#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
CEP104	9731	hgsc.bcm.edu	37	1	3754080	3754080	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:3754080G>A	ENST00000378230.3	-	9	1219	c.895C>T	c.(895-897)Cga>Tga	p.R299*	CEP104_ENST00000460038.1_5'Flank	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	299						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)	p.R299*(1)		breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						AAAGGTCTTCGCATCTAGAGA	0.453																																					p.R299X		Atlas-SNP	.											CEP104,colon,carcinoma,0,1	CEP104	79	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C895T						.						53.0	58.0	56.0					1																	3754080		2203	4300	6503	SO:0001587	stop_gained	9731	exon9			GTCTTCGCATCTA	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.895C>T	chr1.hg19:g.3754080G>A	ENSP00000367476:p.Arg299*	53.0	0.0		61.0	3.0	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Nonsense_Mutation	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	37	6.176452	0.97348	.	.	ENSG00000116198	ENST00000378230	.	.	.	5.44	1.19	0.21007	.	0.639794	0.15563	N	0.255851	.	.	.	.	.	.	0.46167	D	0.998909	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	13.3671	0.60692	0.0:0.0:0.4562:0.5438	.	.	.	.	X	299	.	ENSP00000367476:R299X	R	-	1	2	CEP104	3743940	0.993000	0.37304	0.079000	0.20413	0.216000	0.24613	1.558000	0.36309	-0.035000	0.13691	0.555000	0.69702	CGA	.	.		0.453	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
KLHL21	9903	hgsc.bcm.edu	37	1	6653499	6653499	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:6653499C>T	ENST00000377658.4	-	4	1771	c.1720G>A	c.(1720-1722)Gag>Aag	p.E574K	KLHL21_ENST00000467612.1_Missense_Mutation_p.E207K|KLHL21_ENST00000377663.3_3'UTR	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	574					chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		CTGTCCAACTCGAAGCCACGC	0.687																																					p.E574K		Atlas-SNP	.											KLHL21,right_upper_lobe,carcinoma,0,1	KLHL21	27	.	0			c.G1720A						.						60.0	56.0	58.0					1																	6653499		2203	4300	6503	SO:0001583	missense	9903	exon4			CCAACTCGAAGCC	AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413		"""Kelch-like"", ""BTB/POZ domain containing"""	29041	protein-coding gene	gene with protein product			"""kelch-like 21 (Drosophila)"""				Standard	XM_005263542		Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.1720G>A	chr1.hg19:g.6653499C>T	ENSP00000366886:p.Glu574Lys	50.0	1.0		51.0	3.0	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Missense_Mutation	SNP	ENST00000377658.4	hg19	CCDS30575.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967263	0.53507	.	.	ENSG00000162413	ENST00000377658;ENST00000505933	T	0.72505	-0.66	5.33	4.4	0.53042	.	1.549940	0.03705	N	0.249336	T	0.58764	0.2145	N	0.19112	0.55	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.55477	-0.8135	10	0.54805	T	0.06	.	7.1029	0.25348	0.0:0.8336:0.0:0.1664	.	574	Q9UJP4	KLH21_HUMAN	K	574;12	ENSP00000366886:E574K	ENSP00000366886:E574K	E	-	1	0	KLHL21	6576086	0.229000	0.23729	0.997000	0.53966	0.621000	0.37620	1.751000	0.38339	2.655000	0.90218	0.655000	0.94253	GAG	.	.		0.687	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851	
KAZN	23254	hgsc.bcm.edu	37	1	15287300	15287300	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:15287300C>T	ENST00000376030.2	+	2	641	c.347C>T	c.(346-348)tCg>tTg	p.S116L	KAZN_ENST00000503743.1_Missense_Mutation_p.S116L|KAZN_ENST00000422387.2_Missense_Mutation_p.S116L|KAZN_ENST00000361144.5_Missense_Mutation_p.S110L|KAZN_ENST00000400797.3_Missense_Mutation_p.S22L|KAZN_ENST00000400798.2_Missense_Mutation_p.S22L	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	116					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						GAGGTCCTCTCGGCCACCGAG	0.617																																					p.S116L		Atlas-SNP	.											.	KAZN	57	.	0			c.C347T						.						30.0	29.0	29.0					1																	15287300		2203	4300	6503	SO:0001583	missense	23254	exon2			TCCTCTCGGCCAC	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.347C>T	chr1.hg19:g.15287300C>T	ENSP00000365198:p.Ser116Leu	51.0	0.0		85.0	5.0	NM_015209	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	C	25.6	4.651026	0.88056	.	.	ENSG00000189337	ENST00000376030;ENST00000503743;ENST00000422387;ENST00000361144;ENST00000376028;ENST00000400798;ENST00000400797	T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.67757	0.2927	M	0.68952	2.095	0.80722	D	1	D;D;P;P	0.89917	1.0;1.0;0.519;0.772	D;D;B;B	0.83275	0.991;0.996;0.113;0.078	T	0.62348	-0.6873	10	0.30854	T	0.27	-2.9242	18.8652	0.92289	0.0:1.0:0.0:0.0	.	116;22;110;116	Q674X7-2;Q674X7-4;Q674X7-3;Q674X7	.;.;.;KAZRN_HUMAN	L	116;116;116;110;22;22;22	ENSP00000365198:S116L;ENSP00000426015:S116L;ENSP00000391728:S116L;ENSP00000354727:S110L;ENSP00000365196:S22L;ENSP00000383602:S22L;ENSP00000383601:S22L	ENSP00000354727:S110L	S	+	2	0	KAZN	15159887	1.000000	0.71417	0.952000	0.39060	0.984000	0.73092	7.298000	0.78815	2.709000	0.92574	0.561000	0.74099	TCG	.	.		0.617	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
ZNF683	257101	hgsc.bcm.edu	37	1	26691310	26691310	+	Missense_Mutation	SNP	G	G	C	rs144078461|rs145815386|rs372936882	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:26691310G>C	ENST00000436292.1	-	4	847	c.727C>G	c.(727-729)Ctg>Gtg	p.L243V	ZNF683_ENST00000374204.1_Missense_Mutation_p.L243V|ZNF683_ENST00000349618.3_Missense_Mutation_p.L243V|ZNF683_ENST00000403843.1_Missense_Mutation_p.L243V			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	243					natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L228_W235delLGHPSARW(1)|p.L243_W250delLGHPSARW(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		GGGTGCCCCAGCTCATTGACC	0.637																																					p.L243V		Atlas-SNP	.											.	ZNF683	51	.	2	Deletion - In frame(2)	large_intestine(2)	c.C727G						.						38.0	51.0	46.0					1																	26691310		2111	4285	6396	SO:0001583	missense	257101	exon4			GCCCCAGCTCATT	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"""Zinc fingers, C2H2-type"""	28495	protein-coding gene	gene with protein product	"""hypothetical protein MGC33414"""					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.727C>G	chr1.hg19:g.26691310G>C	ENSP00000388792:p.Leu243Val	0.0	0.0		7.0	6.0	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.901	1.206758	0.22205	.	.	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618;ENST00000455900;ENST00000451801	T;T;T;T;T;T	0.18016	2.9;2.9;2.92;2.92;2.24;2.25	4.74	-1.94	0.07571	.	0.482467	0.17752	N	0.163192	T	0.06050	0.0157	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.004	T	0.34700	-0.9818	10	0.21014	T	0.42	-0.0116	4.8538	0.13549	0.3374:0.2722:0.3904:0.0	.	243;243	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	V	243;243;243;243;251;243	ENSP00000384782:L243V;ENSP00000388792:L243V;ENSP00000363320:L243V;ENSP00000344095:L243V;ENSP00000411289:L251V;ENSP00000411290:L243V	ENSP00000344095:L243V	L	-	1	2	ZNF683	26563897	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.807000	0.04520	-0.257000	0.09459	-0.264000	0.10439	CTG	.	.		0.637	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574	
TINAGL1	64129	hgsc.bcm.edu	37	1	32052549	32052549	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:32052549G>A	ENST00000271064.7	+	12	1449	c.1373G>A	c.(1372-1374)cGc>cAc	p.R458H	TINAGL1_ENST00000481165.1_3'UTR|TINAGL1_ENST00000457433.2_Missense_Mutation_p.R427H	NM_001204415.1|NM_022164.2	NP_001191344.1|NP_071447.1	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	458					endosomal transport (GO:0016197)|immune response (GO:0006955)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type peptidase activity (GO:0008234)|extracellular matrix structural constituent (GO:0005201)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			breast(2)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		GTCTGGGGCCGCGTGGGCATG	0.697																																					p.R458H		Atlas-SNP	.											TINAGL1,right_upper_lobe,carcinoma,0,1	TINAGL1	35	.	0			c.G1373A						.						27.0	32.0	30.0					1																	32052549		2199	4295	6494	SO:0001583	missense	64129	exon12			GGGGCCGCGTGGG	AB050716	CCDS343.1, CCDS55586.1, CCDS72745.1	1p34.3	2014-04-22	2005-08-18	2005-08-18	ENSG00000142910	ENSG00000142910			19168	protein-coding gene	gene with protein product			"""lipocalin 7"", ""TINAG-like 1"""	LCN7		11170462	Standard	NM_022164		Approved	P3ECSL, LIECG3, ARG1, TINAGRP	uc001bta.3	Q9GZM7	OTTHUMG00000003884	ENST00000271064.7:c.1373G>A	chr1.hg19:g.32052549G>A	ENSP00000271064:p.Arg458His	49.0	0.0		10.0	2.0	NM_022164	A8K9Q5|B4DPK6|D3DPN8|Q8TEJ9|Q8WZ23|Q96GZ4|Q96JW3	Missense_Mutation	SNP	ENST00000271064.7	hg19	CCDS343.1	.	.	.	.	.	.	.	.	.	.	g	18.44	3.625174	0.66901	.	.	ENSG00000142910	ENST00000457433;ENST00000271064	T;T	0.69306	-0.39;0.07	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.75895	0.3912	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.76969	-0.2762	10	0.46703	T	0.11	.	15.151	0.72700	0.0:0.0:1.0:0.0	.	427;458	B4DPK6;Q9GZM7	.;TINAL_HUMAN	H	427;458	ENSP00000395137:R427H;ENSP00000271064:R458H	ENSP00000271064:R458H	R	+	2	0	TINAGL1	31825136	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.943000	0.92975	1.932000	0.55993	0.462000	0.41574	CGC	.	.		0.697	TINAGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011072.1	NM_022164	
CSMD2	114784	hgsc.bcm.edu	37	1	34006774	34006774	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:34006774C>T	ENST00000373381.4	-	59	9589	c.9413G>A	c.(9412-9414)tGc>tAc	p.C3138Y		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3110	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCCTTGGTGCAGCTCAGCAC	0.498																																					p.C2994Y		Atlas-SNP	.											.	CSMD2	946	.	0			c.G8981A						.						176.0	159.0	165.0					1																	34006774		2203	4300	6503	SO:0001583	missense	114784	exon58			TTGGTGCAGCTCA	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.9413G>A	chr1.hg19:g.34006774C>T	ENSP00000362479:p.Cys3138Tyr	117.0	0.0		123.0	5.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	25.9	4.683884	0.88639	.	.	ENSG00000121904	ENST00000373381	D	0.92595	-3.07	5.58	5.58	0.84498	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.98157	0.9391	H	0.99435	4.565	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	1.0;1.0	D	0.99572	1.0971	10	0.72032	D	0.01	.	18.5585	0.91093	0.0:1.0:0.0:0.0	.	2994;3138	Q7Z408;E7EUA6	CSMD2_HUMAN;.	Y	3138	ENSP00000362479:C3138Y	ENSP00000241312:C2994Y	C	-	2	0	CSMD2	33779361	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.736000	0.84948	2.622000	0.88805	0.462000	0.41574	TGC	.	.		0.498	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
FOXD3	27022	hgsc.bcm.edu	37	1	63789224	63789224	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:63789224C>T	ENST00000371116.2	+	1	495	c.495C>T	c.(493-495)agC>agT	p.S165S	RP4-792G4.2_ENST00000431294.1_RNA|RP4-792G4.2_ENST00000427268.1_RNA|RP4-792G4.2_ENST00000426393.1_RNA|RP4-792G4.2_ENST00000449386.1_RNA|RP4-792G4.2_ENST00000418244.1_RNA	NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	165					embryonic placenta development (GO:0001892)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|trophectodermal cell differentiation (GO:0001829)	nuclear chromatin (GO:0000790)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5						TGACCCTGAGCGGCATCTGCG	0.587																																					p.S165S	Pancreas(68;276 1750 11966 31252)	Atlas-SNP	.											FOXD3,right_upper_lobe,carcinoma,0,1	FOXD3	15	.	0			c.C495T						.						68.0	76.0	73.0					1																	63789224		2203	4300	6503	SO:0001819	synonymous_variant	27022	exon1			CCTGAGCGGCATC	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140		"""Forkhead boxes"""	3804	protein-coding gene	gene with protein product		611539				8499623	Standard	NM_012183		Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.495C>T	chr1.hg19:g.63789224C>T		70.0	0.0		69.0	3.0	NM_012183	Q9BYM2|Q9UDD1	Silent	SNP	ENST00000371116.2	hg19	CCDS624.1																																																																																			.	.		0.587	FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1		
JAK1	3716	hgsc.bcm.edu	37	1	65335078	65335078	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:65335078T>A	ENST00000342505.4	-	6	811	c.563A>T	c.(562-564)gAg>gTg	p.E188V		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	188	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCCTAGACACTCGTTCTCAAT	0.512			Mis		ALL																																p.E188V		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A563T						.						145.0	139.0	141.0					1																	65335078		2023	4191	6214	SO:0001583	missense	3716	exon6			AGACACTCGTTCT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.563A>T	chr1.hg19:g.65335078T>A	ENSP00000343204:p.Glu188Val	100.0	0.0		123.0	35.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.665413	0.88251	.	.	ENSG00000162434	ENST00000342505	T	0.72725	-0.68	5.33	5.33	0.75918	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);	.	.	.	.	D	0.83004	0.5160	M	0.85859	2.78	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	D	0.86395	0.1738	9	0.87932	D	0	.	15.6084	0.76692	0.0:0.0:0.0:1.0	.	188	P23458	JAK1_HUMAN	V	188	ENSP00000343204:E188V	ENSP00000343204:E188V	E	-	2	0	JAK1	65107666	1.000000	0.71417	0.999000	0.59377	0.767000	0.43475	7.676000	0.84012	2.152000	0.67230	0.533000	0.62120	GAG	.	.		0.512	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
CLCA4	22802	hgsc.bcm.edu	37	1	87045908	87045908	+	Silent	SNP	T	T	A	rs56040873|rs77594462	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:87045908T>A	ENST00000370563.3	+	14	2682	c.2640T>A	c.(2638-2640)acT>acA	p.T880T	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	880					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		ctacacctactcctactccta	0.353																																					p.T880T		Atlas-SNP	.											.	CLCA4	131	.	0			c.T2640A						.						98.0	94.0	95.0					1																	87045908		1847	4080	5927	SO:0001819	synonymous_variant	22802	exon14			ACCTACTCCTACT	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2640T>A	chr1.hg19:g.87045908T>A		43.0	0.0		107.0	26.0	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Silent	SNP	ENST00000370563.3	hg19	CCDS41355.1																																																																																			.	.		0.353	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
PTPN22	26191	hgsc.bcm.edu	37	1	114380935	114380935	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:114380935C>T	ENST00000359785.5	-	13	1222	c.1087G>A	c.(1087-1089)Gca>Aca	p.A363T	PTPN22_ENST00000528414.1_Missense_Mutation_p.A308T|PTPN22_ENST00000525799.1_Missense_Mutation_p.A236T|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Missense_Mutation_p.A363T|PTPN22_ENST00000538253.1_Missense_Mutation_p.A119T	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	363					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTTCTTTTGCACTTATTTCA	0.348																																					p.A363T		Atlas-SNP	.											.	PTPN22	90	.	0			c.G1087A						.						125.0	104.0	111.0					1																	114380935		2203	4300	6503	SO:0001583	missense	26191	exon13			CTTTTGCACTTAT	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9652	protein-coding gene	gene with protein product		600716	"""protein tyrosine phosphatase, non-receptor type 8"""	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1087G>A	chr1.hg19:g.114380935C>T	ENSP00000352833:p.Ala363Thr	99.0	0.0		100.0	4.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	8.282	0.815667	0.16607	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.82	2.71	0.32032	.	0.662724	0.14465	N	0.317950	T	0.09024	0.0223	L	0.43152	1.355	0.09310	N	1	P;P;P;B;P;P	0.48764	0.763;0.915;0.736;0.003;0.828;0.736	B;B;B;B;B;B	0.41946	0.295;0.321;0.205;0.003;0.371;0.205	T	0.11179	-1.0598	10	0.14656	T	0.56	.	6.5743	0.22555	0.0:0.6854:0.1438:0.1707	.	119;236;363;308;363;363	F5H2S8;E9PPI1;E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;.;.;PTN22_HUMAN	T	363;308;119;363;236;363	ENSP00000352833:A363T;ENSP00000435176:A308T;ENSP00000439372:A119T;ENSP00000388229:A363T;ENSP00000432674:A236T	ENSP00000346621:A363T	A	-	1	0	PTPN22	114182458	0.000000	0.05858	0.028000	0.17463	0.006000	0.05464	0.394000	0.20834	0.730000	0.32425	-0.345000	0.07892	GCA	.	.		0.348	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967	
WDR3	10885	hgsc.bcm.edu	37	1	118495158	118495158	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:118495158A>G	ENST00000349139.5	+	19	2071	c.2024A>G	c.(2023-2025)cAc>cGc	p.H675R		NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3	675						nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		CAGGGTCATCACCAGGAAATA	0.393																																					p.H675R		Atlas-SNP	.											.	WDR3	81	.	0			c.A2024G						.						77.0	78.0	78.0					1																	118495158		2203	4300	6503	SO:0001583	missense	10885	exon19			GTCATCACCAGGA	AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183		"""WD repeat domain containing"""	12755	protein-coding gene	gene with protein product		604737				10395803	Standard	NM_006784		Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.2024A>G	chr1.hg19:g.118495158A>G	ENSP00000308179:p.His675Arg	93.0	0.0		93.0	4.0	NM_006784		Missense_Mutation	SNP	ENST00000349139.5	hg19	CCDS898.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784104	0.70222	.	.	ENSG00000065183	ENST00000349139	T	0.59083	0.29	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.043669	0.85682	D	0.000000	T	0.28995	0.0720	N	0.16201	0.385	0.80722	D	1	P	0.36789	0.57	B	0.38106	0.265	T	0.20638	-1.0269	10	0.23891	T	0.37	-15.8671	16.4311	0.83844	1.0:0.0:0.0:0.0	.	675	Q9UNX4	WDR3_HUMAN	R	675	ENSP00000308179:H675R	ENSP00000308179:H675R	H	+	2	0	WDR3	118296681	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.125000	0.94402	2.277000	0.76020	0.528000	0.53228	CAC	.	.		0.393	WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2	NM_006784	
