c.6A>G	c.(4-6)gaA>gaG	p.E2E	AMD1_ENST00000451850.2_Silent_p.E2E|AMD1_ENST00000368882.3_5'UTR|AMD1_ENST00000368877.5_Silent_p.E2E|AMD1_ENST00000368876.1_5'Flank	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	2					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	CGGTGATGGAAGCTGCACATT	0.547																																					p.E2E		Atlas-SNP	.											.	AMD1	23	.	0			c.A6G						.						58.0	52.0	54.0					6																	111196314		2202	4300	6502	SO:0001819	synonymous_variant	262	exon1			GATGGAAGCTGCA	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"""S-adenosylmethionine decarboxylase 1"""				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.6A>G	chr6.hg19:g.111196314A>G		47.0	0.0		63.0	9.0	NM_001634	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Silent	SNP	ENST00000368885.3	hg19	CCDS5086.1																																																																																			.	.		0.547	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1		
MED23	9439	hgsc.bcm.edu	37	6	131941772	131941772	+	Missense_Mutation	SNP	T	T	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:131941772T>C	ENST00000368068.3	-	7	772	c.593A>G	c.(592-594)cAc>cGc	p.H198R	MED23_ENST00000354577.4_Missense_Mutation_p.H198R|MED23_ENST00000368060.3_Missense_Mutation_p.H198R|MED23_ENST00000403834.3_Missense_Mutation_p.H198R|MED23_ENST00000539158.1_Missense_Mutation_p.H198R|MED23_ENST00000368053.4_Missense_Mutation_p.H198R|MED23_ENST00000540546.1_Missense_Mutation_p.H198R|MED23_ENST00000368058.1_Missense_Mutation_p.H198R	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	198					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		ATTTACCCAGTGTGGAAGTTT	0.398																																					p.H198R		Atlas-SNP	.											.	MED23	112	.	0			c.A593G						.						50.0	51.0	51.0					6																	131941772		2203	4300	6503	SO:0001583	missense	9439	exon7			ACCCAGTGTGGAA	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.593A>G	chr6.hg19:g.131941772T>C	ENSP00000357047:p.His198Arg	252.0	0.0		252.0	32.0	NM_015979	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	hg19	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510387	0.64522	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000368053;ENST00000540546;ENST00000539158	T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.82171	0.4979	L	0.57536	1.79	0.80722	D	1	B;D;D	0.89917	0.435;1.0;0.999	B;D;D	0.77557	0.07;0.99;0.983	T	0.81986	-0.0681	10	0.39692	T	0.17	-5.9422	15.6489	0.77076	0.0:0.0:0.0:1.0	.	198;198;198	Q9ULK4-2;Q9ULK4;Q9ULK4-3	.;MED23_HUMAN;.	R	198	ENSP00000346588:H198R;ENSP00000357047:H198R;ENSP00000384536:H198R;ENSP00000357039:H198R;ENSP00000357037:H198R;ENSP00000357032:H198R;ENSP00000437818:H198R;ENSP00000445072:H198R	ENSP00000346588:H198R	H	-	2	0	MED23	131983465	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.698000	0.84413	2.117000	0.64856	0.402000	0.26972	CAC	.	.		0.398	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1		
CREB5	9586	hgsc.bcm.edu	37	7	28547252	28547252	+	Missense_Mutation	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr7:28547252C>T	ENST00000357727.2	+	4	578	c.188C>T	c.(187-189)aCg>aTg	p.T63M	CREB5_ENST00000396300.2_Missense_Mutation_p.T56M|CREB5_ENST00000409603.1_Missense_Mutation_p.T30M|CREB5_ENST00000396299.2_Missense_Mutation_p.T30M	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	63					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						CCGACCCCAACGAGATTCCTG	0.517																																					p.T63M		Atlas-SNP	.											.	CREB5	115	.	0			c.C188T						.						112.0	120.0	117.0					7																	28547252		2203	4300	6503	SO:0001583	missense	9586	exon4			CCCCAACGAGATT	L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"""basic leucine zipper proteins"""	16844	protein-coding gene	gene with protein product	"""cAMP response element binding protein CRE-Bpa"""					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.188C>T	chr7.hg19:g.28547252C>T	ENSP00000350359:p.Thr63Met	106.0	0.0		151.0	11.0	NM_182898	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	hg19	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881284	0.72294	.	.	ENSG00000146592	ENST00000396299;ENST00000424599;ENST00000357727;ENST00000396300;ENST00000409603	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.66117	0.2757	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.71087	-0.4694	10	0.87932	D	0	-18.3352	18.3806	0.90449	0.0:1.0:0.0:0.0	.	63	Q02930	CREB5_HUMAN	M	30;56;63;56;30	ENSP00000379593:T30M;ENSP00000394088:T56M;ENSP00000350359:T63M;ENSP00000379594:T56M;ENSP00000387197:T30M	ENSP00000350359:T63M	T	+	2	0	CREB5	28513777	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.450000	0.80656	2.650000	0.89964	0.655000	0.94253	ACG	.	.		0.517	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904	
ZNF727	442319	hgsc.bcm.edu	37	7	63537704	63537704	+	Missense_Mutation	SNP	G	G	T	rs375815259		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr7:63537704G>T	ENST00000550760.3	+	4	456	c.277G>T	c.(277-279)Gat>Tat	p.D93Y	RP11-3N2.13_ENST00000445978.1_RNA	NM_001159522.1	NP_001152994.1	A8MUV8	ZN727_HUMAN	zinc finger protein 727	93					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|skin(1)|stomach(1)|urinary_tract(1)	8						CGACATAAACGATTCATTTCA	0.388																																					p.D93Y		Atlas-SNP	.											.	ZNF727	35	.	0			c.G277T						.						63.0	54.0	57.0					7																	63537704		692	1591	2283	SO:0001583	missense	442319	exon4			ATAAACGATTCAT			7q11.21	2014-09-09	2014-09-09	2014-09-09	ENSG00000214652	ENSG00000214652		"""Zinc fingers, C2H2-type"", ""-"""	22785	pseudogene	pseudogene			"""zinc finger protein 727, pseudogene"""	ZNF727P			Standard	NM_001159522		Approved		uc011kdm.2	A8MUV8	OTTHUMG00000156536	ENST00000550760.3:c.277G>T	chr7.hg19:g.63537704G>T	ENSP00000447987:p.Asp93Tyr	151.0	0.0		188.0	19.0	NM_001159522		Missense_Mutation	SNP	ENST00000550760.3	hg19	CCDS55113.1	.	.	.	.	.	.	.	.	.	.	G	7.596	0.671815	0.14776	.	.	ENSG00000257482	ENST00000550760	T	0.04917	3.53	0.158	0.158	0.14942	.	.	.	.	.	T	0.08935	0.0221	M	0.88906	2.99	0.09310	N	1	P	0.36535	0.557	B	0.27262	0.078	T	0.20338	-1.0278	8	.	.	.	.	3.729	0.08485	1.0E-4:0.4867:0.5129:2.0E-4	.	93	A8MUV8	ZN727_HUMAN	Y	93	ENSP00000447987:D93Y	.	D	+	1	0	ZNF727	63175139	0.000000	0.05858	0.024000	0.17045	0.023000	0.10783	-0.320000	0.08028	0.202000	0.20498	0.205000	0.17691	GAT	.	.		0.388	ZNF727-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001159522	
AKR1B1	231	hgsc.bcm.edu	37	7	134136358	134136358	+	Nonsense_Mutation	SNP	C	C	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr7:134136358C>A	ENST00000285930.4	-	2	293	c.214G>T	c.(214-216)Gag>Tag	p.E72*	AKR1B1_ENST00000489022.1_5'UTR	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	72					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)			kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	ATGAAGAGCTCCTCACGCTTC	0.587																																					p.E72X		Atlas-SNP	.											AKR1B1,NS,carcinoma,0,1	AKR1B1	32	.	0			c.G214T						.						118.0	97.0	104.0					7																	134136358		2203	4300	6503	SO:0001587	stop_gained	231	exon2			AGAGCTCCTCACG	J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"""Aldo-keto reductases"""	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.214G>T	chr7.hg19:g.134136358C>A	ENSP00000285930:p.Glu72*	51.0	0.0		111.0	44.0	NM_001628	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Nonsense_Mutation	SNP	ENST00000285930.4	hg19	CCDS5831.1	.	.	.	.	.	.	.	.	.	.	C	37	6.060052	0.97246	.	.	ENSG00000085662	ENST00000285930	.	.	.	5.23	5.23	0.72850	.	0.193737	0.53938	D	0.000051	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.1639	0.89718	0.0:1.0:0.0:0.0	.	.	.	.	X	72	.	ENSP00000285930:E72X	E	-	1	0	AKR1B1	133786898	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	5.959000	0.70339	2.608000	0.88229	0.561000	0.74099	GAG	.	.		0.587	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628	
WRN	7486	hgsc.bcm.edu	37	8	30974005	30974005	+	Missense_Mutation	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr8:30974005G>T	ENST00000298139.5	+	20	2658	c.2409G>T	c.(2407-2409)agG>agT	p.R803S		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	803	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTAGCACAAGGAAAGACATTC	0.388			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.R803S	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G2409T						.						120.0	114.0	116.0					8																	30974005		2203	4300	6503	SO:0001583	missense	7486	exon20	Familial Cancer Database	WS, Adult Progeria	CACAAGGAAAGAC		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2409G>T	chr8.hg19:g.30974005G>T	ENSP00000298139:p.Arg803Ser	63.0	0.0		79.0	14.0	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330462	0.41297	.	.	ENSG00000165392	ENST00000298139	D	0.82433	-1.61	5.66	3.86	0.44501	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.94735	0.8301	H	0.99777	4.77	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94247	0.7490	10	0.87932	D	0	-19.7967	8.7149	0.34405	0.2295:0.0:0.7705:0.0	.	213;803	Q59F09;Q14191	.;WRN_HUMAN	S	803	ENSP00000298139:R803S	ENSP00000298139:R803S	R	+	3	2	WRN	31093547	1.000000	0.71417	0.596000	0.28811	0.013000	0.08279	2.176000	0.42500	1.392000	0.46585	0.557000	0.71058	AGG	.	.		0.388	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
KAT6A	7994	hgsc.bcm.edu	37	8	41812897	41812897	+	Silent	SNP	T	T	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr8:41812897T>C	ENST00000396930.3	-	10	2058	c.1515A>G	c.(1513-1515)caA>caG	p.Q505Q	KAT6A_ENST00000406337.1_Silent_p.Q505Q|KAT6A_ENST00000265713.2_Silent_p.Q505Q|KAT6A_ENST00000485568.1_Silent_p.Q505Q	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	505	Catalytic.|Interaction with PML.|Interaction with RUNX1-1.|MYST-type HAT.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GACAGCGGACTTGTGGATCAG	0.423																																					p.Q505Q		Atlas-SNP	.											.	.	.	.	0			c.A1515G						.						93.0	84.0	87.0					8																	41812897		2203	4300	6503	SO:0001819	synonymous_variant	7994	exon10			GCGGACTTGTGGA	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1515A>G	chr8.hg19:g.41812897T>C		94.0	0.0		108.0	13.0	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.423	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
DBH	1621	hgsc.bcm.edu	37	9	136501520	136501520	+	Silent	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr9:136501520C>T	ENST00000393056.2	+	1	39	c.27C>T	c.(25-27)agC>agT	p.S9S		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	9					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCTGGGCCAGCCTGCCCGGCC	0.677																																					p.S9S		Atlas-SNP	.											DBH,NS,carcinoma,0,1	DBH	86	.	0			c.C27T						.						32.0	34.0	33.0					9																	136501520		2203	4298	6501	SO:0001819	synonymous_variant	1621	exon1			GGCCAGCCTGCCC	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.27C>T	chr9.hg19:g.136501520C>T		281.0	0.0		229.0	16.0	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	hg19	CCDS6977.2																																																																																			.	.		0.677	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
WDR37	22884	hgsc.bcm.edu	37	10	1118109	1118109	+	Missense_Mutation	SNP	G	G	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:1118109G>C	ENST00000358220.1	+	2	158	c.14G>C	c.(13-15)aGc>aCc	p.S5T	WDR37_ENST00000263150.4_Missense_Mutation_p.S5T|WDR37_ENST00000381329.1_Missense_Mutation_p.S5T			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	5										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		CCCACAGAAAGCGCAAGTTGT	0.463																																					p.S5T		Atlas-SNP	.											.	WDR37	52	.	0			c.G14C						.						90.0	85.0	87.0					10																	1118109		2203	4300	6503	SO:0001583	missense	22884	exon2			CAGAAAGCGCAAG	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"""WD repeat domain containing"""	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.14G>C	chr10.hg19:g.1118109G>C	ENSP00000350954:p.Ser5Thr	112.0	0.0		107.0	8.0	NM_014023	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Missense_Mutation	SNP	ENST00000358220.1	hg19	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860172	0.51482	.	.	ENSG00000047056	ENST00000358220;ENST00000381329;ENST00000263150	T;T;T	0.73575	-0.07;-0.76;-0.07	5.58	5.58	0.84498	.	0.041495	0.85682	D	0.000000	T	0.67002	0.2847	L	0.31294	0.92	0.53005	D	0.999965	B;B;B	0.15141	0.001;0.001;0.012	B;B;B	0.12156	0.002;0.002;0.007	T	0.60214	-0.7307	10	0.38643	T	0.18	.	19.573	0.95428	0.0:0.0:1.0:0.0	.	5;5;5	A8K976;Q9Y2I8;E7EQ49	.;WDR37_HUMAN;.	T	5	ENSP00000350954:S5T;ENSP00000370730:S5T;ENSP00000263150:S5T	ENSP00000263150:S5T	S	+	2	0	WDR37	1108109	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.394000	0.79862	2.628000	0.89032	0.563000	0.77884	AGC	.	.		0.463	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023	
GPR158	57512	hgsc.bcm.edu	37	10	25888075	25888075	+	Missense_Mutation	SNP	T	T	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:25888075T>A	ENST00000376351.3	+	11	3879	c.3520T>A	c.(3520-3522)Tgg>Agg	p.W1174R	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1174					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GGTTTGTCCTTGGGAGTTTGA	0.448																																					p.W1174R		Atlas-SNP	.											.	GPR158	255	.	0			c.T3520A						.						47.0	51.0	50.0					10																	25888075		2203	4300	6503	SO:0001583	missense	57512	exon11			TGTCCTTGGGAGT	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3520T>A	chr10.hg19:g.25888075T>A	ENSP00000365529:p.Trp1174Arg	31.0	0.0		36.0	16.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.113571	0.56398	.	.	ENSG00000151025	ENST00000376351	T	0.80393	-1.37	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000002	D	0.85084	0.5616	L	0.34521	1.04	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.86915	0.2063	10	0.87932	D	0	.	16.0368	0.80635	0.0:0.0:0.0:1.0	.	1174	Q5T848	GP158_HUMAN	R	1174	ENSP00000365529:W1174R	ENSP00000365529:W1174R	W	+	1	0	GPR158	25928081	1.000000	0.71417	1.000000	0.80357	0.474000	0.32979	5.599000	0.67592	2.183000	0.69458	0.533000	0.62120	TGG	.	.		0.448	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
VSTM4	196740	hgsc.bcm.edu	37	10	50285295	50285295	+	Nonsense_Mutation	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:50285295C>T	ENST00000332853.4	-	4	626	c.603G>A	c.(601-603)tgG>tgA	p.W201*		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	201						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						ACACAGACTGCCAGACGATGA	0.522																																					p.W201X		Atlas-SNP	.											.	VSTM4	83	.	0			c.G603A						.						136.0	107.0	117.0					10																	50285295		2203	4300	6503	SO:0001587	stop_gained	196740	exon4			AGACTGCCAGACG	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"""Immunoglobulin superfamily / V-set domain containing"""	26470	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 72"""	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.603G>A	chr10.hg19:g.50285295C>T	ENSP00000331062:p.Trp201*	74.0	0.0		75.0	4.0	NM_001031746	B4DNI6|Q96MX7	Nonsense_Mutation	SNP	ENST00000332853.4	hg19	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	C	37	6.212578	0.97380	.	.	ENSG00000165633	ENST00000332853	.	.	.	5.4	2.2	0.27929	.	0.238309	0.43416	D	0.000562	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-3.5597	14.7508	0.69525	0.0:0.4146:0.5854:0.0	.	.	.	.	X	201	.	ENSP00000331062:W201X	W	-	3	0	VSTM4	49955301	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.766000	0.26560	0.700000	0.31782	0.655000	0.94253	TGG	.	.		0.522	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984	
KIAA1279	26128	hgsc.bcm.edu	37	10	70775761	70775761	+	Missense_Mutation	SNP	G	G	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:70775761G>C	ENST00000361983.4	+	7	1557	c.1455G>C	c.(1453-1455)atG>atC	p.M485I		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	485					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						ATGATATGATGGATTTGAAGG	0.393																																					p.M485I		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G1455C						.						69.0	65.0	66.0					10																	70775761		2203	4300	6503	SO:0001583	missense	26128	exon7			TATGATGGATTTG	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1455G>C	chr10.hg19:g.70775761G>C	ENSP00000354848:p.Met485Ile	139.0	0.0		116.0	6.0	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	hg19	CCDS7284.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.414728	0.83449	.	.	ENSG00000198954	ENST00000361983	T	0.47528	0.84	5.63	5.63	0.86233	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.56992	0.2023	M	0.68952	2.095	0.80722	D	1	P	0.49253	0.921	P	0.47251	0.542	T	0.56353	-0.7993	10	0.42905	T	0.14	-3.0587	20.0572	0.97657	0.0:0.0:1.0:0.0	.	485	Q96EK5	KBP_HUMAN	I	485	ENSP00000354848:M485I	ENSP00000354848:M485I	M	+	3	0	KIAA1279	70445767	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.777000	0.99008	2.826000	0.97356	0.655000	0.94253	ATG	.	.		0.393	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634	