NBPF10	100132406	hgsc.bcm.edu	37	1	145367777	145367777	+	Missense_Mutation	SNP	G	G	T	rs200743139		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:145367777G>T	ENST00000342960.5	+	83	10408	c.10373G>T	c.(10372-10374)aGg>aTg	p.R3458M	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	755						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		gaaagaagaaggggaagaaaa	0.428																																					p.R3458M		Atlas-SNP	.											NBPF10,NS,carcinoma,0,1	NBPF10	221	.	0			c.G10373T						.																																			SO:0001583	missense	100132406	exon83			GAAGAAGGGGAAG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.10373G>T	chr1.hg19:g.145367777G>T	ENSP00000345684:p.Arg3458Met	2.0	0.0		6.0	3.0	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	hg19	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	10.39	1.335798	0.24253	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.05258	3.47	.	.	.	.	.	.	.	.	T	0.03651	0.0104	L	0.51422	1.61	0.09310	N	1	.	.	.	.	.	.	T	0.38351	-0.9665	4	0.87932	D	0	.	.	.	.	.	.	.	.	M	578;3458	ENSP00000345684:R3458M	ENSP00000345684:R3458M	R	+	2	0	NBPF10	144079134	.	.	.	.	.	.	.	.	.	.	.	.	AGG	.	.		0.428	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
LCE1E	353135	hgsc.bcm.edu	37	1	152759984	152759984	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:152759984C>A	ENST00000368770.3	+	2	262	c.209C>A	c.(208-210)tCt>tAt	p.S70Y	LCE1E_ENST00000368771.1_Missense_Mutation_p.S70Y	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	70	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTGCAGCTCTGGGGGAGGT	0.682																																					p.S70Y		Atlas-SNP	.											.	LCE1E	26	.	0			c.C209A						.						35.0	44.0	41.0					1																	152759984		2203	4298	6501	SO:0001583	missense	353135	exon2			GCAGCTCTGGGGG	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.209C>A	chr1.hg19:g.152759984C>A	ENSP00000357759:p.Ser70Tyr	134.0	0.0		95.0	46.0	NM_178353	D3DV30	Missense_Mutation	SNP	ENST00000368770.3	hg19	CCDS1024.1	.	.	.	.	.	.	.	.	.	.	C	9.777	1.174286	0.21704	.	.	ENSG00000186226	ENST00000368771;ENST00000368770	T;T	0.06294	3.32;3.32	4.06	4.06	0.47325	.	0.000000	0.34959	N	0.003545	T	0.17195	0.0413	M	0.87900	2.915	0.27825	N	0.941652	D	0.69078	0.997	D	0.78314	0.991	T	0.01360	-1.1375	10	0.87932	D	0	.	11.9094	0.52731	0.0:1.0:0.0:0.0	.	70	Q5T753	LCE1E_HUMAN	Y	70	ENSP00000357760:S70Y;ENSP00000357759:S70Y	ENSP00000357759:S70Y	S	+	2	0	LCE1E	151026608	0.996000	0.38824	1.000000	0.80357	0.773000	0.43773	1.958000	0.40402	2.237000	0.73441	0.514000	0.50259	TCT	.	.		0.682	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
DENND4B	9909	hgsc.bcm.edu	37	1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	rs3835302|rs199597671		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						.						23.0	27.0	26.0					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	25.0	0.0		51.0	6.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
SLC50A1	55974	hgsc.bcm.edu	37	1	155110121	155110121	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:155110121G>A	ENST00000368404.4	+	4	429	c.367G>A	c.(367-369)Gag>Aag	p.E123K	SLC50A1_ENST00000484157.1_Missense_Mutation_p.E58K|SLC50A1_ENST00000368401.5_Missense_Mutation_p.E68K|SLC50A1_ENST00000368405.3_Intron|SLC50A1_ENST00000303343.8_Intron	NM_018845.3	NP_061333.2	Q9BRV3	SWET1_HUMAN	solute carrier family 50 (sugar efflux transporter), member 1	123					carbohydrate transport (GO:0008643)|DNA recombination (GO:0006310)|glucoside transport (GO:0042946)|positive regulation of gene expression, epigenetic (GO:0045815)	endomembrane system (GO:0012505)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucoside transmembrane transporter activity (GO:0042947)			endometrium(1)|lung(1)|ovary(1)|skin(1)	4						ACCCAACCCTGAGGCCCGGCT	0.582																																					p.E123K		Atlas-SNP	.											.	SLC50A1	16	.	0			c.G367A						.						74.0	76.0	75.0					1																	155110121		2203	4300	6503	SO:0001583	missense	55974	exon4			AACCCTGAGGCCC	AF126023, AF126024	CCDS1093.1, CCDS44238.1, CCDS44239.1, CCDS72929.1, CCDS72930.1	1q22	2013-07-17	2013-07-17	2010-11-30	ENSG00000169241	ENSG00000169241		"""Solute carriers"""	30657	protein-coding gene	gene with protein product	"""stromal cell protein"""	613683	"""recombination activating gene 1 activating protein 1"""	RAG1AP1		21107422	Standard	NM_018845		Approved	SCP, RP11-540D14.5, slv, RZPDo834D038D, HsSWEET1, SWEET1	uc001fhj.4	Q9BRV3	OTTHUMG00000035333	ENST00000368404.4:c.367G>A	chr1.hg19:g.155110121G>A	ENSP00000357389:p.Glu123Lys	68.0	0.0		97.0	28.0	NM_018845	Q5SR64|Q6IAK6|Q96DC5|Q9UHQ2|Q9UHQ3	Missense_Mutation	SNP	ENST00000368404.4	hg19	CCDS1093.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.440450	0.63067	.	.	ENSG00000169241	ENST00000484157;ENST00000368404;ENST00000368401	.	.	.	5.08	3.15	0.36227	.	0.792831	0.12180	N	0.492158	T	0.10551	0.0258	N	0.08118	0	0.09310	N	0.999997	D;P	0.62365	0.991;0.615	P;B	0.56434	0.798;0.28	T	0.05920	-1.0856	9	0.20519	T	0.43	-1.0217	5.9692	0.19342	0.2946:0.0:0.7054:0.0	.	68;123	Q9BRV3-2;Q9BRV3	.;SWET1_HUMAN	K	58;123;68	.	ENSP00000357386:E68K	E	+	1	0	SLC50A1	153376745	0.016000	0.18221	0.003000	0.11579	0.944000	0.59088	1.819000	0.39022	1.434000	0.47414	0.655000	0.94253	GAG	.	.		0.582	SLC50A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085505.1	NM_018845	
FAM189B	10712	hgsc.bcm.edu	37	1	155223732	155223732	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:155223732A>G	ENST00000361361.2	-	4	940	c.431T>C	c.(430-432)cTc>cCc	p.L144P	SCAMP3_ENST00000472397.1_5'Flank|FAM189B_ENST00000472550.1_Intron|FAM189B_ENST00000350210.2_Intron|FAM189B_ENST00000368368.3_Missense_Mutation_p.L125P	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	144						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						GGGCCGGAGGAGGGGAACAGA	0.607																																					p.L144P		Atlas-SNP	.											.	FAM189B	51	.	0			c.T431C						.						69.0	82.0	77.0					1																	155223732		2203	4300	6503	SO:0001583	missense	10712	exon4			CGGAGGAGGGGAA	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 2"""	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.431T>C	chr1.hg19:g.155223732A>G	ENSP00000354958:p.Leu144Pro	57.0	0.0		95.0	6.0	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	hg19	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	A	10.46	1.355854	0.24598	.	.	ENSG00000160767	ENST00000368368;ENST00000361361	T;T	0.03004	4.08;4.08	4.05	4.05	0.47172	.	0.000000	0.37669	N	0.001983	T	0.01905	0.0060	L	0.34521	1.04	0.52501	D	0.999955	B;B	0.29909	0.261;0.261	B;B	0.38562	0.276;0.161	T	0.52689	-0.8542	10	0.34782	T	0.22	.	9.5821	0.39495	1.0:0.0:0.0:0.0	.	125;144	B1AVS5;P81408	.;F189B_HUMAN	P	125;144	ENSP00000357352:L125P;ENSP00000354958:L144P	ENSP00000354958:L144P	L	-	2	0	FAM189B	153490356	0.992000	0.36948	0.582000	0.28627	0.974000	0.67602	4.108000	0.57817	1.832000	0.53329	0.459000	0.35465	CTC	.	.		0.607	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589	
KIRREL	55243	hgsc.bcm.edu	37	1	158061246	158061246	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:158061246C>T	ENST00000359209.6	+	11	1438	c.1371C>T	c.(1369-1371)acC>acT	p.T457T	KIRREL_ENST00000368173.3_Silent_p.T473T|KIRREL_ENST00000392272.2_Silent_p.T354T|KIRREL_ENST00000360089.4_Silent_p.T293T|KIRREL_ENST00000416935.2_Silent_p.T357T|KIRREL_ENST00000368172.1_Silent_p.T271T			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	457	Ig-like C2-type 5.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)	p.T293T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CCACGCTCACCATCAACAATG	0.577																																					p.T457T		Atlas-SNP	.											KIRREL,NS,carcinoma,0,1	KIRREL	346	.	1	Substitution - coding silent(1)	ovary(1)	c.C1371T						.						158.0	138.0	145.0					1																	158061246		2203	4300	6503	SO:0001819	synonymous_variant	55243	exon11			GCTCACCATCAAC	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1371C>T	chr1.hg19:g.158061246C>T		57.0	0.0		64.0	12.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	ENST00000359209.6	hg19	CCDS1172.2																																																																																			.	.		0.577	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
DCAF6	55827	hgsc.bcm.edu	37	1	168034975	168034975	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:168034975T>C	ENST00000312263.6	+	16	2518	c.2314T>C	c.(2314-2316)Ttt>Ctt	p.F772L	DCAF6_ENST00000367840.3_Missense_Mutation_p.F863L|DCAF6_ENST00000432587.2_Missense_Mutation_p.F832L|DCAF6_ENST00000367843.3_Missense_Mutation_p.F792L	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	772					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						GCCACATCCGTTTGACCCAAG	0.383																																					p.F863L		Atlas-SNP	.											.	DCAF6	99	.	0			c.T2587C						.						66.0	64.0	65.0					1																	168034975		2203	4300	6503	SO:0001583	missense	55827	exon19			CATCCGTTTGACC	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2314T>C	chr1.hg19:g.168034975T>C	ENSP00000311949:p.Phe772Leu	63.0	0.0		87.0	4.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211692	0.79240	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.60171	0.21;0.21;0.21;0.21	5.41	5.41	0.78517	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.161154	0.64402	D	0.000020	T	0.56978	0.2022	L	0.55743	1.74	0.37751	D	0.925968	B;P;B;B;B	0.42620	0.126;0.785;0.191;0.316;0.387	B;P;B;B;B	0.53988	0.28;0.739;0.075;0.229;0.146	T	0.56768	-0.7924	9	0.32370	T	0.25	.	15.7437	0.77922	0.0:0.0:0.0:1.0	.	832;445;863;772;792	B4DNB8;Q9P0U0;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;.;DCAF6_HUMAN;.	L	792;832;772;863	ENSP00000356817:F792L;ENSP00000396238:F832L;ENSP00000311949:F772L;ENSP00000356814:F863L	ENSP00000311949:F772L	F	+	1	0	DCAF6	166301599	1.000000	0.71417	0.919000	0.36401	0.478000	0.33099	7.512000	0.81728	2.184000	0.69523	0.459000	0.35465	TTT	.	.		0.383	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
SLC9C2	284525	hgsc.bcm.edu	37	1	173476077	173476077	+	Missense_Mutation	SNP	A	A	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:173476077A>C	ENST00000367714.3	-	25	3565	c.3143T>G	c.(3142-3144)aTc>aGc	p.I1048S	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	1048					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										ATACACAATGATAACAAATTT	0.333																																					p.I1048S		Atlas-SNP	.											.	.	.	.	0			c.T3143G						.						136.0	125.0	129.0					1																	173476077		2203	4300	6503	SO:0001583	missense	284525	exon25			ACAATGATAACAA	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.3143T>G	chr1.hg19:g.173476077A>C	ENSP00000356687:p.Ile1048Ser	169.0	0.0		184.0	38.0	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356160	0.61293	.	.	ENSG00000162753	ENST00000367714	T	0.06849	3.25	5.58	5.58	0.84498	.	0.215417	0.32671	N	0.005785	T	0.09686	0.0238	M	0.68952	2.095	0.58432	D	0.999997	D	0.54397	0.966	P	0.49012	0.598	T	0.01287	-1.1395	10	0.87932	D	0	-30.2794	12.1245	0.53909	1.0:0.0:0.0:0.0	.	1048	Q5TAH2	S9A11_HUMAN	S	1048	ENSP00000356687:I1048S	ENSP00000356687:I1048S	I	-	2	0	SLC9A11	171742700	0.558000	0.26554	0.206000	0.23566	0.889000	0.51656	4.799000	0.62517	2.123000	0.65237	0.421000	0.28195	ATC	.	.		0.333	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
KIF21B	23046	hgsc.bcm.edu	37	1	200957983	200957983	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:200957983G>A	ENST00000422435.2	-	22	3525	c.3209C>T	c.(3208-3210)tCc>tTc	p.S1070F	KIF21B_ENST00000332129.2_Missense_Mutation_p.S1070F|KIF21B_ENST00000461742.2_Missense_Mutation_p.S1070F|KIF21B_ENST00000360529.5_Missense_Mutation_p.S1070F	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1070					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GTTCTGGGAGGAGCCTGCCAT	0.627																																					p.S1070F		Atlas-SNP	.											.	KIF21B	208	.	0			c.C3209T						.						30.0	30.0	30.0					1																	200957983		2203	4300	6503	SO:0001583	missense	23046	exon22			TGGGAGGAGCCTG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.3209C>T	chr1.hg19:g.200957983G>A	ENSP00000411831:p.Ser1070Phe	90.0	0.0		103.0	6.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.592732	0.66219	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	4.67	4.67	0.58626	Prefoldin (1);	0.063366	0.64402	D	0.000003	D	0.82797	0.5115	L	0.56769	1.78	0.53688	D	0.999976	D;P;P;D	0.63880	0.989;0.93;0.93;0.993	P;P;P;P	0.61132	0.768;0.564;0.564;0.884	D	0.84268	0.0487	10	0.72032	D	0.01	.	11.4646	0.50230	0.0838:0.0:0.9162:0.0	.	1070;1070;1070;1070	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	F	1070	ENSP00000328494:S1070F;ENSP00000353724:S1070F;ENSP00000433808:S1070F;ENSP00000411831:S1070F	ENSP00000328494:S1070F	S	-	2	0	KIF21B	199224606	1.000000	0.71417	0.982000	0.44146	0.682000	0.39822	6.789000	0.75110	2.305000	0.77605	0.491000	0.48974	TCC	.	.		0.627	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
KIF21B	23046	hgsc.bcm.edu	37	1	200978071	200978071	+	Silent	SNP	G	G	A	rs199591058		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:200978071G>A	ENST00000422435.2	-	3	589	c.273C>T	c.(271-273)gcC>gcT	p.A91A	KIF21B_ENST00000332129.2_Silent_p.A91A|KIF21B_ENST00000461742.2_Silent_p.A91A|KIF21B_ENST00000360529.5_Silent_p.A91A	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	91	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A91A(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						ACGTCTTCCCGGCCCCCGTCT	0.602																																					p.A91A		Atlas-SNP	.											KIF21B,NS,carcinoma,0,1	KIF21B	208	.	1	Substitution - coding silent(1)	endometrium(1)	c.C273T						.	G		0,4406		0,0,2203	99.0	84.0	89.0		273	-7.2	0.7	1		89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIF21B	NM_017596.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		91/1625	200978071	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon3			CTTCCCGGCCCCC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.273C>T	chr1.hg19:g.200978071G>A		29.0	0.0		41.0	2.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	G|0.999;A|0.001		0.602	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
IGFN1	91156	hgsc.bcm.edu	37	1	201182025	201182025	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:201182025A>G	ENST00000335211.4	+	12	8134	c.8004A>G	c.(8002-8004)ccA>ccG	p.P2668P	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	0						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ATGAAGGGCCAGGGGGCTTTA	0.617																																					p.P2668P		Atlas-SNP	.											.	IGFN1	220	.	0			c.A8004G						.						12.0	14.0	14.0					1																	201182025		692	1590	2282	SO:0001819	synonymous_variant	91156	exon12			AGGGCCAGGGGGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8004A>G	chr1.hg19:g.201182025A>G		70.0	0.0		95.0	4.0	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.363010	0.24684	.	.	ENSG00000163395	ENST00000412892	.	.	.	3.01	0.454	0.16644	.	.	.	.	.	T	0.21718	0.0523	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	T	0.23726	-1.0180	4	.	.	.	.	2.5428	0.04730	0.4482:0.0:0.1308:0.4209	.	.	.	.	G	86	.	.	R	+	1	2	IGFN1	199448648	0.043000	0.20138	0.001000	0.08648	0.616000	0.37450	0.407000	0.21049	-0.120000	0.11809	0.402000	0.26972	AGG	.	.		0.617	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205306696	205306696	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:205306696G>A	ENST00000367156.3	-	9	1700	c.884C>T	c.(883-885)aCg>aTg	p.T295M	KLHDC8A_ENST00000460687.1_Missense_Mutation_p.T161M|KLHDC8A_ENST00000367155.3_Missense_Mutation_p.T295M|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.T295M|KLHDC8A_ENST00000537168.1_Missense_Mutation_p.T182M	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	295										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			TGCTTCCGCCGTCTCCAGGAC	0.577																																					p.T295M		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.C884T						.						133.0	148.0	143.0					1																	205306696		2203	4300	6503	SO:0001583	missense	55220	exon6			TCCGCCGTCTCCA		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.884C>T	chr1.hg19:g.205306696G>A	ENSP00000356124:p.Thr295Met	46.0	0.0		87.0	5.0	NM_018203	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	hg19	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.574133	0.86542	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253;ENST00000537168	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	5.34	5.34	0.76211	Kelch-type beta propeller (1);	0.047999	0.85682	D	0.000000	D	0.87289	0.6140	M	0.85299	2.745	0.52099	D	0.999941	D;D	0.89917	1.0;0.999	D;D	0.64687	0.923;0.928	D	0.89270	0.3604	10	0.87932	D	0	-17.4262	18.6459	0.91410	0.0:0.0:1.0:0.0	.	182;295	F5H5F1;Q8IYD2	.;KLD8A_HUMAN	M	295;295;295;182	ENSP00000356123:T295M;ENSP00000356124:T295M;ENSP00000442229:T295M;ENSP00000443447:T182M	ENSP00000356123:T295M	T	-	2	0	KLHDC8A	203573319	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	9.094000	0.94168	2.500000	0.84329	0.591000	0.81541	ACG	.	.		0.577	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