C10orf12	26148	hgsc.bcm.edu	37	10	98741959	98741959	+	Missense_Mutation	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:98741959A>G	ENST00000286067.2	+	1	919	c.812A>G	c.(811-813)gAc>gGc	p.D271G		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	271										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GGAGGTGGAGACGTTTCACCT	0.522																																					p.D271G		Atlas-SNP	.											.	C10orf12	94	.	0			c.A812G						.						86.0	88.0	87.0					10																	98741959		2203	4300	6503	SO:0001583	missense	26148	exon1			GTGGAGACGTTTC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.812A>G	chr10.hg19:g.98741959A>G	ENSP00000286067:p.Asp271Gly	130.0	0.0		125.0	7.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	A	0.177	-1.065558	0.01934	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.08282	3.11	6.05	2.36	0.29203	.	0.554792	0.15939	N	0.237297	T	0.04952	0.0133	L	0.27053	0.805	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.09377	0.004;0.004	T	0.38628	-0.9652	10	0.33940	T	0.23	-5.3828	1.9858	0.03436	0.482:0.2682:0.1206:0.1292	.	105;271	A0PJI9;Q8N655	.;CJ012_HUMAN	G	271;105	ENSP00000286067:D271G	ENSP00000286067:D271G	D	+	2	0	C10orf12	98731949	.	.	0.004000	0.12327	0.077000	0.17291	.	.	0.477000	0.27464	0.533000	0.62120	GAC	.	.		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118351992	118351992	+	Missense_Mutation	SNP	G	G	T	rs141478509		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:118351992G>T	ENST00000528052.1	+	4	340	c.269G>T	c.(268-270)cGg>cTg	p.R90L	PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.R90L|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.R90L|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.R90L|PNLIPRP1_ENST00000480870.2_3'UTR			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	90					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		AGAAAGACCCGGTTCATCATC	0.493																																					p.R90L		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G269T						.						128.0	126.0	127.0					10																	118351992		2203	4300	6503	SO:0001583	missense	5407	exon4			AGACCCGGTTCAT	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.269G>T	chr10.hg19:g.118351992G>T	ENSP00000433933:p.Arg90Leu	96.0	0.0		90.0	22.0	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	hg19	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726545	0.48833	.	.	ENSG00000187021	ENST00000531984;ENST00000358834;ENST00000528052;ENST00000442761;ENST00000530319;ENST00000527980;ENST00000471549;ENST00000534537	D;D;D;D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	5.21	4.3	0.51218	Lipase, N-terminal (1);	0.000000	0.64402	D	0.000003	D	0.95956	0.8683	H	0.96080	3.765	0.40664	D	0.982154	D;D	0.89917	1.0;0.994	D;D	0.77557	0.99;0.914	D	0.97114	0.9806	10	0.87932	D	0	-7.899	12.9869	0.58596	0.0801:0.0:0.9199:0.0	.	90;90	P54315;P54315-2	LIPR1_HUMAN;.	L	90	ENSP00000436123:R90L;ENSP00000351695:R90L;ENSP00000433933:R90L;ENSP00000400963:R90L;ENSP00000437263:R90L;ENSP00000433785:R90L;ENSP00000431207:R90L;ENSP00000434159:R90L	ENSP00000351695:R90L	R	+	2	0	PNLIPRP1	118341982	0.988000	0.35896	0.908000	0.35775	0.192000	0.23643	5.700000	0.68318	1.326000	0.45319	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.493	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
CPSF7	79869	hgsc.bcm.edu	37	11	61183611	61183611	+	Missense_Mutation	SNP	T	T	C	rs143271041		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:61183611T>C	ENST00000394888.4	-	6	1103	c.931A>G	c.(931-933)Atg>Gtg	p.M311V	CPSF7_ENST00000448745.1_Missense_Mutation_p.M302V|CPSF7_ENST00000340437.4_Missense_Mutation_p.M354V|CPSF7_ENST00000439958.3_Missense_Mutation_p.M302V	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	311	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GAGGCCTTCATGTAAGTATCT	0.517																																					p.M354V		Atlas-SNP	.											.	CPSF7	46	.	0			c.A1060G						.	T	VAL/MET,VAL/MET,VAL/MET	0,4404		0,0,2202	58.0	65.0	62.0		931,904,1060	5.6	1.0	11	dbSNP_134	62	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense,missense	CPSF7	NM_001136040.2,NM_001142565.1,NM_024811.3	21,21,21	0,1,6497	CC,CT,TT		0.0116,0.0,0.0077	benign,benign,benign	311/472,302/463,354/515	61183611	1,12995	2202	4296	6498	SO:0001583	missense	79869	exon6			CCTTCATGTAAGT		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"""RNA binding motif (RRM) containing"""	30098	protein-coding gene	gene with protein product	"""pre mRNA cleavage factor I, 59 kDa subunit"", ""cleavage factor Im complex 59 kDa subunit"""					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.931A>G	chr11.hg19:g.61183611T>C	ENSP00000378352:p.Met311Val	91.0	0.0		62.0	10.0	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.398025	0.25205	0.0	1.16E-4	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000544147;ENST00000477890	D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09;-2.09	5.61	5.61	0.85477	.	0.461453	0.25383	N	0.031071	T	0.70605	0.3243	N	0.03608	-0.345	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.10450	0.002;0.002;0.002;0.005	T	0.66360	-0.5943	10	0.16896	T	0.51	-4.9219	10.9315	0.47220	0.0:0.0747:0.0:0.9253	.	302;311;354;302	B4DGF8;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	V	354;311;302;302;77;235	ENSP00000345412:M354V;ENSP00000378352:M311V;ENSP00000397203:M302V;ENSP00000407394:M302V;ENSP00000437860:M235V	ENSP00000345412:M354V	M	-	1	0	CPSF7	60940187	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.786000	0.47790	2.126000	0.65437	0.528000	0.53228	ATG	.	T|1.000;C|0.000		0.517	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811	
CARNS1	57571	hgsc.bcm.edu	37	11	67191670	67191670	+	Missense_Mutation	SNP	G	G	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:67191670G>A	ENST00000307823.3	+	9	2534	c.2082G>A	c.(2080-2082)atG>atA	p.M694I	CARNS1_ENST00000531040.1_Missense_Mutation_p.M791I|CARNS1_ENST00000423745.2_Missense_Mutation_p.M694I|CARNS1_ENST00000445895.2_Missense_Mutation_p.M817I	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	694	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						ACCCCCGCATGGGTGGCTTCT	0.617																																					p.M817I		Atlas-SNP	.											.	CARNS1	60	.	0			c.G2451A						.						35.0	39.0	38.0					11																	67191670		2131	4238	6369	SO:0001583	missense	57571	exon10			CCGCATGGGTGGC		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.2082G>A	chr11.hg19:g.67191670G>A	ENSP00000308268:p.Met694Ile	156.0	0.0		114.0	31.0	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	hg19	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.088690	0.76756	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.54	5.54	0.83059	ATP-grasp fold (1);ATP-grasp fold, DUF201-type (1);ATP-grasp fold, subdomain 2 (1);	0.144148	0.46145	D	0.000306	T	0.52677	0.1749	M	0.66297	2.02	0.46609	D	0.999121	P;P	0.51791	0.948;0.899	P;P	0.60117	0.869;0.73	T	0.51779	-0.8662	10	0.59425	D	0.04	-41.5132	18.2385	0.89958	0.0:0.0:1.0:0.0	.	694;833	A5YM72;A5YM72-3	CRNS1_HUMAN;.	I	791;694;791;694;817	ENSP00000431670:M791I;ENSP00000308268:M694I;ENSP00000401519:M694I;ENSP00000389009:M817I	ENSP00000308268:M694I	M	+	3	0	CARNS1	66948246	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.860000	0.75473	2.614000	0.88457	0.543000	0.68304	ATG	.	.		0.617	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
TYR	7299	hgsc.bcm.edu	37	11	88924399	88924399	+	Silent	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:88924399C>T	ENST00000263321.5	+	2	1351	c.849C>T	c.(847-849)aaC>aaT	p.N283N	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	283					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	AGGAGTACAACAGCCATCAGT	0.483																																					p.N283N		Atlas-SNP	.											.	TYR	130	.	0			c.C849T						.						133.0	121.0	125.0					11																	88924399		2201	4299	6500	SO:0001819	synonymous_variant	7299	exon2			GTACAACAGCCAT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.849C>T	chr11.hg19:g.88924399C>T		141.0	0.0		167.0	55.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Silent	SNP	ENST00000263321.5	hg19	CCDS8284.1																																																																																			.	.		0.483	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
SNX19	399979	hgsc.bcm.edu	37	11	130773191	130773191	+	Missense_Mutation	SNP	C	C	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:130773191C>A	ENST00000265909.4	-	8	3101	c.2532G>T	c.(2530-2532)atG>atT	p.M844I	SNX19_ENST00000530356.1_Missense_Mutation_p.M224I|SNX19_ENST00000528555.1_Missense_Mutation_p.M224I|SNX19_ENST00000534726.1_Missense_Mutation_p.M84I|SNX19_ENST00000545537.1_Missense_Mutation_p.M84I|SNX19_ENST00000539184.1_Missense_Mutation_p.M287I|SNX19_ENST00000533318.1_5'UTR	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	844					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GAAACTTTTGCATGTTTTCGG	0.448																																					p.M844I		Atlas-SNP	.											.	SNX19	84	.	0			c.G2532T						.						139.0	123.0	129.0					11																	130773191		2201	4297	6498	SO:0001583	missense	399979	exon8			CTTTTGCATGTTT	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2532G>T	chr11.hg19:g.130773191C>A	ENSP00000265909:p.Met844Ile	129.0	0.0		123.0	5.0	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	C	7.853	0.724442	0.15439	.	.	ENSG00000120451	ENST00000265909;ENST00000534726;ENST00000545537;ENST00000528555;ENST00000530356;ENST00000539184	T;T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86;1.86	5.77	3.91	0.45181	Sorting nexin, C-terminal (1);	0.297494	0.47455	D	0.000229	T	0.13200	0.0320	N	0.17082	0.46	0.39660	D	0.9706	B;B	0.09022	0.002;0.001	B;B	0.14023	0.002;0.01	T	0.09292	-1.0681	10	0.08599	T	0.76	-6.4731	9.3858	0.38342	0.0:0.7375:0.1267:0.1358	.	287;844	F5H5D1;Q92543	.;SNX19_HUMAN	I	844;84;84;224;224;287	ENSP00000265909:M844I;ENSP00000433699:M84I;ENSP00000437982:M84I;ENSP00000435122:M224I;ENSP00000432307:M224I;ENSP00000443480:M287I	ENSP00000265909:M844I	M	-	3	0	SNX19	130278401	0.997000	0.39634	1.000000	0.80357	0.964000	0.63967	0.339000	0.19875	0.905000	0.36596	0.655000	0.94253	ATG	.	.		0.448	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
CS	1431	hgsc.bcm.edu	37	12	56667010	56667010	+	Missense_Mutation	SNP	T	T	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr12:56667010T>C	ENST00000351328.3	-	11	1449	c.1259A>G	c.(1258-1260)tAc>tGc	p.Y420C	CS_ENST00000548567.1_Missense_Mutation_p.Y354C|CS_ENST00000542324.2_Missense_Mutation_p.Y407C	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	420					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		CAGGACCGTGTAGTAATTCAT	0.478																																					p.Y420C		Atlas-SNP	.											.	CS	44	.	0			c.A1259G						.						97.0	88.0	91.0					12																	56667010		2203	4300	6503	SO:0001583	missense	1431	exon11			ACCGTGTAGTAAT		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.1259A>G	chr12.hg19:g.56667010T>C	ENSP00000342056:p.Tyr420Cys	174.0	0.0		152.0	34.0	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	hg19	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056042	0.76074	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000548746;ENST00000542324	.	.	.	5.33	5.33	0.75918	Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.88362	0.6416	H	0.97829	4.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.996	D	0.92482	0.5993	9	0.87932	D	0	-9.2794	14.6005	0.68438	0.0:0.0:0.0:1.0	.	407;375;420	B4DJV2;B3KTN4;O75390	.;.;CISY_HUMAN	C	354;420;93;407	.	ENSP00000342056:Y420C	Y	-	2	0	CS	54953277	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.277000	0.78572	2.137000	0.66172	0.528000	0.53228	TAC	.	.		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33109968	33109968	+	Missense_Mutation	SNP	T	T	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:33109968T>A	ENST00000267068.3	-	2	1361	c.1197A>T	c.(1195-1197)aaA>aaT	p.K399N	N4BP2L2_ENST00000446957.2_Missense_Mutation_p.K399N|N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	399					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ACTTCTGCAATTTATTTAACT	0.373																																					p.K399N		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.A1197T						.						90.0	90.0	90.0					13																	33109968		2203	4300	6503	SO:0001583	missense	10443	exon2			CTGCAATTTATTT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.1197A>T	chr13.hg19:g.33109968T>A	ENSP00000267068:p.Lys399Asn	90.0	0.0		92.0	5.0	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	hg19	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175795	0.38413	.	.	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.47528	0.84;0.85;0.84	5.08	2.67	0.31697	.	.	.	.	.	T	0.43634	0.1256	L	0.31157	0.91	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.56278	0.795;0.795	T	0.23190	-1.0195	9	0.33940	T	0.23	-23.4899	5.8979	0.18949	0.2751:0.0753:0.0:0.6497	.	399;399	D6R968;Q92802	.;N42L2_HUMAN	N	399	ENSP00000394239:K399N;ENSP00000423362:K399N;ENSP00000267068:K399N	ENSP00000267068:K399N	K	-	3	2	N4BP2L2	32007968	0.985000	0.35326	1.000000	0.80357	0.992000	0.81027	0.566000	0.23593	0.991000	0.38814	0.528000	0.53228	AAA	.	.		0.373	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887	
SPG20	23111	hgsc.bcm.edu	37	13	36905735	36905735	+	Splice_Site	SNP	T	T	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:36905735T>C	ENST00000451493.1	-	3	1028		c.e3-2		SPG20_ENST00000438666.2_Splice_Site|SPG20_ENST00000495510.1_Splice_Site|SPG20_ENST00000494062.2_Splice_Site|SPG20_ENST00000355182.4_Splice_Site	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)						abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		GTCACAAACCTGAAAGGATTC	0.308																																					.		Atlas-SNP	.											.	SPG20	87	.	0			c.811-2A>G						.						43.0	43.0	43.0					13																	36905735		2203	4300	6503	SO:0001630	splice_region_variant	23111	exon4			CAAACCTGAAAGG	AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"""spartin"""	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.811-2A>G	chr13.hg19:g.36905735T>C		83.0	0.0		92.0	30.0	NM_015087	O60349|Q86Y67|Q9H1T2|Q9H1T3	Splice_Site	SNP	ENST00000451493.1	hg19	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586730	0.46110	.	.	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	.	.	.	5.69	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0141	0.53303	0.1296:0.0:0.0:0.8704	.	.	.	.	.	-1	.	.	.	-	.	.	SPG20	35803735	1.000000	0.71417	0.818000	0.32626	0.612000	0.37316	7.283000	0.78640	0.957000	0.37930	0.459000	0.35465	.	.	.		0.308	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2		Intron
POSTN	10631	hgsc.bcm.edu	37	13	38153242	38153242	+	Missense_Mutation	SNP	A	A	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:38153242A>G	ENST00000379747.4	-	14	1925	c.1808T>C	c.(1807-1809)cTg>cCg	p.L603P	POSTN_ENST00000379742.4_Missense_Mutation_p.L603P|POSTN_ENST00000379743.4_Missense_Mutation_p.L603P|POSTN_ENST00000541481.1_Missense_Mutation_p.L603P|POSTN_ENST00000541179.1_Missense_Mutation_p.L603P|POSTN_ENST00000379749.4_Missense_Mutation_p.L603P	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	603	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TTCATTCACCAGAAGTGTATC	0.308																																					p.L603P		Atlas-SNP	.											.	POSTN	161	.	0			c.T1808C						.						81.0	73.0	76.0					13																	38153242		2201	4297	6498	SO:0001583	missense	10631	exon14			TTCACCAGAAGTG	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1808T>C	chr13.hg19:g.38153242A>G	ENSP00000369071:p.Leu603Pro	107.0	0.0		154.0	21.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	hg19	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.521274	0.44866	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	5.23	5.23	0.72850	FAS1 domain (5);	0.282386	0.32533	N	0.005968	D	0.93625	0.7964	M	0.73598	2.24	0.80722	D	1	D;P;P;P;D;P;P	0.54601	0.96;0.951;0.86;0.915;0.967;0.731;0.86	P;P;P;P;P;P;P	0.58077	0.832;0.742;0.723;0.635;0.67;0.477;0.723	D	0.93060	0.6473	10	0.37606	T	0.19	.	15.1173	0.72413	1.0:0.0:0.0:0.0	.	603;603;603;603;603;603;603	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	P	603	ENSP00000437959:L603P;ENSP00000369073:L603P;ENSP00000369071:L603P;ENSP00000369067:L603P;ENSP00000369066:L603P;ENSP00000437953:L603P	ENSP00000369066:L603P	L	-	2	0	POSTN	37051242	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.294000	0.72738	1.971000	0.57363	0.383000	0.25322	CTG	.	.		0.308	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