FCAMR	83953	hgsc.bcm.edu	37	1	207133090	207133090	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:207133090T>C	ENST00000324852.4	-	7	1981	c.1507A>G	c.(1507-1509)Atg>Gtg	p.M503V	FCAMR_ENST00000486178.1_5'UTR|FCAMR_ENST00000450945.2_Silent_p.P235P|FCAMR_ENST00000400962.3_Silent_p.P235P	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	458					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						AGGGCCAGCATGGTAGAGACA	0.532																																					p.M503V	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.A1507G						.						147.0	143.0	144.0					1																	207133090		1568	3582	5150	SO:0001583	missense	83953	exon7			CCAGCATGGTAGA	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.1507A>G	chr1.hg19:g.207133090T>C	ENSP00000316491:p.Met503Val	93.0	0.0		88.0	23.0	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	hg19	CCDS53468.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.528754	0.00959	.	.	ENSG00000162897	ENST00000324852	T	0.03663	3.85	4.63	-8.22	0.01037	.	.	.	.	.	T	0.01029	0.0034	.	.	.	0.24552	N	0.994019	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42832	-0.9428	8	0.02654	T	1	-1.0385	2.1438	0.03782	0.2183:0.4507:0.1091:0.2219	.	478;458	D2KTA8;Q8WWV6	.;FCAMR_HUMAN	V	503	ENSP00000316491:M503V	ENSP00000316491:M503V	M	-	1	0	FCAMR	205199713	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.284000	0.02793	-1.872000	0.01136	-1.229000	0.01577	ATG	.	.		0.532	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029	
DNAH14	127602	hgsc.bcm.edu	37	1	225525167	225525167	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:225525167C>T	ENST00000445597.2	+	45	7685	c.7685C>T	c.(7684-7686)gCt>gTt	p.A2562V	DNAH14_ENST00000430092.1_Missense_Mutation_p.A3334V|DNAH14_ENST00000439375.2_Missense_Mutation_p.A3334V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2562					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						ATTGAAAATGCTATGAAGACA	0.458																																					p.A3334V		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10001T						.						41.0	38.0	39.0					1																	225525167		692	1591	2283	SO:0001583	missense	127602	exon65			AAAATGCTATGAA	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7685C>T	chr1.hg19:g.225525167C>T	ENSP00000409472:p.Ala2562Val	283.0	0.0		331.0	59.0	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	hg19		.	.	.	.	.	.	.	.	.	.	C	24.4	4.522249	0.85600	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.31510	1.49;1.49;1.49	5.09	5.09	0.68999	.	0.473555	0.15708	N	0.248553	T	0.70710	0.3255	H	0.96833	3.89	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.80625	-0.1299	10	0.87932	D	0	.	17.6019	0.88027	0.0:1.0:0.0:0.0	.	3334	Q0VDD8-4	.	V	2562;3334;3334	ENSP00000409472:A2562V;ENSP00000414402:A3334V;ENSP00000392061:A3334V	ENSP00000414402:A3334V	A	+	2	0	DNAH14	223591790	0.996000	0.38824	0.412000	0.26496	0.972000	0.66771	3.395000	0.52558	2.529000	0.85273	0.536000	0.68110	GCT	.	.		0.458	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PRSS38	339501	hgsc.bcm.edu	37	1	228033905	228033905	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:228033905T>C	ENST00000366757.3	+	5	1001	c.977T>C	c.(976-978)cTg>cCg	p.L326P		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	326						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						TGGTCAGTGCTGTGAGGTCAG	0.622																																					p.L326P		Atlas-SNP	.											.	PRSS38	55	.	0			c.T977C						.						72.0	68.0	69.0					1																	228033905		2203	4300	6503	SO:0001583	missense	339501	exon5			CAGTGCTGTGAGG		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"""Serine peptidases / Serine peptidases"""	29625	protein-coding gene	gene with protein product	"""marapsin 2"""					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.977T>C	chr1.hg19:g.228033905T>C	ENSP00000355719:p.Leu326Pro	30.0	0.0		52.0	4.0	NM_183062	Q7RTY6	Missense_Mutation	SNP	ENST00000366757.3	hg19	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.619038	0.46736	.	.	ENSG00000185888	ENST00000366757	D	0.89552	-2.53	4.31	3.14	0.36123	.	0.303615	0.18164	N	0.149661	D	0.85660	0.5748	N	0.08118	0	0.23260	N	0.998025	D	0.89917	1.0	D	0.68192	0.956	T	0.76011	-0.3115	10	0.87932	D	0	.	7.422	0.27077	0.1938:0.0:0.0:0.8062	.	326	A1L453	PRS38_HUMAN	P	326	ENSP00000355719:L326P	ENSP00000355719:L326P	L	+	2	0	PRSS38	226100528	0.058000	0.20735	0.019000	0.16419	0.148000	0.21650	1.533000	0.36040	0.734000	0.32515	0.460000	0.39030	CTG	.	.		0.622	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062	
OBSCN	84033	hgsc.bcm.edu	37	1	228511085	228511085	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:228511085A>G	ENST00000422127.1	+	56	15474	c.15430A>G	c.(15430-15432)Agc>Ggc	p.S5144G	OBSCN_ENST00000570156.2_Missense_Mutation_p.S6101G|OBSCN_ENST00000366709.4_Missense_Mutation_p.S2263G|OBSCN_ENST00000284548.11_Missense_Mutation_p.S5144G|OBSCN_ENST00000366707.4_Missense_Mutation_p.S2778G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5144	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTATCCTGTGAGCTTTGACTG	0.517																																					p.S6101G		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A18301G						.						75.0	77.0	77.0					1																	228511085		2130	4228	6358	SO:0001583	missense	84033	exon67			CCTGTGAGCTTTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15430A>G	chr1.hg19:g.228511085A>G	ENSP00000409493:p.Ser5144Gly	90.0	0.0		122.0	5.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928582	0.92389	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81612	0.4859	M	0.79926	2.475	0.39861	D	0.973371	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.82673	-0.0341	10	0.36615	T	0.2	.	14.9992	0.71459	1.0:0.0:0.0:0.0	.	5144;5144	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	5144;5144;2778;2263	ENSP00000284548:S5144G;ENSP00000409493:S5144G;ENSP00000355668:S2778G;ENSP00000355670:S2263G	ENSP00000284548:S5144G	S	+	1	0	OBSCN	226577708	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.073000	0.76784	2.125000	0.65367	0.533000	0.62120	AGC	.	.		0.517	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OBSCN	84033	hgsc.bcm.edu	37	1	228547659	228547659	+	Intron	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:228547659G>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Missense_Mutation_p.G3475W|OBSCN_ENST00000284548.11_Missense_Mutation_p.G6356W|OBSCN_ENST00000366707.4_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAGCTCATCGGGGCATCTCTT	0.647																																					p.G6356W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19066T						.						20.0	23.0	22.0					1																	228547659		1917	4119	6036	SO:0001627	intron_variant	84033	exon81			TCATCGGGGCATC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2618G>T	chr1.hg19:g.228547659G>T		77.0	0.0		113.0	6.0	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932384	0.52866	.	.	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.57273	0.41;0.55	4.3	-1.09	0.09904	.	.	.	.	.	T	0.50103	0.1596	M	0.62723	1.935	0.09310	N	1	D	0.57257	0.979	P	0.47162	0.54	T	0.44982	-0.9292	9	0.59425	D	0.04	.	6.5145	0.22240	0.223:0.363:0.414:0.0	.	6356	Q5VST9-3	.	W	6356;3475	ENSP00000284548:G6356W;ENSP00000355670:G3475W	ENSP00000284548:G6356W	G	+	1	0	OBSCN	226614282	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.552000	0.23376	-0.413000	0.07507	-0.300000	0.09419	GGG	.	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ACTN2	88	hgsc.bcm.edu	37	1	236906307	236906307	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:236906307A>G	ENST00000366578.4	+	11	1385	c.1219A>G	c.(1219-1221)Agg>Ggg	p.R407G	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Missense_Mutation_p.R407G|ACTN2_ENST00000546208.1_5'UTR	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	407					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TGAGAAGTTCAGGCAGAAGGC	0.532																																					p.R407G		Atlas-SNP	.											ACTN2,caecum,carcinoma,0,1	ACTN2	191	.	0			c.A1219G						.						106.0	97.0	100.0					1																	236906307		2203	4300	6503	SO:0001583	missense	88	exon11			AAGTTCAGGCAGA	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1219A>G	chr1.hg19:g.236906307A>G	ENSP00000355537:p.Arg407Gly	48.0	0.0		62.0	3.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	hg19	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.527879	0.27299	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000545611	T;T	0.51071	0.72;0.72	5.47	1.69	0.24217	.	0.618137	0.16636	N	0.205861	T	0.56441	0.1985	M	0.85710	2.77	0.42436	D	0.992697	B;B;B;B	0.31640	0.069;0.002;0.333;0.108	B;B;B;B	0.36567	0.133;0.012;0.228;0.044	T	0.62201	-0.6904	10	0.72032	D	0.01	.	14.3868	0.66949	0.4847:0.5153:0.0:0.0	.	192;407;177;407	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	G	407;407;176	ENSP00000443495:R407G;ENSP00000355537:R407G	ENSP00000355537:R407G	R	+	1	2	ACTN2	234972930	0.042000	0.20092	0.479000	0.27329	0.436000	0.31835	0.578000	0.23773	0.084000	0.17077	0.533000	0.62120	AGG	.	.		0.532	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
FMN2	56776	hgsc.bcm.edu	37	1	240370636	240370636	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:240370636G>T	ENST00000319653.9	+	5	2754	c.2524G>T	c.(2524-2526)Gaa>Taa	p.E842*		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	842	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.E985K(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AACCAGCCACGAACACTCTGT	0.557																																					p.E842X		Atlas-SNP	.											FMN2,NS,malignant_melanoma,0,3	FMN2	451	.	1	Substitution - Missense(1)	skin(1)	c.G2524T						.						105.0	100.0	102.0					1																	240370636		2203	4300	6503	SO:0001587	stop_gained	56776	exon5			AGCCACGAACACT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2524G>T	chr1.hg19:g.240370636G>T	ENSP00000318884:p.Glu842*	88.0	0.0		120.0	5.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Nonsense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	38	6.812801	0.97857	.	.	ENSG00000155816	ENST00000319653	.	.	.	4.09	4.09	0.47781	.	0.190914	0.35436	N	0.003211	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8328	0.52305	0.0:0.1769:0.8231:0.0	.	.	.	.	X	842	.	.	E	+	1	0	FMN2	238437259	0.041000	0.20044	0.720000	0.30636	0.550000	0.35303	1.026000	0.30103	2.270000	0.75569	0.555000	0.69702	GAA	.	.		0.557	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
COLEC11	78989	hgsc.bcm.edu	37	2	3652045	3652045	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:3652045G>A	ENST00000349077.4	+	2	218	c.115G>A	c.(115-117)Gtc>Atc	p.V39I	COLEC11_ENST00000402922.1_5'Flank|AC010907.2_ENST00000456450.1_RNA|COLEC11_ENST00000382062.2_Missense_Mutation_p.V39I|COLEC11_ENST00000418971.2_Missense_Mutation_p.V53I|COLEC11_ENST00000236693.7_Silent_p.S9S|COLEC11_ENST00000404205.1_5'Flank|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000403096.3_5'Flank|COLEC11_ENST00000402794.1_5'Flank	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	39					developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)	p.S9S(1)|p.V53L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		GCAGATCCTCGTCCCTGGCCT	0.642																																					p.V53I		Atlas-SNP	.											COLEC11_ENST00000418971,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	COLEC11	93	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	central_nervous_system(2)	c.G157A						.						119.0	107.0	111.0					2																	3652045		2203	4300	6503	SO:0001583	missense	78989	exon3			ATCCTCGTCCCTG	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.115G>A	chr2.hg19:g.3652045G>A	ENSP00000339168:p.Val39Ile	89.0	0.0		83.0	4.0	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Missense_Mutation	SNP	ENST00000349077.4	hg19	CCDS1649.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.140485	0.37825	.	.	ENSG00000118004	ENST00000382062;ENST00000349077;ENST00000438814;ENST00000418971	D;D;D;D	0.91631	-1.76;-2.03;-2.88;-2.16	4.83	3.95	0.45737	.	0.122413	0.53938	D	0.000042	D	0.88104	0.6347	.	.	.	0.51012	D	0.999905	P;B;P;P	0.38129	0.564;0.109;0.59;0.619	B;B;B;B	0.36989	0.077;0.031;0.113;0.238	D	0.85377	0.1117	9	0.26408	T	0.33	-30.3903	14.5751	0.68240	0.0:0.147:0.853:0.0	.	39;39;39;39	Q9BWP8-5;Q9BWP8-3;Q9BWP8-2;Q9BWP8	.;.;.;COL11_HUMAN	I	39;39;53;53	ENSP00000371494:V39I;ENSP00000339168:V39I;ENSP00000393167:V53I;ENSP00000411770:V53I	ENSP00000339168:V39I	V	+	1	0	COLEC11	3629920	1.000000	0.71417	0.705000	0.30386	0.885000	0.51271	4.185000	0.58330	1.167000	0.42706	-0.150000	0.13652	GTC	.	.		0.642	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
RHOB	388	hgsc.bcm.edu	37	2	20647265	20647265	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:20647265C>T	ENST00000272233.4	+	1	431	c.39C>T	c.(37-39)gaC>gaT	p.D13D		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	13					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	TGGTGGGCGACGGCGCGTGTG	0.682																																					p.D13D		Atlas-SNP	.											RHOB,colon,carcinoma,0,1	RHOB	18	.	0			c.C39T						.						75.0	76.0	76.0					2																	20647265		2203	4300	6503	SO:0001819	synonymous_variant	388	exon1			GGGCGACGGCGCG		CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"""oncogene RHO H6"""	165370	"""ras homolog gene family, member B"""	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.39C>T	chr2.hg19:g.20647265C>T		33.0	0.0		27.0	2.0	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Silent	SNP	ENST00000272233.4	hg19	CCDS1699.1																																																																																			.	.		0.682	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040	
ATAD2B	54454	hgsc.bcm.edu	37	2	23980414	23980414	+	Missense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:23980414G>T	ENST00000238789.5	-	25	4295	c.3952C>A	c.(3952-3954)Cca>Aca	p.P1318T	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1318						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAGTTTCTGGTTTTTCTTTT	0.393																																					p.P1318T		Atlas-SNP	.											.	ATAD2B	110	.	0			c.C3952A						.						181.0	175.0	177.0					2																	23980414		1823	4085	5908	SO:0001583	missense	54454	exon25			TTTCTGGTTTTTC	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.3952C>A	chr2.hg19:g.23980414G>T	ENSP00000238789:p.Pro1318Thr	186.0	0.0		219.0	53.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.12|11.12	1.545640|1.545640	0.27652|0.27652	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000381024|ENST00000238789;ENST00000546030	.|D	.|0.91351	.|-2.83	5.27|5.27	3.36|3.36	0.38483|0.38483	.|.	.|2.650130	.|0.01891	.|N	.|0.038537	D|D	0.82426|0.82426	0.5034|0.5034	N|N	0.12182|0.12182	0.205|0.205	0.31462|0.31462	N|N	0.669472|0.669472	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.001;0.002	T|T	0.72261|0.72261	-0.4345|-0.4345	5|10	.|0.24483	.|T	.|0.36	.|.	6.5557|6.5557	0.22460|0.22460	0.077:0.1065:0.6428:0.1738|0.077:0.1065:0.6428:0.1738	.|.	.|1318;1313	.|Q9ULI0;Q9ULI0-2	.|ATD2B_HUMAN;.	K|T	593|1318;486	.|ENSP00000238789:P1318T	.|ENSP00000238789:P1318T	N|P	-|-	3|1	2|0	ATAD2B|ATAD2B	23833918|23833918	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.989000|0.989000	0.77384|0.77384	1.311000|1.311000	0.33562|0.33562	1.355000|1.355000	0.45865|0.45865	0.563000|0.563000	0.77884|0.77884	AAC|CCA	.	.		0.393	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
C2orf44	80304	hgsc.bcm.edu	37	2	24261849	24261849	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:24261849C>T	ENST00000295148.4	-	2	573	c.516G>A	c.(514-516)gtG>gtA	p.V172V	C2orf44_ENST00000406895.3_Silent_p.V172V	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	172									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTACTGCCACCACCAGCCTCA	0.547			T	ALK	NSCLC																																p.V172V		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.G516A						.						53.0	47.0	49.0					2																	24261849		2203	4300	6503	SO:0001819	synonymous_variant	80304	exon2			TGCCACCACCAGC	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.516G>A	chr2.hg19:g.24261849C>T		77.0	0.0		83.0	21.0	NM_025203	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	hg19	CCDS1705.1																																																																																			.	.		0.547	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
AGBL5	60509	hgsc.bcm.edu	37	2	27278977	27278977	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:27278977G>A	ENST00000360131.4	+	7	1495	c.1336G>A	c.(1336-1338)Gga>Aga	p.G446R	AGBL5_ENST00000323064.8_Missense_Mutation_p.G446R|RP11-503P10.1_ENST00000607407.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	446					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATGTACGGAAACAGCTT	0.502																																					p.G446R		Atlas-SNP	.											AGBL5_ENST00000323064,lower_third,carcinoma,0,2	AGBL5	126	.	0			c.G1336A						.						124.0	124.0	124.0					2																	27278977		2203	4300	6503	SO:0001583	missense	60509	exon7			ATGTACGGAAACA	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 5"""	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.1336G>A	chr2.hg19:g.27278977G>A	ENSP00000353249:p.Gly446Arg	40.0	0.0		48.0	2.0	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	G	33	5.231204	0.95207	.	.	ENSG00000084693	ENST00000323064;ENST00000360131	T;T	0.33865	1.39;1.39	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.73001	0.3531	M	0.94142	3.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.79799	-0.1651	10	0.87932	D	0	-21.4622	20.0291	0.97531	0.0:0.0:1.0:0.0	.	446;446;446	Q8NDL9;Q8NDL9-3;Q8NDL9-2	CBPC5_HUMAN;.;.	R	446	ENSP00000323681:G446R;ENSP00000353249:G446R	ENSP00000323681:G446R	G	+	1	0	AGBL5	27132481	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.359000	0.97115	2.838000	0.97847	0.561000	0.74099	GGA	.	.		0.502	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831	
IFT172	26160	hgsc.bcm.edu	37	2	27679434	27679434	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:27679434T>C	ENST00000260570.3	-	30	3418	c.3315A>G	c.(3313-3315)agA>agG	p.R1105R		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	1105					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TATTAAGCAGTCTAACTGCAG	0.562																																					p.R1105R		Atlas-SNP	.											.	IFT172	119	.	0			c.A3315G						.						127.0	119.0	121.0					2																	27679434		2203	4300	6503	SO:0001819	synonymous_variant	26160	exon30			AAGCAGTCTAACT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.3315A>G	chr2.hg19:g.27679434T>C		74.0	0.0		81.0	4.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Silent	SNP	ENST00000260570.3	hg19	CCDS1755.1																																																																																			.	.		0.562	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
CYP26B1	56603	hgsc.bcm.edu	37	2	72359542	72359542	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:72359542C>T	ENST00000001146.2	-	6	1556	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L	CYP26B1_ENST00000412253.1_Silent_p.L260L|CYP26B1_ENST00000546307.1_Silent_p.L376L	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	451					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						CCAGCACCTTCAGGAACAGCT	0.672																																					p.L451L		Atlas-SNP	.											.	CYP26B1	73	.	0			c.G1353A						.						48.0	43.0	45.0					2																	72359542		2203	4300	6503	SO:0001819	synonymous_variant	56603	exon6			CACCTTCAGGAAC		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"""Cytochrome P450s"""	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1353G>A	chr2.hg19:g.72359542C>T		94.0	0.0		93.0	4.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Silent	SNP	ENST00000001146.2	hg19	CCDS1919.1																																																																																			.	.		0.672	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885	
INO80B	83444	hgsc.bcm.edu	37	2	74682605	74682605	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:74682605A>G	ENST00000233331.7	+	2	225	c.131A>G	c.(130-132)aAg>aGg	p.K44R	WBP1_ENST00000233615.2_5'Flank|WBP1_ENST00000409737.1_5'Flank|INO80B_ENST00000409917.1_Missense_Mutation_p.K44R|WBP1_ENST00000393972.3_5'Flank|INO80B_ENST00000469849.1_Intron	NM_031288.3	NP_112578.2	Q9C086	IN80B_HUMAN	INO80 complex subunit B	44	Lys-rich.				chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	13						aagaagcacaagaagaaacac	0.547																																					p.K44R		Atlas-SNP	.											INO80B,NS,carcinoma,0,1	INO80B	37	.	0			c.A131G						.						75.0	89.0	84.0					2																	74682605		2203	4300	6503	SO:0001583	missense	83444	exon2			AGCACAAGAAGAA	AB054538	CCDS1942.2	2p13.1	2011-07-06	2008-08-07	2008-08-07	ENSG00000115274	ENSG00000115274		"""Zinc fingers, HIT-type"", ""INO80 complex subunits"""	13324	protein-coding gene	gene with protein product	"""PAP-1 binding protein"", ""IES2 homolog (S. cerevisiae)"""		"""high mobility group AT-hook 1-like 4"", ""zinc finger, HIT type 4"""	HMGA1L4, ZNHIT4		16230350	Standard	NM_031288		Approved	HMGIYL4, PAPA-1, hIes2, PAP-1BP, IES2	uc002slg.3	Q9C086	OTTHUMG00000129959	ENST00000233331.7:c.131A>G	chr2.hg19:g.74682605A>G	ENSP00000233331:p.Lys44Arg	39.0	0.0		49.0	2.0	NM_031288		Missense_Mutation	SNP	ENST00000233331.7	hg19	CCDS1942.2	.	.	.	.	.	.	.	.	.	.	A	26.1	4.709684	0.89018	.	.	ENSG00000115274	ENST00000233331;ENST00000431187;ENST00000409917;ENST00000409493	T;T;T;T	0.55930	0.58;0.54;0.57;0.49	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.50514	0.1620	N	0.08118	0	0.52501	D	0.999956	D;D;D;D	0.69078	0.997;0.993;0.993;0.988	D;D;D;D	0.75020	0.985;0.968;0.956;0.981	T	0.52366	-0.8585	10	0.23891	T	0.37	-23.5868	13.4809	0.61334	1.0:0.0:0.0:0.0	.	62;44;44;44	B4DJ31;B4DJ22;Q9C086;B8ZZ93	.;.;IN80B_HUMAN;.	R	44;44;44;49	ENSP00000233331:K44R;ENSP00000389887:K44R;ENSP00000387267:K44R;ENSP00000386937:K49R	ENSP00000233331:K44R	K	+	2	0	INO80B	74536113	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.616000	0.83018	2.067000	0.61834	0.460000	0.39030	AAG	.	.		0.547	INO80B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252223.2	NM_031288	
DNAH6	1768	hgsc.bcm.edu	37	2	84932627	84932627	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:84932627C>A	ENST00000237449.6	+	51	8491	c.8483C>A	c.(8482-8484)gCa>gAa	p.A2828E	DNAH6_ENST00000389394.3_Missense_Mutation_p.A2828E			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2828	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGGCCATCAGCAAAGCAACTT	0.328																																					p.A2828E		Atlas-SNP	.											.	DNAH6	194	.	0			c.C8483A						.						61.0	50.0	53.0					2																	84932627		692	1591	2283	SO:0001583	missense	1768	exon52			CATCAGCAAAGCA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.8483C>A	chr2.hg19:g.84932627C>A	ENSP00000237449:p.Ala2828Glu	65.0	0.0		105.0	19.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580866	0.86748	.	.	ENSG00000115423	ENST00000389394;ENST00000237449	T;T	0.80480	-1.38;-1.38	5.49	5.49	0.81192	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.47455	D	0.000226	D	0.93986	0.8074	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95827	0.8855	10	0.87932	D	0	.	18.5012	0.90882	0.0:1.0:0.0:0.0	.	2828	Q9C0G6	DYH6_HUMAN	E	2828	ENSP00000374045:A2828E;ENSP00000237449:A2828E	ENSP00000237449:A2828E	A	+	2	0	DNAH6	84786138	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.845000	0.55880	2.727000	0.93392	0.650000	0.86243	GCA	.	.		0.328	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
REV1	51455	hgsc.bcm.edu	37	2	100019562	100019562	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:100019562C>A	ENST00000258428.3	-	20	3402	c.3174G>T	c.(3172-3174)aaG>aaT	p.K1058N	RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000393445.3_Missense_Mutation_p.K1057N|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1058					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.K1058K(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTAAAGGATTCTTTGGCACTA	0.358								Direct reversal of damage																													p.K1058N		Atlas-SNP	.											REV1,colon,carcinoma,0,1	REV1	100	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3174T						.						31.0	28.0	29.0					2																	100019562		2201	4297	6498	SO:0001583	missense	51455	exon20			AGGATTCTTTGGC	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3174G>T	chr2.hg19:g.100019562C>A	ENSP00000258428:p.Lys1058Asn	50.0	0.0		51.0	3.0	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.748285	0.69533	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.33865	1.39;1.39	5.95	3.16	0.36331	.	0.043184	0.85682	D	0.000000	T	0.51770	0.1694	M	0.73598	2.24	0.52099	D	0.999949	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.987	T	0.51260	-0.8728	10	0.56958	D	0.05	.	3.4149	0.07372	0.0:0.4766:0.1973:0.3261	.	1058;1057	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	N	1057;1058	ENSP00000377091:K1057N;ENSP00000258428:K1058N	ENSP00000258428:K1058N	K	-	3	2	REV1	99385994	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.918000	0.28678	0.839000	0.34971	0.655000	0.94253	AAG	.	.		0.358	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
TBC1D8	11138	hgsc.bcm.edu	37	2	101656711	101656711	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:101656711C>T	ENST00000376840.4	-	6	963	c.964G>A	c.(964-966)Gcc>Acc	p.A322T	TBC1D8_ENST00000409318.1_Missense_Mutation_p.A337T			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	322	GRAM 2.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.A337T(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CTGTCAGAGGCGAACATCCGC	0.577																																					p.A322T		Atlas-SNP	.											TBC1D8,NS,carcinoma,0,1	TBC1D8	169	.	1	Substitution - Missense(1)	ovary(1)	c.G964A						.						69.0	73.0	72.0					2																	101656711		2042	4188	6230	SO:0001583	missense	11138	exon6			CAGAGGCGAACAT	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.964G>A	chr2.hg19:g.101656711C>T	ENSP00000366036:p.Ala322Thr	60.0	0.0		61.0	3.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	hg19	CCDS46375.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.583712	0.28268	.	.	ENSG00000204634	ENST00000376840;ENST00000409318	D;D	0.86769	-2.17;-2.17	5.86	-7.1	0.01547	GRAM (2);	0.503517	0.20539	N	0.090356	T	0.66247	0.2770	N	0.08118	0	0.09310	N	0.999995	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.52586	-0.8556	10	0.41790	T	0.15	-9.2577	8.092	0.30805	0.1779:0.4128:0.0:0.4093	.	337;322	B7Z6L4;O95759	.;TBCD8_HUMAN	T	322;337	ENSP00000366036:A322T;ENSP00000386856:A337T	ENSP00000366036:A322T	A	-	1	0	TBC1D8	101023143	0.000000	0.05858	0.054000	0.19295	0.601000	0.36947	-0.415000	0.07106	-1.140000	0.02877	-1.147000	0.01851	GCC	.	.		0.577	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
LCT	3938	hgsc.bcm.edu	37	2	136566972	136566972	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:136566972C>T	ENST00000264162.2	-	8	2955	c.2945G>A	c.(2944-2946)cGg>cAg	p.R982Q	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	982	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	TGGGAAAATCCGAGACCAGGA	0.498																																					p.R982Q		Atlas-SNP	.											.	LCT	309	.	0			c.G2945A						.						74.0	79.0	77.0					2																	136566972		2203	4300	6503	SO:0001583	missense	3938	exon8			AAAATCCGAGACC	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2945G>A	chr2.hg19:g.136566972C>T	ENSP00000264162:p.Arg982Gln	68.0	0.0		85.0	5.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	32	5.188696	0.94923	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.61158	0.13	5.78	5.78	0.91487	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.047713	0.85682	D	0.000000	D	0.84853	0.5564	H	0.96365	3.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89003	0.3423	10	0.87932	D	0	-30.6945	20.0139	0.97470	0.0:1.0:0.0:0.0	.	982	P09848	LPH_HUMAN	Q	982;414	ENSP00000264162:R982Q	ENSP00000264162:R982Q	R	-	2	0	LCT	136283442	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.818000	0.86416	2.724000	0.93272	0.563000	0.77884	CGG	.	.		0.498	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
PKP4	8502	hgsc.bcm.edu	37	2	159481873	159481873	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:159481873C>T	ENST00000389759.3	+	7	1199	c.1087C>T	c.(1087-1089)Caa>Taa	p.Q363*	PKP4_ENST00000389757.3_Nonsense_Mutation_p.Q363*	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	363					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TGACATGGAGCAATTCGGACA	0.552										HNSCC(62;0.18)																											p.Q363X		Atlas-SNP	.											.	PKP4	133	.	0			c.C1087T						.						86.0	73.0	78.0					2																	159481873		2203	4300	6503	SO:0001587	stop_gained	8502	exon7			ATGGAGCAATTCG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.1087C>T	chr2.hg19:g.159481873C>T	ENSP00000374409:p.Gln363*	223.0	0.0		268.0	48.0	NM_001005476	Q86W91	Nonsense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	C	37	6.094775	0.97276	.	.	ENSG00000144283	ENST00000428353;ENST00000389757;ENST00000389759	.	.	.	5.67	4.78	0.61160	.	0.353767	0.29646	N	0.011565	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-1.4514	16.2064	0.82133	0.1343:0.8657:0.0:0.0	.	.	.	.	X	215;363;363	.	ENSP00000374407:Q363X	Q	+	1	0	PKP4	159190119	0.995000	0.38212	0.289000	0.24876	0.998000	0.95712	5.278000	0.65592	1.499000	0.48617	0.655000	0.94253	CAA	.	.		0.552	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
FAP	2191	hgsc.bcm.edu	37	2	163031427	163031427	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:163031427A>G	ENST00000188790.4	-	22	2126	c.1919T>C	c.(1918-1920)cTt>cCt	p.L640P	FAP_ENST00000443424.1_Missense_Mutation_p.L615P|AC007750.5_ENST00000418968.3_RNA	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						ACATTTGAAAAGACCAGTTCC	0.398																																					p.L640P		Atlas-SNP	.											.	FAP	122	.	0			c.T1919C						.						122.0	108.0	113.0					2																	163031427		2203	4300	6503	SO:0001583	missense	2191	exon22			TTGAAAAGACCAG	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"""seprase"""	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1919T>C	chr2.hg19:g.163031427A>G	ENSP00000188790:p.Leu640Pro	86.0	0.0		93.0	4.0	NM_004460		Missense_Mutation	SNP	ENST00000188790.4	hg19	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.565427	0.65651	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	T;T	0.49432	0.78;0.78	5.42	5.42	0.78866	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.238619	0.37715	N	0.001973	T	0.47210	0.1433	L	0.39085	1.19	0.80722	D	1	B;B;B	0.28605	0.007;0.005;0.217	B;B;B	0.38616	0.078;0.021;0.277	T	0.48885	-0.8995	10	0.56958	D	0.05	-20.5135	15.7747	0.78204	1.0:0.0:0.0:0.0	.	615;119;640	B4DLR2;Q12884-2;Q12884	.;.;SEPR_HUMAN	P	640;615	ENSP00000188790:L640P;ENSP00000411391:L615P	ENSP00000188790:L640P	L	-	2	0	FAP	162739673	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.777000	0.91781	2.194000	0.70268	0.533000	0.62120	CTT	.	.		0.398	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2		
TNS1	7145	hgsc.bcm.edu	37	2	218713231	218713231	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:218713231T>C	ENST00000171887.4	-	17	2086	c.1634A>G	c.(1633-1635)gAc>gGc	p.D545G	TNS1_ENST00000419504.1_Missense_Mutation_p.D545G|TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Missense_Mutation_p.D545G	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	545					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GTAGGACTTGTCCAGACCGTT	0.657																																					p.D545G		Atlas-SNP	.											.	TNS1	251	.	0			c.A1634G						.						53.0	60.0	57.0					2																	218713231		2203	4299	6502	SO:0001583	missense	7145	exon17			GACTTGTCCAGAC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1634A>G	chr2.hg19:g.218713231T>C	ENSP00000171887:p.Asp545Gly	95.0	0.0		67.0	4.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.072243	0.36566	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.95069	-2.98;-2.98;-2.99;-3.6	4.79	4.79	0.61399	.	0.587686	0.17541	N	0.170538	D	0.94974	0.8374	L	0.55990	1.75	0.80722	D	1	D;D;P;P;P	0.59357	0.958;0.985;0.89;0.89;0.791	P;P;B;B;B	0.55923	0.604;0.787;0.318;0.318;0.272	D	0.93468	0.6816	10	0.30854	T	0.27	.	14.4915	0.67654	0.0:0.0:0.0:1.0	.	545;599;545;545;545	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	G	545;545;545;670	ENSP00000171887:D545G;ENSP00000408724:D545G;ENSP00000406016:D545G;ENSP00000405460:D670G	ENSP00000171887:D545G	D	-	2	0	TNS1	218421476	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	4.390000	0.59646	2.013000	0.59113	0.459000	0.35465	GAC	.	.		0.657	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
TNS1	7145	hgsc.bcm.edu	37	2	218762666	218762666	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:218762666T>A	ENST00000171887.4	-	6	475	c.23A>T	c.(22-24)gAg>gTg	p.E8V	TNS1_ENST00000419504.1_Missense_Mutation_p.E8V|TNS1_ENST00000310858.6_Missense_Mutation_p.E39V|TNS1_ENST00000430930.1_Missense_Mutation_p.E8V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	8	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		ACAGCTGTCCTCCATGGTCCG	0.587																																					p.E8V		Atlas-SNP	.											.,2	TNS1	251	.	0			c.A23T						.						126.0	93.0	104.0					2																	218762666		2203	4300	6503	SO:0001583	missense	7145	exon6			CTGTCCTCCATGG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.23A>T	chr2.hg19:g.218762666T>A	ENSP00000171887:p.Glu8Val	44.0	0.0		48.0	4.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	T	33	5.205287	0.95033	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858;ENST00000413280;ENST00000439083;ENST00000423413;ENST00000449814	D;D;D;D;D;D;D;D;D	0.99252	-3.18;-3.17;-3.18;-3.63;-3.97;-3.93;-5.63;-4.93;-4.72	5.42	5.42	0.78866	Phosphatase tensin type (1);	0.050950	0.85682	D	0.000000	D	0.99248	0.9738	M	0.67517	2.055	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.981;0.997;1.0;1.0;1.0	D;P;D;D;D;D	0.85130	0.997;0.874;0.946;0.982;0.997;0.997	D	0.99509	1.0955	10	0.87932	D	0	.	15.6246	0.76845	0.0:0.0:0.0:1.0	.	8;62;39;8;8;8	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.;.;.;TENS1_HUMAN;.;.	V	8;8;8;133;76;39;8;8;73;8	ENSP00000171887:E8V;ENSP00000408724:E8V;ENSP00000406016:E8V;ENSP00000405460:E133V;ENSP00000400383:E76V;ENSP00000308321:E39V;ENSP00000395615:E8V;ENSP00000404477:E8V;ENSP00000411349:E73V	ENSP00000171887:E8V	E	-	2	0	TNS1	218470911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.066000	0.71185	2.274000	0.75844	0.533000	0.62120	GAG	.	.		0.587	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