COL4A2	1284	hgsc.bcm.edu	37	13	111125290	111125290	+	Nonsense_Mutation	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:111125290C>T	ENST00000360467.5	+	29	2524	c.2218C>T	c.(2218-2220)Cga>Tga	p.R740*		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	740	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CATAGGACCCCGAGGATCCAA	0.592																																					p.R740X		Atlas-SNP	.											.	COL4A2	178	.	0			c.C2218T						.						9.0	9.0	9.0					13																	111125290		1800	4036	5836	SO:0001587	stop_gained	1284	exon29			GGACCCCGAGGAT	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.2218C>T	chr13.hg19:g.111125290C>T	ENSP00000353654:p.Arg740*	207.0	0.0		198.0	14.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Nonsense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	C	42	9.381156	0.99155	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	.	.	.	5.37	4.43	0.53597	.	0.000000	0.43747	D	0.000533	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	13.9817	0.64308	0.2362:0.7638:0.0:0.0	.	.	.	.	X	740	.	ENSP00000257309:R740X	R	+	1	2	COL4A2	109923291	0.995000	0.38212	1.000000	0.80357	0.854000	0.48673	0.941000	0.29005	2.516000	0.84829	0.563000	0.77884	CGA	.	.		0.592	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
PSMC6	5706	hgsc.bcm.edu	37	14	53175062	53175062	+	Nonsense_Mutation	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr14:53175062G>T	ENST00000606149.1	+	2	137	c.121G>T	c.(121-123)Gaa>Taa	p.E41*	PSMC6_ENST00000445930.2_Nonsense_Mutation_p.E55*	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	41					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					CAAGCAGTATGAAAAGTCTGA	0.363																																					p.E55X		Atlas-SNP	.											.	PSMC6	71	.	0			c.G163T						.						112.0	110.0	111.0					14																	53175062		2203	4300	6503	SO:0001587	stop_gained	5706	exon2			CAGTATGAAAAGT		CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.121G>T	chr14.hg19:g.53175062G>T	ENSP00000475721:p.Glu41*	147.0	0.0		132.0	42.0	NM_002806	B2R975|P49719|Q6IBU3|Q92524	Nonsense_Mutation	SNP	ENST00000606149.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.0|27.0	4.788983|4.788983	0.90367|0.90367	.|.	.|.	ENSG00000100519|ENSG00000100519	ENST00000445930|ENST00000556813	.|.	.|.	.|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.25106|.	T|.	0.35|.	.|.	19.0331|19.0331	0.92965|0.92965	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	55|40	.|.	ENSP00000401802:E55X|.	E|X	+|+	1|2	0|2	PSMC6|PSMC6	52244812|52244812	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	9.378000|9.378000	0.97191|0.97191	2.570000|2.570000	0.86706|0.86706	0.561000|0.561000	0.74099|0.74099	GAA|TGA	.	.		0.363	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806	
GCNT3	9245	hgsc.bcm.edu	37	15	59911450	59911450	+	Missense_Mutation	SNP	G	G	A	rs142393489		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr15:59911450G>A	ENST00000396065.1	+	3	1461	c.1013G>A	c.(1012-1014)cGt>cAt	p.R338H	GCNT3_ENST00000560585.1_Missense_Mutation_p.R338H	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	338					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACCCTTCAGCGTGCACGGTGG	0.507																																					p.R338H		Atlas-SNP	.											GCNT3,NS,carcinoma,+1,1	GCNT3	42	.	0			c.G1013A						.						120.0	111.0	114.0					15																	59911450		2190	4290	6480	SO:0001583	missense	9245	exon3			TTCAGCGTGCACG	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.1013G>A	chr15.hg19:g.59911450G>A	ENSP00000379377:p.Arg338His	109.0	0.0		135.0	7.0	NM_004751		Missense_Mutation	SNP	ENST00000396065.1	hg19	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.991162	0.93106	.	.	ENSG00000140297	ENST00000396065	T	0.11277	2.79	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.27054	-1.0085	10	0.49607	T	0.09	.	19.4741	0.94979	0.0:0.0:1.0:0.0	.	338	O95395	GCNT3_HUMAN	H	338	ENSP00000379377:R338H	ENSP00000379377:R338H	R	+	2	0	GCNT3	57698742	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	9.869000	0.99810	2.595000	0.87683	0.655000	0.94253	CGT	.	G|1.000;C|0.000		0.507	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751	
TBL3	10607	hgsc.bcm.edu	37	16	2025894	2025894	+	Missense_Mutation	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:2025894G>T	ENST00000568546.1	+	11	1201	c.1073G>T	c.(1072-1074)tGc>tTc	p.C358F		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	358					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AATAGCCCCTGCCTAAAAGTG	0.637																																					p.C358F	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.G1073T						.						70.0	68.0	69.0					16																	2025894		2198	4300	6498	SO:0001583	missense	10607	exon11			GCCCCTGCCTAAA	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1073G>T	chr16.hg19:g.2025894G>T	ENSP00000454836:p.Cys358Phe	209.0	0.0		113.0	18.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.465845	0.43839	.	.	ENSG00000183751	ENST00000332704	.	.	.	4.75	3.78	0.43462	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.715221	0.13405	N	0.390350	T	0.31451	0.0797	N	0.22421	0.69	0.40625	D	0.981806	B;B	0.30439	0.001;0.279	B;B	0.27608	0.0;0.081	T	0.13791	-1.0496	9	0.15499	T	0.54	-14.1595	5.077	0.14636	0.289:0.0:0.711:0.0	.	120;358	A0JLS5;Q12788	.;TBL3_HUMAN	F	358	.	ENSP00000331815:C358F	C	+	2	0	TBL3	1965895	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.045000	0.71020	2.194000	0.70268	0.561000	0.74099	TGC	.	.		0.637	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
TBL3	10607	hgsc.bcm.edu	37	16	2025898	2025898	+	Silent	SNP	A	A	G	rs556701886		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:2025898A>G	ENST00000568546.1	+	11	1205	c.1077A>G	c.(1075-1077)ctA>ctG	p.L359L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	359					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GCCCCTGCCTAAAAGTGTTTG	0.637																																					p.L359L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A1077G						.						68.0	66.0	66.0					16																	2025898		2198	4300	6498	SO:0001819	synonymous_variant	10607	exon11			CTGCCTAAAAGTG	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1077A>G	chr16.hg19:g.2025898A>G		208.0	0.0		120.0	20.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	hg19	CCDS10453.1																																																																																			.	.		0.637	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
MT1H	4496	hgsc.bcm.edu	37	16	56704900	56704900	+	Silent	SNP	G	G	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:56704900G>A	ENST00000332374.4	+	3	256	c.185G>A	c.(184-186)tGa>tAa	p.*62*	MT1G_ENST00000379811.3_5'Flank|MT1G_ENST00000444837.2_5'Flank|MT1H_ENST00000569155.1_3'UTR|MT1G_ENST00000568675.1_5'Flank|MT1G_ENST00000569500.1_5'Flank	NM_005951.2	NP_005942.1	P80294	MT1H_HUMAN	metallothionein 1H	0					cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			lung(5)	5						TGCTGTGCCTGATGTCGGGAC	0.512																																					p.X62X		Atlas-SNP	.											.	MT1H	19	.	0			c.G185A						.						87.0	81.0	83.0					16																	56704900		2198	4300	6498	SO:0001819	synonymous_variant	4496	exon3			GTGCCTGATGTCG	BC008408	CCDS10767.1	16q13	2008-02-05			ENSG00000205358	ENSG00000205358		"""Metallothioneins"""	7400	protein-coding gene	gene with protein product		156354		MT1		2286373, 8049263	Standard	NM_005951		Approved		uc002ejw.3	P80294	OTTHUMG00000133283	ENST00000332374.4:c.185G>A	chr16.hg19:g.56704900G>A		62.0	0.0		44.0	8.0	NM_005951	B2RUY6	Silent	SNP	ENST00000332374.4	hg19	CCDS10767.1																																																																																			.	.		0.512	MT1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257063.1	NM_005951	
VPS9D1	9605	hgsc.bcm.edu	37	16	89783145	89783145	+	Silent	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:89783145G>T	ENST00000389386.3	-	3	385	c.261C>A	c.(259-261)gcC>gcA	p.A87A	VPS9D1-AS1_ENST00000562298.1_RNA|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Silent_p.A17A	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	87					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CACCAAGCTTGGCGGCCGTCG	0.647																																					p.A87A		Atlas-SNP	.											.	.	.	.	0			c.C261A						.						23.0	29.0	27.0					16																	89783145		1915	4111	6026	SO:0001819	synonymous_variant	9605	exon3			AAGCTTGGCGGCC	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.261C>A	chr16.hg19:g.89783145G>T		89.0	0.0		82.0	4.0	NM_004913		Silent	SNP	ENST00000389386.3	hg19	CCDS42220.1																																																																																			.	.		0.647	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
DNAH9	1770	hgsc.bcm.edu	37	17	11515011	11515011	+	Missense_Mutation	SNP	C	C	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:11515011C>G	ENST00000262442.4	+	4	886	c.818C>G	c.(817-819)aCg>aGg	p.T273R	DNAH9_ENST00000579828.1_Missense_Mutation_p.T273R|DNAH9_ENST00000454412.2_Missense_Mutation_p.T273R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	273	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGAACAATAACGGTGAGGGGC	0.448																																					p.T273R		Atlas-SNP	.											.	DNAH9	695	.	0			c.C818G						.						144.0	129.0	134.0					17																	11515011		2203	4300	6503	SO:0001583	missense	1770	exon4			CAATAACGGTGAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.818C>G	chr17.hg19:g.11515011C>G	ENSP00000262442:p.Thr273Arg	139.0	0.0		127.0	10.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.312430	0.00237	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.53857	0.6;0.6	5.69	2.32	0.28847	Dynein heavy chain, domain-1 (1);	0.476491	0.22576	N	0.058271	T	0.13756	0.0333	N	0.00446	-1.495	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.30446	-0.9978	10	0.07482	T	0.82	.	4.8323	0.13447	0.56:0.1552:0.2848:0.0	.	273;273	Q9NYC9;E7EP17	DYH9_HUMAN;.	R	273	ENSP00000262442:T273R;ENSP00000414874:T273R	ENSP00000262442:T273R	T	+	2	0	DNAH9	11455736	0.994000	0.37717	0.004000	0.12327	0.010000	0.07245	2.496000	0.45346	0.443000	0.26582	-0.311000	0.09066	ACG	.	.		0.448	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
SEPT4	5414	hgsc.bcm.edu	37	17	56604304	56604304	+	Silent	SNP	T	T	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:56604304T>A	ENST00000317268.3	-	2	272	c.96A>T	c.(94-96)ggA>ggT	p.G32G	SEPT4_ENST00000317256.6_Silent_p.G13G|SEPT4_ENST00000580791.1_5'UTR|SEPT4_ENST00000579371.1_Intron|SEPT4_ENST00000580844.1_Intron|SEPT4_ENST00000580809.1_Intron|SEPT4_ENST00000583114.1_5'UTR|SEPT4_ENST00000426861.1_Silent_p.G13G|RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000412945.3_Silent_p.G24G|SEPT4_ENST00000393086.1_Silent_p.G13G|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_Silent_p.G47G	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	32					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCTCAGTTCTCCATCATCCG	0.592																																					p.G47G		Atlas-SNP	.											.	SEPT4	48	.	0			c.A141T						.						76.0	82.0	80.0					17																	56604304		2203	4300	6503	SO:0001819	synonymous_variant	5414	exon3			CAGTTCTCCATCA	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"""Septins"""	9165	protein-coding gene	gene with protein product	"""bradeoin"", ""septin-M"""	603696	"""peanut-like 2 (Drosophila)"""	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.96A>T	chr17.hg19:g.56604304T>A		82.0	0.0		57.0	14.0	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	hg19	CCDS11610.1																																																																																			.	.		0.592	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
CLTC	1213	hgsc.bcm.edu	37	17	57724931	57724931	+	Missense_Mutation	SNP	G	G	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:57724931G>A	ENST00000269122.3	+	3	697	c.423G>A	c.(421-423)atG>atA	p.M141I	CLTC_ENST00000393043.1_Missense_Mutation_p.M141I|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	141	Globular terminal domain.|WD40-like repeat 3.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CAGTGAAAATGTTTGATCGCC	0.418			T	"""ALK, TFE3"""	"""ALCL, renal """																																p.M141I		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	.	CLTC	124	.	0			c.G423A						.						177.0	162.0	168.0					17																	57724931		2203	4300	6503	SO:0001583	missense	1213	exon3			GAAAATGTTTGAT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.423G>A	chr17.hg19:g.57724931G>A	ENSP00000269122:p.Met141Ile	168.0	0.0		186.0	13.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.649531	0.29336	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.20332	2.08;2.08	5.79	5.79	0.91817	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.047357	0.85682	D	0.000000	T	0.18130	0.0435	L	0.28740	0.885	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.003	T	0.10200	-1.0640	10	0.11182	T	0.66	.	20.0411	0.97590	0.0:0.0:1.0:0.0	.	141;141	Q00610;Q00610-2	CLH1_HUMAN;.	I	141	ENSP00000269122:M141I;ENSP00000376763:M141I	ENSP00000269122:M141I	M	+	3	0	CLTC	55079713	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	3.453000	0.52978	2.739000	0.93911	0.655000	0.94253	ATG	.	.		0.418	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
CEP112	201134	hgsc.bcm.edu	37	17	64128831	64128831	+	Missense_Mutation	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:64128831G>T	ENST00000392769.2	-	5	739	c.521C>A	c.(520-522)cCa>cAa	p.P174Q	CEP112_ENST00000537949.1_Missense_Mutation_p.P174Q|CEP112_ENST00000535342.2_Missense_Mutation_p.P174Q	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	174					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						TCTGTGAGTTGGACTCAAGGA	0.383																																					p.P174Q		Atlas-SNP	.											.	CEP112	192	.	0			c.C521A						.						108.0	100.0	103.0					17																	64128831		2203	4300	6503	SO:0001583	missense	201134	exon5			TGAGTTGGACTCA	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.521C>A	chr17.hg19:g.64128831G>T	ENSP00000376522:p.Pro174Gln	89.0	0.0		112.0	5.0	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	hg19	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.755511	0.31046	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000537949	T;T;T	0.47528	0.92;0.92;0.84	4.82	3.85	0.44370	.	0.439424	0.19202	N	0.120158	T	0.50274	0.1606	M	0.67953	2.075	0.80722	D	1	P;P	0.41131	0.739;0.739	P;P	0.45232	0.474;0.474	T	0.50964	-0.8765	10	0.52906	T	0.07	-4.6798	9.1486	0.36948	0.1024:0.0:0.8976:0.0	.	174;174	F5GYE8;Q8N8E3	.;CE112_HUMAN	Q	174	ENSP00000442784:P174Q;ENSP00000376522:P174Q;ENSP00000440775:P174Q	ENSP00000376522:P174Q	P	-	2	0	CEP112	61559293	1.000000	0.71417	0.625000	0.29200	0.561000	0.35649	3.465000	0.53064	1.161000	0.42604	0.655000	0.94253	CCA	.	.		0.383	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
BPTF	2186	hgsc.bcm.edu	37	17	65916145	65916145	+	Nonsense_Mutation	SNP	G	G	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:65916145G>T	ENST00000321892.4	+	15	5882	c.5821G>T	c.(5821-5823)Gaa>Taa	p.E1941*	BPTF_ENST00000306378.6_Nonsense_Mutation_p.E1815*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.E1802*|BPTF_ENST00000335221.5_Nonsense_Mutation_p.E1941*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1941					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATCCGAAACTGAAATCACAAC	0.343																																					p.E1941X		Atlas-SNP	.											.	BPTF	415	.	0			c.G5821T						.						117.0	120.0	119.0					17																	65916145		2203	4300	6503	SO:0001587	stop_gained	2186	exon15			GAAACTGAAATCA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.5821G>T	chr17.hg19:g.65916145G>T	ENSP00000315454:p.Glu1941*	93.0	0.0		82.0	4.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Nonsense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	G	48	14.022587	0.99775	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-19.2322	19.7228	0.96150	0.0:0.0:1.0:0.0	.	.	.	.	X	1815;1941;1941	.	ENSP00000307208:E1815X	E	+	1	0	BPTF	63346607	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.023000	0.88764	2.667000	0.90743	0.655000	0.94253	GAA	.	.		0.343	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