FEV	54738	hgsc.bcm.edu	37	2	219849754	219849754	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:219849754T>C	ENST00000295727.1	-	1	625	c.44A>G	c.(43-45)tAc>tGc	p.Y15C		NM_017521.2	NP_059991.1	Q99581	FEV_HUMAN	FEV (ETS oncogene family)	15					cell differentiation (GO:0030154)|neuron fate specification (GO:0048665)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)		EWSR1/FEV(11)|FUS/FEV(2)	large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCTGGCAGGTACATGTTGAT	0.697			T	"""EWSR1,  FUS"""	Ewing sarcoma																																p.Y15C	NSCLC(198;941 2228 4658 24163 34665)	Atlas-SNP	.		Dom	yes		2	2q36	54738	FEV protein - (HSRNAFEV)		M	.	FEV	10	.	0			c.A44G						.						9.0	9.0	9.0					2																	219849754		2130	4192	6322	SO:0001583	missense	54738	exon1			GGCAGGTACATGT		CCDS2428.1	2q36	2008-02-05			ENSG00000163497	ENSG00000163497			18562	protein-coding gene	gene with protein product		607150	"""FEV (fifth Ewing variant)"""			9121764	Standard	NM_017521		Approved	Pet-1	uc002vji.1	Q99581	OTTHUMG00000133080	ENST00000295727.1:c.44A>G	chr2.hg19:g.219849754T>C	ENSP00000295727:p.Tyr15Cys	48.0	0.0		73.0	4.0	NM_017521		Missense_Mutation	SNP	ENST00000295727.1	hg19	CCDS2428.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019993	0.54576	.	.	ENSG00000163497	ENST00000295727	T	0.40476	1.03	3.6	3.6	0.41247	.	1.997360	0.02604	U	0.101365	T	0.50871	0.1641	N	0.14661	0.345	0.47276	D	0.999378	D	0.67145	0.996	D	0.74674	0.984	T	0.41556	-0.9502	10	0.45353	T	0.12	.	11.3339	0.49492	0.0:0.0:0.0:1.0	.	15	Q99581	FEV_HUMAN	C	15	ENSP00000295727:Y15C	ENSP00000295727:Y15C	Y	-	2	0	FEV	219557998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.737000	0.62066	1.496000	0.48567	0.460000	0.39030	TAC	.	.		0.697	FEV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256725.1		
SPEG	10290	hgsc.bcm.edu	37	2	220333895	220333895	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:220333895T>C	ENST00000312358.7	+	13	3641	c.3509T>C	c.(3508-3510)aTg>aCg	p.M1170T	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1170					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.M1170R(1)		breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTGGAGAAGATGCCATCCATT	0.672																																					p.M1170T		Atlas-SNP	.											SPEG,NS,carcinoma,0,1	SPEG	272	.	1	Substitution - Missense(1)	kidney(1)	c.T3509C						.						37.0	44.0	42.0					2																	220333895		2173	4275	6448	SO:0001583	missense	10290	exon13			AGAAGATGCCATC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3509T>C	chr2.hg19:g.220333895T>C	ENSP00000311684:p.Met1170Thr	69.0	0.0		63.0	4.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.752470	0.49362	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.64260	-0.09	4.77	4.77	0.60923	.	0.000000	0.51477	D	0.000098	T	0.67878	0.2940	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	T	0.72330	-0.4326	10	0.72032	D	0.01	.	14.4658	0.67482	0.0:0.0:0.0:1.0	.	1170	Q15772	SPEG_HUMAN	T	1170	ENSP00000311684:M1170T	ENSP00000265327:M1170T	M	+	2	0	SPEG	220042139	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.829000	0.86735	2.015000	0.59207	0.533000	0.62120	ATG	.	.		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
COL4A4	1286	hgsc.bcm.edu	37	2	228012135	228012135	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:228012135C>T	ENST00000396625.3	-	2	272	c.65G>A	c.(64-66)gGt>gAt	p.G22D	COL4A4_ENST00000329662.7_Missense_Mutation_p.G22D	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	22					axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCACCAGGGACCTGTGGCCAA	0.413																																					p.G22D		Atlas-SNP	.											.	COL4A4	215	.	0			c.G65A						.						246.0	258.0	254.0					2																	228012135		1919	4135	6054	SO:0001583	missense	1286	exon2			CAGGGACCTGTGG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.65G>A	chr2.hg19:g.228012135C>T	ENSP00000379866:p.Gly22Asp	62.0	0.0		56.0	8.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	c	0.261	-0.999385	0.02128	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.90004	-2.6;-2.55	4.59	-6.5	0.01884	.	.	.	.	.	T	0.69931	0.3166	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60219	-0.7306	9	0.11182	T	0.66	.	2.3552	0.04293	0.1402:0.3799:0.1208:0.3591	.	22	P53420	CO4A4_HUMAN	D	22	ENSP00000379866:G22D;ENSP00000328553:G22D	ENSP00000328553:G22D	G	-	2	0	COL4A4	227720379	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.870000	0.04228	-1.041000	0.03266	-1.945000	0.00491	GGT	.	.		0.413	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
SH3BP4	23677	hgsc.bcm.edu	37	2	235950464	235950464	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:235950464A>G	ENST00000409212.1	+	4	1558	c.1051A>G	c.(1051-1053)Acc>Gcc	p.T351A	SH3BP4_ENST00000392011.2_Missense_Mutation_p.T351A|SH3BP4_ENST00000344528.4_Missense_Mutation_p.T351A			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	351					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CCCTGGGGAGACCCAGCAGAT	0.622																																					p.T351A		Atlas-SNP	.											.	SH3BP4	109	.	0			c.A1051G						.						28.0	30.0	29.0					2																	235950464		2203	4300	6503	SO:0001583	missense	23677	exon4			GGGGAGACCCAGC	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1051A>G	chr2.hg19:g.235950464A>G	ENSP00000386862:p.Thr351Ala	54.0	0.0		68.0	4.0	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	A	8.864	0.947616	0.18356	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528	T;T;T	0.41065	1.01;1.01;1.01	5.62	5.62	0.85841	ZU5 (1);	0.190156	0.56097	D	0.000036	T	0.42040	0.1185	L	0.53249	1.67	0.42239	D	0.991924	B;B	0.24823	0.112;0.112	B;B	0.30029	0.11;0.11	T	0.27297	-1.0078	10	0.30854	T	0.27	-0.5749	14.651	0.68797	1.0:0.0:0.0:0.0	.	351;351	A8K594;Q9P0V3	.;SH3B4_HUMAN	A	351	ENSP00000375867:T351A;ENSP00000386862:T351A;ENSP00000340237:T351A	ENSP00000340237:T351A	T	+	1	0	SH3BP4	235615203	0.846000	0.29590	0.912000	0.35992	0.946000	0.59487	5.972000	0.70448	2.129000	0.65627	0.533000	0.62120	ACC	.	.		0.622	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
COL6A3	1293	hgsc.bcm.edu	37	2	238289663	238289663	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:238289663C>T	ENST00000295550.4	-	5	2244	c.1792G>A	c.(1792-1794)Gac>Aac	p.D598N	COL6A3_ENST00000409809.1_Missense_Mutation_p.D392N|COL6A3_ENST00000392004.3_Missense_Mutation_p.D392N|COL6A3_ENST00000346358.4_Missense_Mutation_p.D598N|COL6A3_ENST00000353578.4_Missense_Mutation_p.D392N|COL6A3_ENST00000392003.2_Missense_Mutation_p.D191N|COL6A3_ENST00000472056.1_Missense_Mutation_p.D191N|COL6A3_ENST00000347401.3_Missense_Mutation_p.D397N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	598	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D598N(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AGGGAGGAGTCGAAAGCGATC	0.592																																					p.D598N		Atlas-SNP	.											COL6A3_ENST00000392004,colon,carcinoma,0,3	COL6A3	608	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1792A						.						81.0	74.0	77.0					2																	238289663		2203	4300	6503	SO:0001583	missense	1293	exon5			AGGAGTCGAAAGC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1792G>A	chr2.hg19:g.238289663C>T	ENSP00000295550:p.Asp598Asn	49.0	0.0		56.0	3.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893663	0.52121	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.81	5.81	0.92471	von Willebrand factor, type A (3);	0.109102	0.40064	N	0.001193	D	0.89026	0.6598	L	0.55017	1.72	0.20563	N	0.999885	P;D;D;D;D;P	0.89917	0.854;0.999;0.992;1.0;1.0;0.854	B;D;D;D;D;B	0.76575	0.141;0.97;0.912;0.982;0.988;0.141	T	0.80547	-0.1334	10	0.20519	T	0.43	.	20.0804	0.97772	0.0:1.0:0.0:0.0	.	598;191;191;392;392;598	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	N	598;397;392;191;392;598;392;191;598	ENSP00000295550:D598N;ENSP00000315609:D397N;ENSP00000315873:D392N;ENSP00000418285:D191N;ENSP00000386844:D392N;ENSP00000295546:D598N;ENSP00000375861:D392N;ENSP00000375860:D191N;ENSP00000389539:D598N	ENSP00000295550:D598N	D	-	1	0	COL6A3	237954402	0.923000	0.31300	0.610000	0.28997	0.125000	0.20455	2.267000	0.43329	2.738000	0.93877	0.655000	0.94253	GAC	.	.		0.592	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
ILKAP	80895	hgsc.bcm.edu	37	2	239079271	239079271	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:239079271C>T	ENST00000254654.3	-	12	1260	c.1085G>A	c.(1084-1086)cGc>cAc	p.R362H		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	362	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		TGCTTCGTAGCGGGCGTCGGC	0.612																																					p.R362H		Atlas-SNP	.											ILKAP,NS,carcinoma,0,1	ILKAP	42	.	0			c.G1085A						.						43.0	43.0	43.0					2																	239079271		2203	4300	6503	SO:0001583	missense	80895	exon12			TCGTAGCGGGCGT	AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	15566	protein-coding gene	gene with protein product			"""integrin-linked kinase-associated serine/threonine phosphatase 2C"""				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.1085G>A	chr2.hg19:g.239079271C>T	ENSP00000254654:p.Arg362His	111.0	0.0		69.0	3.0	NM_030768	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	hg19	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.719602	0.48728	.	.	ENSG00000132323	ENST00000254654	T	0.17213	2.29	5.69	5.69	0.88448	Protein phosphatase 2C-like (5);	0.112628	0.64402	D	0.000012	T	0.15825	0.0381	L	0.42632	1.34	0.44852	D	0.997862	B	0.31125	0.309	B	0.33042	0.157	T	0.05582	-1.0876	10	0.12766	T	0.61	-0.4038	13.5499	0.61726	0.156:0.844:0.0:0.0	.	362	Q9H0C8	ILKAP_HUMAN	H	362	ENSP00000254654:R362H	ENSP00000254654:R362H	R	-	2	0	ILKAP	238744010	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	2.581000	0.46077	2.688000	0.91661	0.563000	0.77884	CGC	.	.		0.612	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768	
OR6B3	150681	hgsc.bcm.edu	37	2	240984862	240984862	+	Missense_Mutation	SNP	G	G	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:240984862G>C	ENST00000319423.4	-	1	627	c.628C>G	c.(628-630)Cca>Gca	p.P210A	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(10)|lung(4)|ovary(2)|prostate(1)	18		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GCCAGGAGTGGAAACACCAGG	0.587																																					p.P210A		Atlas-SNP	.											.	OR6B3	37	.	0			c.C628G						.						63.0	70.0	68.0					2																	240984862		2141	4244	6385	SO:0001583	missense	150681	exon1			GGAGTGGAAACAC		CCDS42837.1	2q37.3	2013-09-23	2002-11-13	2002-11-15	ENSG00000178586	ENSG00000178586		"""GPCR / Class A : Olfactory receptors"""	15042	protein-coding gene	gene with protein product			"""olfactory receptor, family 6, subfamily B, member 3 pseudogene"""	OR6B3P			Standard	NM_173351		Approved	OR6B3Q	uc010zoe.2	Q8NGW1	OTTHUMG00000152399	ENST00000319423.4:c.628C>G	chr2.hg19:g.240984862G>C	ENSP00000322435:p.Pro210Ala	256.0	0.0		279.0	55.0	NM_173351	Q6IFH3	Missense_Mutation	SNP	ENST00000319423.4	hg19	CCDS42837.1	.	.	.	.	.	.	.	.	.	.	g	10.32	1.317894	0.23994	.	.	ENSG00000178586	ENST00000319423	T	0.56275	0.47	4.09	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.145705	0.31519	N	0.007506	T	0.66056	0.2751	M	0.64676	1.99	0.33789	D	0.625263	D	0.76494	0.999	D	0.75484	0.986	T	0.73786	-0.3873	10	0.36615	T	0.2	.	12.1077	0.53821	0.0:0.1752:0.8248:0.0	.	210	Q8NGW1	OR6B3_HUMAN	A	210	ENSP00000322435:P210A	ENSP00000322435:P210A	P	-	1	0	OR6B3	240633535	0.263000	0.24083	0.177000	0.23020	0.045000	0.14185	0.989000	0.29629	1.267000	0.44247	-0.243000	0.11985	CCA	.	.		0.587	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1		
SCN11A	11280	hgsc.bcm.edu	37	3	38921489	38921489	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:38921489T>C	ENST00000302328.3	-	19	3543	c.3345A>G	c.(3343-3345)ggA>ggG	p.G1115G	SCN11A_ENST00000450244.1_Silent_p.G1115G|SCN11A_ENST00000456224.3_Silent_p.G1077G|SCN11A_ENST00000444237.2_Silent_p.G1115G	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1115					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGAAATACTTTCCAAATCCGA	0.403																																					p.G1115G		Atlas-SNP	.											.	SCN11A	296	.	0			c.A3345G						.						76.0	72.0	73.0					3																	38921489		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon19			ATACTTTCCAAAT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.3345A>G	chr3.hg19:g.38921489T>C		80.0	0.0		88.0	4.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.403	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
WDR6	11180	hgsc.bcm.edu	37	3	49052272	49052272	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:49052272T>C	ENST00000608424.1	+	6	2956	c.2917T>C	c.(2917-2919)Tcc>Ccc	p.S973P	WDR6_ENST00000448293.1_Missense_Mutation_p.S922P|WDR6_ENST00000395474.3_Missense_Mutation_p.S1003P|WDR6_ENST00000415265.2_Missense_Mutation_p.S421P|DALRD3_ENST00000496568.1_5'Flank			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	973					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		TGGCACCCCCTCCCTGACTCT	0.617																																					p.S1003P		Atlas-SNP	.											.	WDR6	79	.	0			c.T3007C						.						76.0	82.0	80.0					3																	49052272		2203	4300	6503	SO:0001583	missense	11180	exon6			ACCCCCTCCCTGA	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"""WD repeat domain containing"""	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.2917T>C	chr3.hg19:g.49052272T>C	ENSP00000477389:p.Ser973Pro	62.0	0.0		104.0	5.0	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	hg19		.	.	.	.	.	.	.	.	.	.	T	9.177	1.022694	0.19433	.	.	ENSG00000178252	ENST00000395474;ENST00000415265;ENST00000448293	T;T;T	0.65549	-0.16;0.21;0.21	5.21	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.380708	0.31484	N	0.007567	T	0.39860	0.1094	N	0.08118	0	0.20074	N	0.999939	P;B;B	0.35328	0.495;0.175;0.002	B;B;B	0.38264	0.269;0.126;0.01	T	0.21759	-1.0236	10	0.35671	T	0.21	-11.6107	6.665	0.23035	0.0:0.0809:0.2938:0.6253	.	421;973;922	E9PBK6;Q9NNW5;E9PDU5	.;WDR6_HUMAN;.	P	1003;421;922	ENSP00000378857:S1003P;ENSP00000412195:S421P;ENSP00000413432:S922P	ENSP00000378857:S1003P	S	+	1	0	WDR6	49027276	0.697000	0.27767	0.749000	0.31150	0.233000	0.25261	1.839000	0.39220	0.921000	0.36994	0.459000	0.35465	TCC	.	.		0.617	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1		
USP4	7375	hgsc.bcm.edu	37	3	49362451	49362451	+	Missense_Mutation	SNP	C	C	A	rs117411669	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:49362451C>A	ENST00000265560.4	-	5	555	c.509G>T	c.(508-510)cGg>cTg	p.R170L	USP4_ENST00000416417.1_Missense_Mutation_p.R170L|USP4_ENST00000415188.1_Missense_Mutation_p.R170L|USP4_ENST00000351842.4_Missense_Mutation_p.R170L	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	170	Necessary for interaction with SART3. {ECO:0000269|PubMed:20595234}.|Ubiquitin-like 1.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		GAATAGCTTCCGCATCTCTTT	0.488																																					p.R170L		Atlas-SNP	.											.	USP4	72	.	0			c.G509T						.						162.0	162.0	162.0					3																	49362451		2203	4300	6503	SO:0001583	missense	7375	exon5			AGCTTCCGCATCT	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.509G>T	chr3.hg19:g.49362451C>A	ENSP00000265560:p.Arg170Leu	131.0	0.0		150.0	42.0	NM_001251877	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	hg19	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966271	0.92855	.	.	ENSG00000114316	ENST00000351842;ENST00000265560;ENST00000416417;ENST00000415188	T;T;T	0.30981	2.01;2.16;1.51	5.51	5.51	0.81932	.	0.061185	0.64402	D	0.000002	T	0.57198	0.2037	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.94	T	0.56282	-0.8005	10	0.46703	T	0.11	-17.6222	17.9838	0.89150	0.0:1.0:0.0:0.0	.	170;170	Q13107-2;Q13107	.;UBP4_HUMAN	L	170	ENSP00000341028:R170L;ENSP00000265560:R170L;ENSP00000400623:R170L	ENSP00000265560:R170L	R	-	2	0	USP4	49337455	1.000000	0.71417	0.951000	0.38953	0.626000	0.37791	5.974000	0.70465	2.604000	0.88044	0.491000	0.48974	CGG	.	C|0.999;T|0.001		0.488	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
CACNA2D2	9254	hgsc.bcm.edu	37	3	50413239	50413239	+	Splice_Site	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:50413239C>T	ENST00000479441.1	-	20	1845		c.e20+1		CACNA2D2_ENST00000424201.2_Splice_Site|CACNA2D2_ENST00000429770.1_Splice_Site|CACNA2D2_ENST00000395083.1_Splice_Site|CACNA2D2_ENST00000266039.3_Splice_Site|CACNA2D2_ENST00000360963.3_Splice_Site|CACNA2D2_ENST00000435965.1_Splice_Site|CACNA2D2_ENST00000423994.2_Splice_Site			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2						energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TGCCTCCTTACCTCATCCAGG	0.627																																					.		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.1845+1G>A						.						86.0	77.0	80.0					3																	50413239		2203	4300	6503	SO:0001630	splice_region_variant	9254	exon21			TCCTTACCTCATC	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"""Calcium channel subunits"""	1400	protein-coding gene	gene with protein product	"""gene 26"""	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.1845+1G>A	chr3.hg19:g.50413239C>T		58.0	0.0		76.0	4.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Splice_Site	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.622034	0.66787	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0303	0.58839	0.0:0.9186:0.0:0.0814	.	.	.	.	.	-1	.	.	.	-	.	.	CACNA2D2	50388243	1.000000	0.71417	0.996000	0.52242	0.677000	0.39632	7.647000	0.83462	2.126000	0.65437	0.462000	0.41574	.	.	.		0.627	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	Intron