ELAC1	55520	hgsc.bcm.edu	37	18	48510826	48510826	+	Missense_Mutation	SNP	T	T	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr18:48510826T>G	ENST00000269466.3	+	3	625	c.518T>G	c.(517-519)tTt>tGt	p.F173C	ELAC1_ENST00000591429.1_Missense_Mutation_p.F173C|RP11-729L2.2_ENST00000588256.1_Intron|RP11-729L2.2_ENST00000590722.2_Intron|ELAC1_ENST00000588577.1_Intron|SMAD4_ENST00000452201.2_Intron	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	173					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)	p.F173C(1)		kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		GATGAACAATTTGTTGTAAAA	0.398																																					p.F173C		Atlas-SNP	.											ELAC1,colon,carcinoma,0,1	ELAC1	17	.	1	Substitution - Missense(1)	large_intestine(1)	c.T518G						.						66.0	65.0	65.0					18																	48510826		2203	4300	6503	SO:0001583	missense	55520	exon3			AACAATTTGTTGT	AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"""tRNA Z (short form)"", ""RNaseZ(S)"""	608079	"""elaC (E. coli) homolog 1"", ""elaC homolog 1 (E. coli)"""			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.518T>G	chr18.hg19:g.48510826T>G	ENSP00000269466:p.Phe173Cys	113.0	0.0		138.0	14.0	NM_018696	Q9NS99	Missense_Mutation	SNP	ENST00000269466.3	hg19	CCDS11949.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295390	0.81025	.	.	ENSG00000141642	ENST00000269466	T	0.77229	-1.08	5.95	5.95	0.96441	Beta-lactamase-like (1);	0.000000	0.85682	D	0.000000	D	0.86973	0.6062	M	0.70903	2.155	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.969	D	0.88267	0.2927	10	0.87932	D	0	.	15.4149	0.74960	0.0:0.0:0.0:1.0	.	173;173	Q53EY2;Q9H777	.;RNZ1_HUMAN	C	173	ENSP00000269466:F173C	ENSP00000269466:F173C	F	+	2	0	ELAC1	46764824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.906000	0.75719	2.281000	0.76405	0.528000	0.53228	TTT	.	.		0.398	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2		
SERPINB3	6317	hgsc.bcm.edu	37	18	61323171	61323171	+	Missense_Mutation	SNP	G	G	A	rs377088096		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr18:61323171G>A	ENST00000283752.5	-	8	1036	c.893C>T	c.(892-894)aCg>aTg	p.T298M	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.T246M	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	298					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)	p.T298M(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GGTTCTCAACGTGTCCTTGAG	0.488																																					p.T298M		Atlas-SNP	.											SERPINB3,NS,carcinoma,0,1	SERPINB3	90	.	1	Substitution - Missense(1)	lung(1)	c.C893T						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	180.0	154.0	163.0		893	-3.2	0.0	18		163	0,8600		0,0,4300	no	missense	SERPINB3	NM_006919.2	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	298/391	61323171	1,13005	2203	4300	6503	SO:0001583	missense	6317	exon8			CTCAACGTGTCCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.893C>T	chr18.hg19:g.61323171G>A	ENSP00000283752:p.Thr298Met	114.0	0.0		147.0	24.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	G	8.978	0.974626	0.18736	2.27E-4	0.0	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.84800	-1.9;-1.9	3.07	-3.17	0.05202	Serpin domain (3);	1.383540	0.04944	N	0.459085	D	0.87732	0.6251	M	0.80746	2.51	0.09310	N	1	B;D	0.55385	0.334;0.971	B;P	0.47941	0.146;0.562	T	0.81123	-0.1076	10	0.66056	D	0.02	.	11.7335	0.51752	0.6699:0.0:0.3301:0.0	.	246;298	P29508-2;P29508	.;SPB3_HUMAN	M	298;246	ENSP00000283752:T298M;ENSP00000329498:T246M	ENSP00000283752:T298M	T	-	2	0	SERPINB3	59474151	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-3.514000	0.00445	-0.831000	0.04256	-0.403000	0.06358	ACG	.	.		0.488	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
ZNF407	55628	hgsc.bcm.edu	37	18	72344756	72344756	+	Nonsense_Mutation	SNP	C	C	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr18:72344756C>G	ENST00000299687.5	+	1	1781	c.1781C>G	c.(1780-1782)tCa>tGa	p.S594*	ZNF407_ENST00000582337.1_Nonsense_Mutation_p.S594*|ZNF407_ENST00000577538.1_Nonsense_Mutation_p.S594*|ZNF407_ENST00000309902.6_Nonsense_Mutation_p.S594*	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	594					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CAGTGTTGTTCATTTATATCC	0.378																																					p.S594X		Atlas-SNP	.											.	ZNF407	231	.	0			c.C1781G						.						158.0	162.0	161.0					18																	72344756		1900	4118	6018	SO:0001587	stop_gained	55628	exon1			GTTGTTCATTTAT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1781C>G	chr18.hg19:g.72344756C>G	ENSP00000299687:p.Ser594*	110.0	0.0		117.0	7.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Nonsense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	39	7.389618	0.98255	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	.	.	.	5.76	4.89	0.63831	.	0.178214	0.23696	U	0.045466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	14.8311	0.70149	0.0:0.931:0.0:0.069	.	.	.	.	X	594	.	ENSP00000299687:S594X	S	+	2	0	ZNF407	70473744	0.977000	0.34250	0.001000	0.08648	0.793000	0.44817	3.184000	0.50926	-1.847000	0.01173	-0.710000	0.03640	TCA	.	.		0.378	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
DPF1	8193	hgsc.bcm.edu	37	19	38713312	38713312	+	Missense_Mutation	SNP	G	G	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr19:38713312G>C	ENST00000420980.2	-	2	173	c.147C>G	c.(145-147)caC>caG	p.H49Q	DPF1_ENST00000456296.1_Missense_Mutation_p.H23Q|DPF1_ENST00000414789.1_5'UTR|DPF1_ENST00000412732.1_5'UTR|DPF1_ENST00000355526.4_Missense_Mutation_p.H49Q|DPF1_ENST00000416611.1_Missense_Mutation_p.H23Q	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1	49					apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AACTGCGGCAGTGCTCGATGG	0.687																																					p.H49Q		Atlas-SNP	.											.	DPF1	54	.	0			c.C147G						.						26.0	26.0	26.0					19																	38713312		2200	4298	6498	SO:0001583	missense	8193	exon2			GCGGCAGTGCTCG	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"""Zinc fingers, PHD-type"""	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.147C>G	chr19.hg19:g.38713312G>C	ENSP00000397354:p.His49Gln	164.0	0.0		121.0	23.0	NM_001135155	B3KSY8|Q08AJ0	Missense_Mutation	SNP	ENST00000420980.2	hg19	CCDS33008.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	7.524|7.524	0.657360|0.657360	0.14580|0.14580	.|.	.|.	ENSG00000011332|ENSG00000011332	ENST00000420980;ENST00000437720;ENST00000416611;ENST00000456296;ENST00000434076|ENST00000355526	D;D;D|.	0.89123|.	-2.02;-2.0;-2.47|.	3.36|3.36	3.36|3.36	0.38483|0.38483	.|.	0.078481|.	0.48767|.	N|.	0.000168|.	T|T	0.32224|0.32224	0.0822|0.0822	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B;D;P;B|.	0.89917|.	0.004;0.004;1.0;0.916;0.379|.	B;B;D;P;B|.	0.97110|.	0.007;0.012;1.0;0.821;0.241|.	T|T	0.08166|0.08166	-1.0735|-1.0735	10|5	0.13108|.	T|.	0.6|.	-17.1432|-17.1432	8.1585|8.1585	0.31185|0.31185	0.1178:0.0:0.8822:0.0|0.1178:0.0:0.8822:0.0	.|.	23;23;22;49;49|.	B4DMQ8;E9PDV3;C8C3P2;Q92782-2;Q92782|.	.;.;.;.;DPF1_HUMAN|.	Q|V	49;49;23;23;23|42	ENSP00000397354:H49Q;ENSP00000390223:H23Q;ENSP00000411569:H23Q|.	ENSP00000390223:H23Q|.	H|L	-|-	3|1	2|2	DPF1|DPF1	43405152|43405152	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	0.351000|0.351000	0.20096|0.20096	1.902000|1.902000	0.55061|0.55061	0.394000|0.394000	0.25966|0.25966	CAC|CTG	.	.		0.687	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1		
EID2B	126272	hgsc.bcm.edu	37	19	40023135	40023135	+	Missense_Mutation	SNP	C	C	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr19:40023135C>A	ENST00000326282.4	-	1	359	c.308G>T	c.(307-309)aGc>aTc	p.S103I	CTB-60E11.9_ENST00000594676.1_RNA|EID2B_ENST00000601837.1_Intron	NM_152361.1	NP_689574.1			EP300 interacting inhibitor of differentiation 2B											endometrium(1)|lung(1)|urinary_tract(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AATCATGGAGCTACCATCCAG	0.592																																					p.S103I		Atlas-SNP	.											.	EID2B	9	.	0			c.G308T						.						50.0	52.0	52.0					19																	40023135		2203	4300	6503	SO:0001583	missense	126272	exon1			ATGGAGCTACCAT	AK096263	CCDS12539.1	19q13.2	2008-02-05				ENSG00000176401			26796	protein-coding gene	gene with protein product						15970276	Standard	NM_152361		Approved	EID-3, FLJ38944	uc002olz.1	Q96D98		ENST00000326282.4:c.308G>T	chr19.hg19:g.40023135C>A	ENSP00000317564:p.Ser103Ile	350.0	0.0		324.0	30.0	NM_152361		Missense_Mutation	SNP	ENST00000326282.4	hg19	CCDS12539.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070823	0.55539	.	.	ENSG00000176401	ENST00000326282	T	0.32023	1.47	2.23	-4.47	0.03525	.	.	.	.	.	T	0.11452	0.0279	N	0.14661	0.345	0.09310	N	1	P	0.35821	0.523	B	0.22601	0.04	T	0.10847	-1.0612	9	0.45353	T	0.12	.	4.6015	0.12356	0.0:0.2675:0.179:0.5535	.	103	Q96D98	EID2B_HUMAN	I	103	ENSP00000317564:S103I	ENSP00000317564:S103I	S	-	2	0	EID2B	44714975	0.000000	0.05858	0.000000	0.03702	0.950000	0.60333	-1.118000	0.03280	-1.268000	0.02439	0.306000	0.20318	AGC	.	.		0.592	EID2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464961.1	NM_152361	
PANK2	80025	hgsc.bcm.edu	37	20	3897669	3897669	+	Missense_Mutation	SNP	C	C	T			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr20:3897669C>T	ENST00000316562.4	+	5	1514	c.1508C>T	c.(1507-1509)tCa>tTa	p.S503L	PANK2_ENST00000497424.1_Missense_Mutation_p.S212L|MIR103A2_ENST00000362154.1_RNA|PANK2_ENST00000610179.1_Missense_Mutation_p.S380L|PANK2_ENST00000464452.1_3'UTR	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	503					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						AACATTGGCTCAATAGCAAGA	0.453																																					p.S503L		Atlas-SNP	.											.	PANK2	37	.	0			c.C1508T						.						144.0	121.0	129.0					20																	3897669		2203	4300	6503	SO:0001583	missense	80025	exon5			TTGGCTCAATAGC	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"""Hallervorden-Spatz syndrome"""	606157	"""neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"""	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.1508C>T	chr20.hg19:g.3897669C>T	ENSP00000313377:p.Ser503Leu	166.0	0.0		133.0	25.0	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Missense_Mutation	SNP	ENST00000316562.4	hg19	CCDS13071.2	.	.	.	.	.	.	.	.	.	.	C	34	5.383593	0.95967	.	.	ENSG00000125779	ENST00000497424;ENST00000316562;ENST00000399552	D;D	0.99548	-6.14;-6.14	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.99468	0.9811	M	0.63208	1.945	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.98446	1.0589	10	0.66056	D	0.02	.	16.3012	0.82816	0.0:1.0:0.0:0.0	.	503	Q9BZ23	PANK2_HUMAN	L	212;503;319	ENSP00000417609:S212L;ENSP00000313377:S503L	ENSP00000313377:S503L	S	+	2	0	PANK2	3845669	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.579000	0.82511	2.713000	0.92767	0.655000	0.94253	TCA	.	.		0.453	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960	
TCFL5	10732	hgsc.bcm.edu	37	20	61491546	61491546	+	Silent	SNP	T	T	C			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr20:61491546T>C	ENST00000335351.3	-	2	854	c.762A>G	c.(760-762)caA>caG	p.Q254Q	TCFL5_ENST00000217162.5_Silent_p.Q206Q	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	254					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					GGTATGTAAATTGCAAAGCAG	0.373																																					p.Q254Q		Atlas-SNP	.											.	TCFL5	43	.	0			c.A762G						.						152.0	147.0	149.0					20																	61491546		2203	4300	6503	SO:0001819	synonymous_variant	10732	exon2			TGTAAATTGCAAA	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"""Basic helix-loop-helix proteins"""	11646	protein-coding gene	gene with protein product	"""HPV-16 E2 binding protein 1"""	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.762A>G	chr20.hg19:g.61491546T>C		163.0	0.0		130.0	23.0	NM_006602	O94771|Q9BYW0	Silent	SNP	ENST00000335351.3	hg19	CCDS13506.1																																																																																			.	.		0.373	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602	
AP1B1	162	hgsc.bcm.edu	37	22	29727788	29727788	+	Silent	SNP	C	C	G			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr22:29727788C>G	ENST00000405198.1	-	17	2458	c.2427G>C	c.(2425-2427)ctG>ctC	p.L809L	AP1B1_ENST00000472057.1_5'UTR|SNORD125_ENST00000459538.1_RNA|AP1B1_ENST00000317368.7_Silent_p.L782L|AP1B1_ENST00000415447.1_Silent_p.L802L|AP1B1_ENST00000357586.2_Silent_p.L809L|AP1B1_ENST00000402502.1_Silent_p.L802L|AP1B1_ENST00000356015.2_Silent_p.L802L|AP1B1_ENST00000432560.2_Silent_p.L802L			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	809					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGAGGTTGTTCAGAGGCTCCA	0.652																																					p.L809L		Atlas-SNP	.											.	AP1B1	72	.	0			c.G2427C						.						71.0	66.0	68.0					22																	29727788		2203	4300	6503	SO:0001819	synonymous_variant	162	exon18			GTTGTTCAGAGGC	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.2427G>C	chr22.hg19:g.29727788C>G		143.0	0.0		94.0	12.0	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Silent	SNP	ENST00000405198.1	hg19	CCDS13855.1																																																																																			.	.		0.652	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127	
MT-CO1	4512	hgsc.bcm.edu	37	M	7326	7326	+	Missense_Mutation	SNP	G	G	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chrM:7326G>A	ENST00000361624.2	+	1	1423	c.1423G>A	c.(1423-1425)Gcc>Acc	p.A475T	MT-TG_ENST00000387429.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TW_ENST00000387382.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-CO2_ENST00000361739.1_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	475					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						TGATTTGAGAAGCCTTCGCTT	0.428																																					p.A475T		Atlas-SNP	.											.	.	.	.	0			c.G1423A						.																																			SO:0001583	missense	5742	exon1			TGAGAAGCCTTCG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.1423G>A	chrM.hg19:g.7326G>A	ENSP00000354499:p.Ala475Thr	13.0	0.0		81.0	7.0	ENST00000361624	Q34770	Missense_Mutation	SNP	ENST00000361624.2	hg19																																																																																				.	.		0.428	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
MT-ND5	4540	hgsc.bcm.edu	37	M	12730	12730	+	Missense_Mutation	SNP	G	G	A			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chrM:12730G>A	ENST00000361567.2	+	1	394	c.394G>A	c.(394-396)Gtt>Att	p.V132I	MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	132					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TACTAATCTTAGTTACCGCTA	0.393																																					p.V132I		Atlas-SNP	.											.	.	.	.	0			c.G394A						.																																			SO:0001583	missense	0	exon1			ATCTTAGTTACCG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.394G>A	chrM.hg19:g.12730G>A	ENSP00000354813:p.Val132Ile	15.0	0.0		105.0	17.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.393	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
PPP2R5C	5527	hgsc.bcm.edu	37	14	102356589	102356590	+	Frame_Shift_Del	DEL	AG	AG	-	rs4617782		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr14:102356589_102356590delAG	ENST00000334743.5	+	6	693_694	c.645_646delAG	c.(643-648)acagagfs	p.E216fs	PPP2R5C_ENST00000445439.3_Frame_Shift_Del_p.E216fs|PPP2R5C_ENST00000350249.3_Frame_Shift_Del_p.E216fs|PPP2R5C_ENST00000422945.2_Frame_Shift_Del_p.E247fs|PPP2R5C_ENST00000328724.5_Frame_Shift_Del_p.E271fs|PPP2R5C_ENST00000557095.1_Frame_Shift_Del_p.E216fs	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	216					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TTTATGAAACAGAGCATCATAA	0.386																																					p.270_270del		Atlas-INDEL	.											.	PPP2R5C	74	.	0			c.809_810del						.																																			SO:0001589	frameshift_variant	5527	exon8			.	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9311	protein-coding gene	gene with protein product		601645	"""protein phosphatase 2, regulatory subunit B (B56), gamma isoform"", ""protein phosphatase 2, regulatory subunit B', gamma isoform"""			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.645_646delAG	chr14.hg19:g.102356591_102356592delAG	ENSP00000333905:p.Glu216fs	137.0	0.0		115.0	27.0	NM_001161726	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Frame_Shift_Del	DEL	ENST00000334743.5	hg19	CCDS9964.1																																																																																			.	.		0.386	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	