HEMK1	51409	hgsc.bcm.edu	37	3	50614592	50614592	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:50614592T>C	ENST00000232854.4	+	5	1076	c.524T>C	c.(523-525)cTc>cCc	p.L175P	HEMK1_ENST00000455834.1_Missense_Mutation_p.L175P|HEMK1_ENST00000434410.1_Missense_Mutation_p.L175P	NM_016173.3	NP_057257.1	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1	175					DNA methylation (GO:0006306)	mitochondrion (GO:0005739)	DNA binding (GO:0003677)|N-methyltransferase activity (GO:0008170)|protein methyltransferase activity (GO:0008276)			lung(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000283)|KIRC - Kidney renal clear cell carcinoma(197;0.0179)|Kidney(197;0.0212)		GCCATCTCCCTCAGCCTGCTG	0.632																																					p.L175P		Atlas-SNP	.											.	HEMK1	17	.	0			c.T524C						.						51.0	53.0	52.0					3																	50614592		2203	4300	6503	SO:0001583	missense	51409	exon5			TCTCCCTCAGCCT	AF172244	CCDS2830.1	3p21	2008-02-05			ENSG00000114735	ENSG00000114735			24923	protein-coding gene	gene with protein product						10690633	Standard	XM_005265218		Approved	MTQ1	uc003dav.3	Q9Y5R4	OTTHUMG00000156849	ENST00000232854.4:c.524T>C	chr3.hg19:g.50614592T>C	ENSP00000232854:p.Leu175Pro	73.0	0.0		69.0	4.0	NM_016173		Missense_Mutation	SNP	ENST00000232854.4	hg19	CCDS2830.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.483225	0.63962	.	.	ENSG00000114735	ENST00000434410;ENST00000232854;ENST00000455834;ENST00000443894	T;T;T;T	0.68765	2.28;2.28;2.28;-0.35	5.2	5.2	0.72013	Methyltransferase small (1);	0.066463	0.64402	D	0.000011	D	0.86727	0.6002	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90005	0.4117	10	0.72032	D	0.01	-19.166	11.3894	0.49804	0.0:0.0:0.0:1.0	.	175	Q9Y5R4	HEMK1_HUMAN	P	175;175;175;13	ENSP00000404843:L175P;ENSP00000232854:L175P;ENSP00000404334:L175P;ENSP00000404168:L13P	ENSP00000232854:L175P	L	+	2	0	HEMK1	50589596	1.000000	0.71417	0.993000	0.49108	0.633000	0.38033	5.195000	0.65131	2.198000	0.70561	0.533000	0.62120	CTC	.	.		0.632	HEMK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346231.1	NM_016173	
GNL3	26354	hgsc.bcm.edu	37	3	52727767	52727767	+	Missense_Mutation	SNP	G	G	C	rs111396798|rs374163260	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:52727767G>C	ENST00000418458.1	+	13	1617	c.1444G>C	c.(1444-1446)Gag>Cag	p.E482Q	SNORD69_ENST00000391150.1_RNA|SNORD19B_ENST00000459623.1_RNA|GNL3_ENST00000394799.2_Missense_Mutation_p.E470Q|SNORD19_ENST00000410413.1_RNA|GLT8D1_ENST00000463827.1_5'Flank	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	482	Acidic. {ECO:0000250}.				cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		AAGGAAGCAGGAGGAGAGGGA	0.418																																					p.E482Q		Atlas-SNP	.											GNL3,NS,carcinoma,0,1	GNL3	37	.	0			c.G1444C						.						93.0	112.0	105.0					3																	52727767		2202	4300	6502	SO:0001583	missense	26354	exon13			AAGCAGGAGGAGA	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.1444G>C	chr3.hg19:g.52727767G>C	ENSP00000395772:p.Glu482Gln	123.0	0.0		134.0	10.0	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Missense_Mutation	SNP	ENST00000418458.1	hg19	CCDS2861.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122420	0.37436	.	.	ENSG00000163938	ENST00000418458;ENST00000394799	T;T	0.30981	1.51;1.51	5.23	4.36	0.52297	.	0.635861	0.18255	N	0.146817	T	0.17280	0.0415	N	0.08118	0	0.25314	N	0.989178	P	0.49961	0.93	B	0.42319	0.383	T	0.04281	-1.0963	10	0.41790	T	0.15	.	11.162	0.48520	0.0843:0.0:0.9157:0.0	.	482	Q9BVP2	GNL3_HUMAN	Q	482;470	ENSP00000395772:E482Q;ENSP00000378278:E470Q	ENSP00000378278:E470Q	E	+	1	0	GNL3	52702807	0.272000	0.24172	0.650000	0.29550	0.067000	0.16453	1.481000	0.35476	1.443000	0.47586	0.511000	0.50034	GAG	.	.		0.418	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366	
FAM208A	23272	hgsc.bcm.edu	37	3	56680996	56680996	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:56680996G>A	ENST00000493960.2	-	14	1779	c.1769C>T	c.(1768-1770)tCa>tTa	p.S590L	FAM208A_ENST00000431842.2_Missense_Mutation_p.S194L|FAM208A_ENST00000355628.5_Missense_Mutation_p.S590L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	590							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TCTGGGAGCTGAGTATAAGAA	0.303																																					p.S590L		Atlas-SNP	.											.	FAM208A	113	.	0			c.C1769T						.						30.0	33.0	32.0					3																	56680996		2198	4294	6492	SO:0001583	missense	23272	exon14			GGAGCTGAGTATA	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1769C>T	chr3.hg19:g.56680996G>A	ENSP00000417509:p.Ser590Leu	201.0	0.0		241.0	31.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	9.606	1.129899	0.21041	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.11821	2.74;2.91;2.91	5.38	5.38	0.77491	.	0.246251	0.29178	N	0.012916	T	0.11879	0.0289	N	0.25647	0.755	0.34260	D	0.679742	B;P;P	0.35272	0.045;0.493;0.493	B;B;B	0.39258	0.031;0.215;0.295	T	0.21177	-1.0253	10	0.26408	T	0.33	-1.2621	12.6157	0.56576	0.0747:0.0:0.9253:0.0	.	590;590;194	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	L	194;590;590	ENSP00000399410:S194L;ENSP00000417509:S590L;ENSP00000347845:S590L	ENSP00000347845:S590L	S	-	2	0	C3orf63	56656036	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.899000	0.63245	2.793000	0.96121	0.655000	0.94253	TCA	.	.		0.303	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
MORC1	27136	hgsc.bcm.edu	37	3	108723940	108723940	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:108723940C>A	ENST00000483760.1	-	18	1970	c.1927G>T	c.(1927-1929)Gtc>Ttc	p.V643F	MORC1_ENST00000232603.5_Missense_Mutation_p.V664F					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GCTAGTTTGACATTTTCTGGC	0.338																																					p.V664F		Atlas-SNP	.											.	MORC1	211	.	0			c.G1990T						.						96.0	100.0	99.0					3																	108723940		2203	4300	6503	SO:0001583	missense	27136	exon19			GTTTGACATTTTC	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1927G>T	chr3.hg19:g.108723940C>A	ENSP00000417282:p.Val643Phe	108.0	0.0		119.0	25.0	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.09	2.729876	0.48833	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.08193	3.14;3.12	4.44	-0.535	0.11879	.	0.929268	0.08916	N	0.875125	T	0.04679	0.0127	L	0.27053	0.805	0.09310	N	1	P;P	0.40476	0.718;0.718	B;B	0.33690	0.168;0.168	T	0.38542	-0.9656	10	0.33940	T	0.23	0.1732	4.2726	0.10794	0.0:0.4279:0.1757:0.3964	.	643;664	E7ERX1;Q86VD1	.;MORC1_HUMAN	F	664;643	ENSP00000232603:V664F;ENSP00000417282:V643F	ENSP00000232603:V664F	V	-	1	0	MORC1	110206630	0.000000	0.05858	0.000000	0.03702	0.740000	0.42216	-0.877000	0.04197	-0.114000	0.11936	0.557000	0.71058	GTC	.	.		0.338	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
CASR	846	hgsc.bcm.edu	37	3	121980604	121980604	+	Missense_Mutation	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:121980604A>T	ENST00000490131.1	+	4	1094	c.722A>T	c.(721-723)gAa>gTa	p.E241V	CASR_ENST00000296154.5_Missense_Mutation_p.E241V|CASR_ENST00000498619.1_Missense_Mutation_p.E241V	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	241					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GACTTCAGTGAACTCATCTCC	0.512																																					p.E241V		Atlas-SNP	.											.	CASR	190	.	0			c.A722T						.						165.0	177.0	173.0					3																	121980604		2203	4300	6503	SO:0001583	missense	846	exon4			TCAGTGAACTCAT	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.722A>T	chr3.hg19:g.121980604A>T	ENSP00000418685:p.Glu241Val	182.0	0.0		221.0	20.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.542488	0.27563	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.87729	-2.29;-2.29;-2.29	6.17	6.17	0.99709	Extracellular ligand-binding receptor (1);	0.045100	0.85682	D	0.000000	D	0.83580	0.5285	L	0.42008	1.315	0.53005	D	0.99996	B;B	0.32409	0.37;0.248	B;B	0.30316	0.114;0.047	D	0.83400	0.0022	10	0.72032	D	0.01	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	241;241	E7ENE0;P41180	.;CASR_HUMAN	V	241	ENSP00000418685:E241V;ENSP00000420194:E241V;ENSP00000296154:E241V	ENSP00000296154:E241V	E	+	2	0	CASR	123463294	1.000000	0.71417	0.921000	0.36526	0.354000	0.29330	7.211000	0.77933	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.512	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388	
PDIA5	10954	hgsc.bcm.edu	37	3	122849447	122849447	+	Silent	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:122849447C>A	ENST00000316218.7	+	11	989	c.894C>A	c.(892-894)gtC>gtA	p.V298V		NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	298	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CTGTCCTCGTCATGTTCCACG	0.562																																					p.V298V		Atlas-SNP	.											.	PDIA5	66	.	0			c.C894A						.						144.0	119.0	127.0					3																	122849447		2203	4300	6503	SO:0001819	synonymous_variant	10954	exon11			CCTCGTCATGTTC	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.894C>A	chr3.hg19:g.122849447C>A		113.0	0.0		121.0	26.0	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	hg19	CCDS3020.1																																																																																			.	.		0.562	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
CPNE4	131034	hgsc.bcm.edu	37	3	131624109	131624109	+	Splice_Site	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:131624109T>A	ENST00000512055.1	-	6	2305	c.179A>T	c.(178-180)gAg>gTg	p.E60V	CPNE4_ENST00000429747.1_Splice_Site_p.E60V|CPNE4_ENST00000502818.1_Splice_Site_p.E78V|CPNE4_ENST00000511604.1_Splice_Site_p.E60V|CPNE4_ENST00000512332.1_Splice_Site_p.E78V			Q96A23	CPNE4_HUMAN	copine IV	60	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CATGCCTACCTCAAACCACTG	0.443																																					p.E60V		Atlas-SNP	.											.	CPNE4	112	.	0			c.A179T						.						135.0	125.0	129.0					3																	131624109		2203	4300	6503	SO:0001630	splice_region_variant	131034	exon2			CCTACCTCAAACC	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.180+1A>T	chr3.hg19:g.131624109T>A		126.0	0.0		133.0	27.0	NM_130808	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195935	0.78902	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881;ENST00000514999;ENST00000505957	T;T;T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;1.06	5.56	5.56	0.83823	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048095	0.85682	D	0.000000	D	0.83912	0.5357	M	0.89785	3.06	0.80722	D	1	D;D	0.61697	0.99;0.99	P;D	0.64321	0.854;0.924	D	0.87615	0.2506	10	0.87932	D	0	-14.8361	15.7219	0.77718	0.0:0.0:0.0:1.0	.	78;60	Q96A23-2;Q96A23	.;CPNE4_HUMAN	V	60;60;78;60;78;60;60;60	ENSP00000421705:E60V;ENSP00000411904:E60V;ENSP00000424853:E78V;ENSP00000423811:E60V;ENSP00000421646:E78V;ENSP00000425506:E60V;ENSP00000427561:E60V;ENSP00000421394:E60V	ENSP00000411904:E60V	E	-	2	0	CPNE4	133106799	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	7.698000	0.84413	2.112000	0.64535	0.533000	0.62120	GAG	.	.		0.443	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	Missense_Mutation
ACAD11	84129	hgsc.bcm.edu	37	3	132337601	132337601	+	Missense_Mutation	SNP	C	C	T	rs542883164		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:132337601C>T	ENST00000264990.6	-	11	2262	c.1291G>A	c.(1291-1293)Gag>Aag	p.E431K	ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000481970.2_Missense_Mutation_p.E431K|ACAD11_ENST00000355458.3_Missense_Mutation_p.E431K	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	431					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						CAGAGACCCTCGACTTTGGCC	0.418													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15389	0.0		0.0	False		,,,				2504	0.0				p.E431K		Atlas-SNP	.											.	ACAD11	78	.	0			c.G1291A						.						68.0	65.0	66.0					3																	132337601		2203	4300	6503	SO:0001583	missense	84129	exon11			GACCCTCGACTTT	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"""acyl-Coenzyme A dehydrogenase family, member 11"""				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1291G>A	chr3.hg19:g.132337601C>T	ENSP00000264990:p.Glu431Lys	202.0	0.0		238.0	63.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	hg19	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361158	0.82353	.	.	ENSG00000240303	ENST00000355458;ENST00000264990;ENST00000481970	D;D;T	0.99701	-6.45;-6.45;1.85	5.52	5.52	0.82312	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	.	.	.	.	D	0.99507	0.9824	M	0.66560	2.04	0.80722	D	1	P;D	0.64830	0.908;0.994	B;P	0.57101	0.158;0.813	D	0.98826	1.0749	9	0.56958	D	0.05	.	19.3995	0.94621	0.0:1.0:0.0:0.0	.	431;431	D6RDI8;Q709F0	.;ACD11_HUMAN	K	431	ENSP00000347636:E431K;ENSP00000264990:E431K;ENSP00000420907:E431K	ENSP00000264990:E431K	E	-	1	0	ACAD11	133820291	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	4.549000	0.60726	2.754000	0.94517	0.650000	0.86243	GAG	.	.		0.418	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169	
ATP11B	23200	hgsc.bcm.edu	37	3	182566270	182566270	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:182566270C>T	ENST00000323116.5	+	10	1036	c.776C>T	c.(775-777)gCg>gTg	p.A259V	ATP11B_ENST00000482794.1_3'UTR	NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	259					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			ACAGGTGTTGCGGTATACACT	0.303																																					p.A259V		Atlas-SNP	.											ATP11B,NS,carcinoma,0,1	ATP11B	115	.	0			c.C776T						.						54.0	56.0	55.0					3																	182566270		2203	4294	6497	SO:0001583	missense	23200	exon10			GTGTTGCGGTATA	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"""ATPases / P-type"""	13553	protein-coding gene	gene with protein product		605869	"""ATPase, Class VI, type 11B"""			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.776C>T	chr3.hg19:g.182566270C>T	ENSP00000321195:p.Ala259Val	190.0	0.0		232.0	59.0	NM_014616	Q96FN1|Q9UKK7	Missense_Mutation	SNP	ENST00000323116.5	hg19	CCDS33896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.272222|4.272222	0.80580|0.80580	.|.	.|.	ENSG00000058063|ENSG00000058063	ENST00000323116|ENST00000498086	D|.	0.82803|.	-1.65|.	5.4|5.4	5.4|5.4	0.78164|0.78164	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54224|0.54224	0.1845|0.1845	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.76071|.	0.987|.	T|T	0.49021|0.49021	-0.8982|-0.8982	10|5	0.02654|.	T|.	1|.	.|.	19.2267|19.2267	0.93820|0.93820	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	259|.	Q9Y2G3|.	AT11B_HUMAN|.	V|W	259|60	ENSP00000321195:A259V|.	ENSP00000321195:A259V|.	A|R	+|+	2|1	0|2	ATP11B|ATP11B	184048964|184048964	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.542000|0.542000	0.35054|0.35054	7.360000|7.360000	0.79487|0.79487	2.563000|2.563000	0.86464|0.86464	0.551000|0.551000	0.68910|0.68910	GCG|CGG	.	.		0.303	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	
HRG	3273	hgsc.bcm.edu	37	3	186383833	186383833	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:186383833A>G	ENST00000232003.4	+	1	93	c.13A>G	c.(13-15)Att>Gtt	p.I5V	HRG_ENST00000468154.1_Intron|RP11-134F2.2_ENST00000455926.1_RNA|RP11-134F2.2_ENST00000428501.1_RNA	NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	5					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GAAGGCACTCATTGCAGCACT	0.448																																					p.I5V		Atlas-SNP	.											.	HRG	81	.	0			c.A13G						.						104.0	90.0	94.0					3																	186383833		2203	4300	6503	SO:0001583	missense	3273	exon1			GCACTCATTGCAG		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.13A>G	chr3.hg19:g.186383833A>G	ENSP00000232003:p.Ile5Val	106.0	0.0		111.0	26.0	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	hg19	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.547153	0.00926	.	.	ENSG00000113905	ENST00000232003	T	0.16897	2.31	5.6	-8.96	0.00761	.	1.332170	0.04902	N	0.451571	T	0.09905	0.0243	L	0.39898	1.24	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43572	-0.9383	10	0.02654	T	1	5.4587	9.548	0.39293	0.2499:0.541:0.2092:0.0	.	5	P04196	HRG_HUMAN	V	5	ENSP00000232003:I5V	ENSP00000232003:I5V	I	+	1	0	HRG	187866527	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.547000	0.00931	-1.503000	0.01812	-0.316000	0.08728	ATT	.	.		0.448	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
HES1	3280	hgsc.bcm.edu	37	3	193854818	193854818	+	Silent	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:193854818G>A	ENST00000232424.3	+	3	509	c.273G>A	c.(271-273)ctG>ctA	p.L91L		NM_005524.3	NP_005515.1	P30042	ES1_HUMAN	hes family bHLH transcription factor 1	0						mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)		TCCGGAACCTGCAGCGGGCGC	0.627																																					p.L91L		Atlas-SNP	.											HES1,NS,carcinoma,0,1	HES1	23	.	0			c.G273A						.						48.0	51.0	50.0					3																	193854818		2203	4300	6503	SO:0001819	synonymous_variant	3280	exon3			GAACCTGCAGCGG	L19314	CCDS3305.1	3q28-q29	2013-10-17	2013-10-17	2003-01-10	ENSG00000114315	ENSG00000114315		"""Basic helix-loop-helix proteins"""	5192	protein-coding gene	gene with protein product		139605	"""hairy homolog (Drosophila)"", ""hairy and enhancer of split 1, (Drosophila)"""	HRY		8020957	Standard	NM_005524		Approved	FLJ20408, HES-1, Hes1, bHLHb39	uc003ftq.2	Q14469	OTTHUMG00000155984	ENST00000232424.3:c.273G>A	chr3.hg19:g.193854818G>A		59.0	0.0		64.0	3.0	NM_005524	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Silent	SNP	ENST00000232424.3	hg19	CCDS3305.1																																																																																			.	.		0.627	HES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342632.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511811	195511811	+	Missense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:195511811G>T	ENST00000463781.3	-	2	7099	c.6640C>A	c.(6640-6642)Cct>Act	p.P2214T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2214T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGGGCTGGTGACA	0.597																																					p.P2214T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6640A						.						40.0	33.0	35.0					3																	195511811		690	1590	2280	SO:0001583	missense	4585	exon2			AGGAAGGGCTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6640C>A	chr3.hg19:g.195511811G>T	ENSP00000417498:p.Pro2214Thr	139.0	0.0		118.0	6.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	hg19	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	3.380	-0.126487	0.06795	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30981	1.51;1.52	.	.	.	.	.	.	.	.	T	0.12178	0.0296	N	0.19112	0.55	0.18873	N	0.999982	B	0.14805	0.011	B	0.04013	0.001	T	0.22243	-1.0222	6	.	.	.	.	.	.	.	.	2214	E7ESK3	.	T	2214	ENSP00000417498:P2214T;ENSP00000420243:P2214T	.	P	-	1	0	MUC4	196996206	0.000000	0.05858	0.010000	0.14722	0.013000	0.08279	-2.224000	0.01213	-2.656000	0.00421	-2.446000	0.00210	CCT	.	.		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM157A	728262	hgsc.bcm.edu	37	3	197880164	197880164	+	lincRNA	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr3:197880164G>A	ENST00000437428.2	+	0	44							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						agcagcagcagcagcagcaAC	0.527																																					p.Q81Q		Atlas-SNP	.											.	FAM157A	4	.	0			c.G243A						.						3.0	6.0	5.0					3																	197880164		474	1113	1587			728262	exon2			GCAGCAGCAGCAG			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			chr3.hg19:g.197880164G>A		192.0	0.0		213.0	26.0	NM_001145248		Silent	SNP	ENST00000437428.2	hg19																																																																																				.	.		0.527	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
SLBP	7884	hgsc.bcm.edu	37	4	1701341	1701341	+	Missense_Mutation	SNP	G	G	C	rs200085408		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:1701341G>C	ENST00000489418.1	-	5	795	c.429C>G	c.(427-429)aaC>aaG	p.N143K	SLBP_ENST00000488267.1_Missense_Mutation_p.N108K|SLBP_ENST00000429429.2_Missense_Mutation_p.N104K|SLBP_ENST00000318386.4_Missense_Mutation_p.N150K	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	143	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			TCTTCCCATAGTTGATCTGCT	0.423																																					p.N143K		Atlas-SNP	.											.	SLBP	12	.	0			c.C429G						.						169.0	155.0	160.0					4																	1701341		2203	4300	6503	SO:0001583	missense	7884	exon5			CCCATAGTTGATC	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"""histone binding protein"""	602422	"""stem-loop (histone) binding protein"""			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.429C>G	chr4.hg19:g.1701341G>C	ENSP00000417686:p.Asn143Lys	195.0	0.0		264.0	49.0	NM_006527	B3KRJ5	Missense_Mutation	SNP	ENST00000489418.1	hg19	CCDS3350.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.50|19.50|19.50	3.838587|3.838587|3.838587	0.71373|0.71373|0.71373	.|.|.	.|.|.	ENSG00000163950|ENSG00000163950|ENSG00000163950	ENST00000480936|ENST00000429429;ENST00000489418;ENST00000460392;ENST00000318386;ENST00000488267|ENST00000483348	.|.|.	.|.|.	.|.|.	5.19|5.19|5.19	3.16|3.16|3.16	0.36331|0.36331|0.36331	.|.|.	.|0.144333|.	.|0.64402|.	.|D|.	.|0.000012|.	T|T|T	0.63070|0.63070|0.63070	0.2480|0.2480|0.2480	M|M|M	0.66939|0.66939|0.66939	2.045|2.045|2.045	0.58432|0.58432|0.58432	D|D|D	0.999994|0.999994|0.999994	.|D;P;P;P;P|.	.|0.62365|.	.|0.991;0.915;0.835;0.734;0.915|.	.|P;P;P;P;P|.	.|0.54026|.	.|0.74;0.72;0.466;0.549;0.72|.	T|T|T	0.61451|0.61451|0.61451	-0.7060|-0.7060|-0.7060	5|9|5	.|0.39692|.	.|T|.	.|0.17|.	-5.3723|-5.3723|-5.3723	9.3219|9.3219|9.3219	0.37968|0.37968|0.37968	0.2754:0.0:0.7246:0.0|0.2754:0.0:0.7246:0.0|0.2754:0.0:0.7246:0.0	.|.|.	.|108;150;104;123;143|.	.|E7EUV9;F8W8D3;B3KRJ5;C9IY53;Q14493|.	.|.;.;.;.;SLBP_HUMAN|.	V|K|S	151|104;143;123;150;108|98	.|.|.	.|ENSP00000316490:N150K|.	L|N|T	-|-|-	1|3|2	2|2|0	SLBP|SLBP|SLBP	1671139|1671139|1671139	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	2.337000|2.337000|2.337000	0.43947|0.43947|0.43947	1.201000|1.201000|1.201000	0.43203|0.43203|0.43203	0.644000|0.644000|0.644000	0.83932|0.83932|0.83932	CTA|AAC|ACT	.	G|0.999;C|0.001		0.423	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527	
EVC2	132884	hgsc.bcm.edu	37	4	5642500	5642500	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:5642500T>C	ENST00000344408.5	-	10	1264	c.1211A>G	c.(1210-1212)aAg>aGg	p.K404R	EVC2_ENST00000344938.1_Missense_Mutation_p.K404R|EVC2_ENST00000310917.2_Missense_Mutation_p.K324R	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	404					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						aatgatatccttgctgatttg	0.433																																					p.K404R		Atlas-SNP	.											.	EVC2	202	.	0			c.A1211G						.						89.0	88.0	88.0					4																	5642500		2203	4300	6503	SO:0001583	missense	132884	exon10			ATATCCTTGCTGA	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1211A>G	chr4.hg19:g.5642500T>C	ENSP00000342144:p.Lys404Arg	115.0	0.0		141.0	6.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275725	0.23307	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.80214	-1.35;-1.35;-1.35	4.25	0.463	0.16700	.	0.288637	0.28859	N	0.013920	T	0.69967	0.3170	L	0.46157	1.445	0.31990	N	0.604743	B	0.21688	0.059	B	0.24541	0.054	T	0.63341	-0.6659	10	0.32370	T	0.25	-11.5439	7.5097	0.27566	0.0:0.2685:0.0:0.7315	.	404	Q86UK5	LBN_HUMAN	R	404;324;404	ENSP00000339954:K404R;ENSP00000311683:K324R;ENSP00000342144:K404R	ENSP00000311683:K324R	K	-	2	0	EVC2	5693401	1.000000	0.71417	0.974000	0.42286	0.550000	0.35303	1.198000	0.32223	0.161000	0.19458	0.482000	0.46254	AAG	.	.		0.433	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
EVC	2121	hgsc.bcm.edu	37	4	5798818	5798818	+	Silent	SNP	C	C	T	rs535012160		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:5798818C>T	ENST00000264956.6	+	14	2140	c.1956C>T	c.(1954-1956)cgC>cgT	p.R652R	EVC_ENST00000382674.2_Silent_p.R652R|EVC_ENST00000515113.1_3'UTR	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	652					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TGGCACTCCGCGGCAACGCCC	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		18521	0.0		0.001	False		,,,				2504	0.0				p.R652R		Atlas-SNP	.											EVC,NS,carcinoma,0,1	EVC	90	.	0			c.C1956T						.						42.0	42.0	42.0					4																	5798818		2203	4298	6501	SO:0001819	synonymous_variant	2121	exon14			ACTCCGCGGCAAC	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1956C>T	chr4.hg19:g.5798818C>T		143.0	0.0		122.0	5.0	NM_153717		Silent	SNP	ENST00000264956.6	hg19	CCDS3383.1																																																																																			.	.		0.672	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
WDR1	9948	hgsc.bcm.edu	37	4	10099482	10099482	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:10099482A>G	ENST00000499869.2	-	5	604	c.411T>C	c.(409-411)tcT>tcC	p.S137S	WDR1_ENST00000382452.2_Silent_p.S137S|WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382451.2_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	137					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CGCCCACAGAAGAGCCACTAT	0.493																																					p.S137S		Atlas-SNP	.											.	WDR1	93	.	0			c.T411C						.						52.0	52.0	52.0					4																	10099482		1989	4172	6161	SO:0001819	synonymous_variant	9948	exon5			CACAGAAGAGCCA	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"""WD repeat domain containing"""	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.411T>C	chr4.hg19:g.10099482A>G		57.0	0.0		92.0	4.0	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Silent	SNP	ENST00000499869.2	hg19	CCDS54740.1																																																																																			.	.		0.493	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	rs112275895		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	158.0	0.0		221.0	21.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
UCP1	7350	hgsc.bcm.edu	37	4	141484320	141484320	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:141484320T>C	ENST00000262999.3	-	4	647	c.572A>G	c.(571-573)gAg>gGg	p.E191G		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	191					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					TGTTACTAGCTCTGTACAATT	0.343																																					p.E191G		Atlas-SNP	.											.	UCP1	33	.	0			c.A572G						.						132.0	131.0	132.0					4																	141484320		2203	4300	6503	SO:0001583	missense	7350	exon4			ACTAGCTCTGTAC	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"""Solute carriers"""	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.572A>G	chr4.hg19:g.141484320T>C	ENSP00000262999:p.Glu191Gly	139.0	0.0		122.0	6.0	NM_021833	Q13218|Q4KMZ3|Q68G66	Missense_Mutation	SNP	ENST00000262999.3	hg19	CCDS3753.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.341173	0.81911	.	.	ENSG00000109424	ENST00000262999	T	0.78246	-1.16	5.22	5.22	0.72569	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.88194	0.6371	M	0.83012	2.62	0.54753	D	0.999982	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	D	0.89852	0.4010	10	0.87932	D	0	.	13.3259	0.60459	0.0:0.0:0.0:1.0	.	190;191	Q4KMT7;P25874	.;UCP1_HUMAN	G	191	ENSP00000262999:E191G	ENSP00000262999:E191G	E	-	2	0	UCP1	141703770	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.388000	0.79795	2.105000	0.64084	0.491000	0.48974	GAG	.	.		0.343	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1		
WWC2	80014	hgsc.bcm.edu	37	4	184233492	184233492	+	Splice_Site	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:184233492A>G	ENST00000403733.3	+	22	3583		c.e22-1		WWC2_ENST00000448232.2_Splice_Site|WWC2_ENST00000513834.1_Splice_Site|WWC2_ENST00000508747.1_Splice_Site|WWC2_ENST00000504005.1_Splice_Site	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2						negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.?(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TCCCTTTTCCAGGCTGAACAG	0.463																																					.		Atlas-SNP	.											WWC2,NS,carcinoma,0,1	WWC2	78	.	1	Unknown(1)	lung(1)	c.3385-2A>G						.						103.0	109.0	107.0					4																	184233492		2203	4300	6503	SO:0001630	splice_region_variant	80014	exon22			TTTTCCAGGCTGA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3385-1A>G	chr4.hg19:g.184233492A>G		28.0	0.0		27.0	2.0	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Splice_Site	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	10.66	1.413279	0.25465	.	.	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1939	0.59728	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WWC2	184470486	1.000000	0.71417	0.998000	0.56505	0.099000	0.18886	5.182000	0.65059	2.037000	0.60232	0.529000	0.55759	.	.	.		0.463	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	Intron
PRIMPOL	201973	hgsc.bcm.edu	37	4	185615700	185615700	+	Missense_Mutation	SNP	G	G	A	rs372438124|rs145762735|rs200746705	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr4:185615700G>A	ENST00000314970.6	+	14	1883	c.1450G>A	c.(1450-1452)Gca>Aca	p.A484T	PRIMPOL_ENST00000510864.1_3'UTR|PRIMPOL_ENST00000515774.1_Missense_Mutation_p.A355T|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.A484T|PRIMPOL_ENST00000512834.1_Missense_Mutation_p.A483T	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	484	Interaction with RPA1.				mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										AACAGATGAAGCAGATGAAAC	0.408																																					p.A484T		Atlas-SNP	.											.,1	CCDC111	43	.	0			c.G1450A						.																																			SO:0001583	missense	201973	exon14			GATGAAGCAGATG	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1450G>A	chr4.hg19:g.185615700G>A	ENSP00000313816:p.Ala484Thr	71.0	0.0		53.0	8.0	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	hg19	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	G	9.738	1.164122	0.21538	.	.	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834;ENST00000508001	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	4.03	-1.96	0.07525	.	0.576826	0.13630	N	0.373802	T	0.09247	0.0228	N	0.01576	-0.805	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.38520	-0.9657	10	0.13108	T	0.6	-9.4298	9.7225	0.40311	0.6661:0.0:0.3339:0.0	.	355;484;483	D3DP56;Q96LW4;D6RDM1	.;CC111_HUMAN;.	T	484;355;484;483;158	ENSP00000313816:A484T;ENSP00000421913:A355T;ENSP00000420860:A484T;ENSP00000425316:A483T	ENSP00000313816:A484T	A	+	1	0	CCDC111	185852694	0.000000	0.05858	0.003000	0.11579	0.213000	0.24496	-0.261000	0.08694	-0.358000	0.08162	0.543000	0.68304	GCA	.	.		0.408	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
ISL1	3670	hgsc.bcm.edu	37	5	50683549	50683549	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:50683549T>C	ENST00000230658.7	+	3	1029	c.444T>C	c.(442-444)agT>agC	p.S148S	ISL1_ENST00000505475.2_3'UTR|ISL1_ENST00000511384.1_Silent_p.S148S	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	148					atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				ACCCGCTCAGTCCCCTGCATC	0.662																																					p.S148S		Atlas-SNP	.											.	ISL1	65	.	0			c.T444C						.						34.0	37.0	36.0					5																	50683549		2042	4189	6231	SO:0001819	synonymous_variant	3670	exon3			GCTCAGTCCCCTG	BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"""Homeoboxes / LIM class"""	6132	protein-coding gene	gene with protein product		600366	"""ISL1 transcription factor, LIM/homeodomain, (islet-1)"""			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.444T>C	chr5.hg19:g.50683549T>C		107.0	0.0		99.0	4.0	NM_002202	P20663|P47894	Silent	SNP	ENST00000230658.7	hg19	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	T	4.727	0.135128	0.09032	.	.	ENSG00000016082	ENST00000505475	.	.	.	5.41	1.03	0.20045	.	0.088274	0.85682	D	0.000000	T	0.63331	0.2502	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63193	-0.6692	6	0.87932	D	0	.	9.0877	0.36592	0.0:0.6683:0.0:0.3317	.	.	.	.	P	95	.	ENSP00000421737:S95P	S	+	1	0	ISL1	50719306	0.993000	0.37304	0.999000	0.59377	0.271000	0.26615	0.370000	0.20433	0.129000	0.18514	0.374000	0.22700	TCC	.	.		0.662	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202	
ADAMTS6	11174	hgsc.bcm.edu	37	5	64748641	64748641	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:64748641C>T	ENST00000536360.1	-	5	1549	c.736G>A	c.(736-738)Gtg>Atg	p.V246M				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	246						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		TCAATGCTCACTGATCTCTTC	0.433																																					p.V246M		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G736A						.						211.0	182.0	192.0					5																	64748641		2203	4300	6503	SO:0001583	missense	11174	exon5			TGCTCACTGATCT	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	222	protein-coding gene	gene with protein product	"""a disintegrin and metalloproteinase with thrombospondin motifs 6"""	605008	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"""			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.736G>A	chr5.hg19:g.64748641C>T	ENSP00000440995:p.Val246Met	251.0	0.0		324.0	58.0	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Missense_Mutation	SNP	ENST00000536360.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.04	2.417701	0.42918	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	T;T;T	0.62105	0.11;0.23;0.05	5.49	3.72	0.42706	Metallopeptidase, catalytic domain (1);	0.188644	0.45606	D	0.000349	T	0.51924	0.1703	L	0.36672	1.1	0.51012	D	0.999902	B	0.23806	0.091	B	0.28784	0.094	T	0.49283	-0.8956	10	0.59425	D	0.04	.	9.9769	0.41789	0.0:0.7833:0.0:0.2167	.	246	Q9UKP5	ATS6_HUMAN	M	246	ENSP00000370443:V246M;ENSP00000423551:V246M;ENSP00000440995:V246M	ENSP00000261306:V246M	V	-	1	0	ADAMTS6	64784397	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.373000	0.34272	0.689000	0.31550	0.563000	0.77884	GTG	.	.		0.433	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941	
GFM2	84340	hgsc.bcm.edu	37	5	74021855	74021855	+	Missense_Mutation	SNP	T	T	A	rs145997856		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:74021855T>A	ENST00000296805.3	-	18	2280	c.1823A>T	c.(1822-1824)gAg>gTg	p.E608V	GFM2_ENST00000509430.1_Missense_Mutation_p.E608V|RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000345239.2_Missense_Mutation_p.E561V	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		ATACTCAAACTCAATCACAGG	0.418																																					p.E608V		Atlas-SNP	.											.	GFM2	38	.	0			c.A1823T						.						124.0	127.0	126.0					5																	74021855		2203	4300	6503	SO:0001583	missense	84340	exon18			TCAAACTCAATCA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1823A>T	chr5.hg19:g.74021855T>A	ENSP00000296805:p.Glu608Val	102.0	0.0		122.0	10.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	-	0.827	-0.746541	0.03065	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.45276	0.9;0.9;0.9	.	.	.	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.349225	0.33309	N	0.005048	T	0.23688	0.0573	N	0.14661	0.345	0.09310	N	1	B;.;B	0.31752	0.0;.;0.338	B;.;B	0.36030	0.009;.;0.216	T	0.16512	-1.0400	8	0.87932	D	0	.	.	.	.	.	608;561;608	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	V	608;561;608	ENSP00000296805:E608V;ENSP00000296804:E561V;ENSP00000427004:E608V	ENSP00000296805:E608V	E	-	2	0	GFM2	74057611	0.640000	0.27243	0.005000	0.12908	0.054000	0.15201	0.784000	0.26816	0.000000	0.14550	0.000000	0.15137	GAG	.	.		0.418	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
ERAP2	64167	hgsc.bcm.edu	37	5	96237302	96237302	+	Silent	SNP	C	C	T	rs560261135		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:96237302C>T	ENST00000437043.3	+	11	2376	c.1665C>T	c.(1663-1665)gaC>gaT	p.D555D	ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Silent_p.D510D|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	555					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D555D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TTAAACAAGACGGGTGTTCAC	0.537																																					p.D555D		Atlas-SNP	.											ERAP2,NS,carcinoma,0,2	ERAP2	77	.	1	Substitution - coding silent(1)	prostate(1)	c.C1665T						.						74.0	73.0	73.0					5																	96237302		2203	4300	6503	SO:0001819	synonymous_variant	64167	exon11			ACAAGACGGGTGT	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1665C>T	chr5.hg19:g.96237302C>T		60.0	0.0		44.0	2.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	hg19	CCDS4086.1																																																																																			.	.		0.537	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503780	140503780	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:140503780C>T	ENST00000194152.1	+	1	2200	c.2200C>T	c.(2200-2202)Cat>Tat	p.H734Y		NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	734					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTTCCAGGGCATCTGGTGGA	0.647																																					p.H734Y		Atlas-SNP	.											PCDHB4,right_upper_lobe,carcinoma,0,1	PCDHB4	177	.	0			c.C2200T						.						81.0	93.0	89.0					5																	140503780		2203	4300	6503	SO:0001583	missense	56131	exon1			CCAGGGCATCTGG	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.2200C>T	chr5.hg19:g.140503780C>T	ENSP00000194152:p.His734Tyr	47.0	0.0		33.0	2.0	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	hg19	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.234736	0.22626	.	.	ENSG00000081818	ENST00000194152	T	0.49432	0.78	4.57	4.57	0.56435	.	.	.	.	.	T	0.60495	0.2273	H	0.94582	3.555	0.31702	N	0.640558	B	0.20368	0.044	B	0.19666	0.026	T	0.68731	-0.5331	9	0.72032	D	0.01	.	11.7507	0.51847	0.1759:0.8241:0.0:0.0	.	734	Q9Y5E5	PCDB4_HUMAN	Y	734	ENSP00000194152:H734Y	ENSP00000194152:H734Y	H	+	1	0	PCDHB4	140483964	0.000000	0.05858	0.994000	0.49952	0.084000	0.17831	-0.274000	0.08537	2.533000	0.85409	0.561000	0.74099	CAT	.	.		0.647	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
PCDH12	51294	hgsc.bcm.edu	37	5	141335035	141335035	+	Silent	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:141335035G>A	ENST00000231484.3	-	1	3592	c.2382C>T	c.(2380-2382)tcC>tcT	p.S794S	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	794					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATCTTTGTGGGACTGCCCGA	0.617																																					p.S794S		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2382T						.						38.0	33.0	35.0					5																	141335035		2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			TTTGTGGGACTGC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2382C>T	chr5.hg19:g.141335035G>A		70.0	0.0		77.0	4.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.617	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
SLC6A7	6534	hgsc.bcm.edu	37	5	149578931	149578931	+	Splice_Site	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:149578931T>C	ENST00000230671.2	+	5	1094		c.e5+2		SLC6A7_ENST00000524041.1_Splice_Site	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7						proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	TCGggcaaggtgaagcctggg	0.607																																					.		Atlas-SNP	.											.	SLC6A7	52	.	0			c.723+2T>C						.						70.0	67.0	68.0					5																	149578931		2203	4300	6503	SO:0001630	splice_region_variant	6534	exon5			GCAAGGTGAAGCC	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"""Solute carriers"""	11054	protein-coding gene	gene with protein product	"""brain-specific L-proline transporter"", ""sodium-dependent proline transporter"""	606205	"""solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"""			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.723+2T>C	chr5.hg19:g.149578931T>C		78.0	0.0		95.0	4.0	NM_014228	Q0VG81|Q52LU6	Splice_Site	SNP	ENST00000230671.2	hg19	CCDS4305.1																																																																																			.	.		0.607	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228	Intron
SLIT3	6586	hgsc.bcm.edu	37	5	168093513	168093513	+	Silent	SNP	C	C	T	rs558199905		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:168093513C>T	ENST00000519560.1	-	36	4937	c.4518G>A	c.(4516-4518)tcG>tcA	p.S1506S	SLIT3_ENST00000332966.8_Silent_p.S1513S|CTC-558O2.2_ENST00000520041.1_RNA	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1506	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTCTACAAACGAGGAGCCGT	0.632													c|||	1	0.000199681	0.0008	0.0	5008	,	,		14541	0.0		0.0	False		,,,				2504	0.0				p.S1513S	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											SLIT3,NS,lymphoid_neoplasm,0,1	SLIT3	224	.	0			c.G4539A						.						44.0	35.0	38.0					5																	168093513		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon36			TACAAACGAGGAG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.4518G>A	chr5.hg19:g.168093513C>T		31.0	0.0		49.0	2.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.632	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
BTNL9	153579	hgsc.bcm.edu	37	5	180486679	180486679	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr5:180486679C>T	ENST00000327705.9	+	11	1656	c.1425C>T	c.(1423-1425)caC>caT	p.H475H	BTNL9_ENST00000376842.3_Silent_p.H476H	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	475	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)		p.H475H(1)		breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCACCTTCCACGACACCTTCT	0.672																																					p.H475H		Atlas-SNP	.											BTNL9,NS,carcinoma,0,1	BTNL9	58	.	1	Substitution - coding silent(1)	lung(1)	c.C1425T						.						38.0	37.0	38.0					5																	180486679		2203	4299	6502	SO:0001819	synonymous_variant	153579	exon11			CTTCCACGACACC	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.1425C>T	chr5.hg19:g.180486679C>T		45.0	0.0		42.0	2.0	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	hg19	CCDS4460.2																																																																																			.	.		0.672	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
GCM2	9247	hgsc.bcm.edu	37	6	10877430	10877430	+	Missense_Mutation	SNP	C	C	T	rs550449754		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:10877430C>T	ENST00000379491.4	-	2	433	c.286G>A	c.(286-288)Ggt>Agt	p.G96S	SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	96					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.G96C(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				AGGCGGGAACCGTCGGGCAGG	0.627													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.G96S		Atlas-SNP	.											GCM2,NS,carcinoma,0,1	GCM2	81	.	1	Substitution - Missense(1)	lung(1)	c.G286A						.						76.0	69.0	72.0					6																	10877430		2203	4300	6503	SO:0001583	missense	9247	exon2			GGGAACCGTCGGG	AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"""glial cells missing (Drosophila) homolog b"""	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.286G>A	chr6.hg19:g.10877430C>T	ENSP00000368805:p.Gly96Ser	42.0	1.0		52.0	3.0	NM_004752	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	hg19	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	C	32	5.112433	0.94339	.	.	ENSG00000124827	ENST00000379491	D	0.84800	-1.9	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.91734	0.7386	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91804	0.5454	10	0.72032	D	0.01	-26.3182	19.8215	0.96599	0.0:1.0:0.0:0.0	.	96	O75603	GCM2_HUMAN	S	96	ENSP00000368805:G96S	ENSP00000368805:G96S	G	-	1	0	GCM2	10985416	1.000000	0.71417	0.986000	0.45419	0.580000	0.36256	7.434000	0.80377	2.679000	0.91253	0.650000	0.86243	GGT	.	.		0.627	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1		
MUC21	394263	hgsc.bcm.edu	37	6	30955247	30955247	+	Missense_Mutation	SNP	C	C	T	rs144122059		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:30955247C>T	ENST00000376296.3	+	2	1536	c.1295C>T	c.(1294-1296)gCc>gTc	p.A432V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	432	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAACACAGCC	0.582																																					p.A432V		Atlas-SNP	.											.	MUC21	98	.	0			c.C1295T						.						129.0	124.0	126.0					6																	30955247		2203	4300	6503	SO:0001583	missense	394263	exon2			GTGGGGCCAACAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1295C>T	chr6.hg19:g.30955247C>T	ENSP00000365473:p.Ala432Val	87.0	0.0		163.0	10.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	hg19	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	10.36	1.328172	0.24080	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02737	4.18	3.94	-0.192	0.13248	.	.	.	.	.	T	0.00412	0.0013	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43766	-0.9371	9	0.30854	T	0.27	-0.829	4.0611	0.09839	0.0:0.4049:0.1757:0.4193	.	432	Q5SSG8	MUC21_HUMAN	V	282;432	ENSP00000365473:A432V	ENSP00000365473:A432V	A	+	2	0	MUC21	31063226	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.873000	0.04214	0.118000	0.18165	-0.464000	0.05259	GCC	.	.		0.582	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PRRC2A	7916	hgsc.bcm.edu	37	6	31599160	31599160	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:31599160C>A	ENST00000376033.2	+	16	2944	c.2710C>A	c.(2710-2712)Cgc>Agc	p.R904S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R904S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	904	4 X 57 AA type A repeats.			PARGVGSGGQ -> LPASRSGA (in Ref. 1; AAA35585/AAA35586 and 8; CAA78744). {ECO:0000305}.		cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						AAAGCCTGCCCGCGGAGTCGG	0.647																																					p.R904S		Atlas-SNP	.											PRRC2A,NS,carcinoma,0,1	PRRC2A	152	.	0			c.C2710A						.						24.0	20.0	22.0					6																	31599160		1508	2707	4215	SO:0001583	missense	7916	exon16			CCTGCCCGCGGAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.2710C>A	chr6.hg19:g.31599160C>A	ENSP00000365201:p.Arg904Ser	71.0	0.0		44.0	2.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	7.015	0.557633	0.13436	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01665	4.7;4.7	4.93	4.93	0.64822	.	0.271232	0.27072	N	0.021080	T	0.00608	0.0020	N	0.19112	0.55	0.35546	D	0.803462	P	0.44090	0.826	B	0.35510	0.204	T	0.60919	-0.7167	10	0.87932	D	0	-9.0305	7.311	0.26475	0.0:0.8212:0.0:0.1788	.	904	P48634	PRC2A_HUMAN	S	904;893;904;904;129	ENSP00000365175:R904S;ENSP00000365201:R904S	ENSP00000365175:R904S	R	+	1	0	PRRC2A	31707139	0.005000	0.15991	0.925000	0.36789	0.496000	0.33645	0.874000	0.28065	2.566000	0.86566	0.561000	0.74099	CGC	.	.		0.647	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
MEA1	4201	hgsc.bcm.edu	37	6	42980713	42980713	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:42980713C>A	ENST00000244711.3	-	3	511	c.357G>T	c.(355-357)gaG>gaT	p.E119D	KLHDC3_ENST00000244670.8_5'Flank|KLHDC3_ENST00000326974.4_5'Flank	NM_014623.2	NP_055438.1	Q16626	MEA1_HUMAN	male-enhanced antigen 1	119					cell differentiation (GO:0030154)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(3)|lung(1)|skin(1)	6			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TAGCTCCCTCCTCATCTTCAT	0.493																																					p.E119D		Atlas-SNP	.											.	MEA1	11	.	0			c.G357T						.						201.0	186.0	191.0					6																	42980713		2203	4300	6503	SO:0001583	missense	4201	exon3			TCCCTCCTCATCT		CCDS4879.1	6p21.3-p21.1	2008-08-15	2005-06-02	2005-06-02	ENSG00000124733	ENSG00000124733			6986	protein-coding gene	gene with protein product		143170	"""male-enhanced antigen"""	MEA		2813404, 12444059	Standard	NM_014623		Approved		uc003otk.3	Q16626	OTTHUMG00000014717	ENST00000244711.3:c.357G>T	chr6.hg19:g.42980713C>A	ENSP00000244711:p.Glu119Asp	74.0	0.0		120.0	9.0	NM_014623	Q5TC36|Q9BV01	Missense_Mutation	SNP	ENST00000244711.3	hg19	CCDS4879.1	.	.	.	.	.	.	.	.	.	.	c	11.38	1.620830	0.28889	.	.	ENSG00000124733	ENST00000244711	T	0.54479	0.57	5.8	3.1	0.35709	.	0.195088	0.45606	D	0.000344	T	0.16938	0.0407	N	0.24115	0.695	0.32265	N	0.56969	P	0.41978	0.767	B	0.38683	0.279	T	0.08953	-1.0697	10	0.17369	T	0.5	-9.8121	10.9106	0.47106	0.0:0.7931:0.0:0.2069	.	119	Q16626	MEA1_HUMAN	D	119	ENSP00000244711:E119D	ENSP00000244711:E119D	E	-	3	2	MEA1	43088691	0.514000	0.26202	0.993000	0.49108	0.338000	0.28826	-0.081000	0.11321	0.403000	0.25479	-0.964000	0.02622	GAG	.	.		0.493	MEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040574.2		
CAPN11	11131	hgsc.bcm.edu	37	6	44148727	44148727	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:44148727T>C	ENST00000398776.1	+	18	1900	c.1862T>C	c.(1861-1863)cTc>cCc	p.L621P	CAPN11_ENST00000542245.1_Missense_Mutation_p.L621P	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	621	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ATGATCAACCTCATGGATGTA	0.582																																					p.L621P		Atlas-SNP	.											.	CAPN11	66	.	0			c.T1862C						.						243.0	247.0	246.0					6																	44148727		2045	4194	6239	SO:0001583	missense	11131	exon18			TCAACCTCATGGA	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1862T>C	chr6.hg19:g.44148727T>C	ENSP00000381758:p.Leu621Pro	56.0	0.0		98.0	4.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	t	18.80	3.701779	0.68501	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	T;T	0.79940	-1.32;-1.32	5.01	3.85	0.44370	EF-hand-like domain (1);	0.556403	0.15143	N	0.278189	D	0.90181	0.6931	H	0.96691	3.865	0.58432	D	0.999996	D;D	0.76494	0.999;0.993	D;P	0.67382	0.951;0.879	D	0.90751	0.4657	10	0.87932	D	0	.	9.9795	0.41804	0.0:0.0798:0.0:0.9202	.	275;621	B4DT90;Q9UMQ6	.;CAN11_HUMAN	P	621	ENSP00000381758:L621P;ENSP00000441078:L621P	ENSP00000381758:L621P	L	+	2	0	CAPN11	44256705	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	6.108000	0.71522	0.941000	0.37499	-0.507000	0.04495	CTC	.	.		0.582	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
DEFB113	245927	hgsc.bcm.edu	37	6	49936572	49936572	+	Nonsense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:49936572T>A	ENST00000398718.1	-	2	66	c.67A>T	c.(67-69)Aaa>Taa	p.K23*		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	23					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					CTTGTTTTTTTCTGTGGAACT	0.353																																					p.K23X		Atlas-SNP	.											.	DEFB113	18	.	0			c.A67T						.						83.0	80.0	81.0					6																	49936572		1845	4089	5934	SO:0001587	stop_gained	245927	exon2			TTTTTTTCTGTGG	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"""Defensins, beta"""	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.67A>T	chr6.hg19:g.49936572T>A	ENSP00000381703:p.Lys23*	99.0	0.0		97.0	21.0	NM_001037729		Nonsense_Mutation	SNP	ENST00000398718.1	hg19	CCDS43472.1	.	.	.	.	.	.	.	.	.	.	T	7.878	0.729576	0.15507	.	.	ENSG00000214642	ENST00000398718	.	.	.	4.15	-1.11	0.09840	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.3815	3.9562	0.09391	0.0:0.2118:0.3772:0.411	.	.	.	.	X	23	.	.	K	-	1	0	DEFB113	50044531	0.942000	0.31987	0.098000	0.21074	0.081000	0.17604	0.491000	0.22419	-0.040000	0.13580	-0.472000	0.04984	AAA	.	.		0.353	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1		
BMP5	653	hgsc.bcm.edu	37	6	55639030	55639030	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:55639030T>C	ENST00000370830.3	-	4	1542	c.844A>G	c.(844-846)Aac>Gac	p.N282D	BMP5_ENST00000446683.2_Missense_Mutation_p.N282D	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	282					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			GATTTTACGTTGATACTGCGT	0.428																																					p.N282D		Atlas-SNP	.											.	BMP5	94	.	0			c.A844G						.						162.0	143.0	150.0					6																	55639030		2203	4300	6503	SO:0001583	missense	653	exon4			TTACGTTGATACT		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.844A>G	chr6.hg19:g.55639030T>C	ENSP00000359866:p.Asn282Asp	175.0	0.0		230.0	32.0	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	hg19	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489979	0.26686	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	T;T	0.63744	-0.06;-0.06	5.74	5.74	0.90152	Transforming growth factor-beta, N-terminal (1);	0.167852	0.64402	D	0.000006	T	0.45357	0.1338	N	0.26130	0.795	0.50171	D	0.999852	P;P	0.46621	0.866;0.881	P;P	0.48921	0.515;0.595	T	0.41305	-0.9516	10	0.22109	T	0.4	.	16.0486	0.80740	0.0:0.0:0.0:1.0	.	282;282	B4E0Y4;P22003	.;BMP5_HUMAN	D	282	ENSP00000359866:N282D;ENSP00000391818:N282D	ENSP00000359866:N282D	N	-	1	0	BMP5	55746989	1.000000	0.71417	0.998000	0.56505	0.145000	0.21501	7.694000	0.84235	2.183000	0.69458	0.533000	0.62120	AAC	.	.		0.428	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
MCHR2	84539	hgsc.bcm.edu	37	6	100382375	100382375	+	Silent	SNP	C	C	A	rs267600746		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:100382375C>A	ENST00000281806.2	-	5	920	c.606G>T	c.(604-606)acG>acT	p.T202T	MCHR2_ENST00000369212.2_Silent_p.T202T	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T202T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		AAGTTGTTATCGTCAAATAAA	0.333													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18433	0.0		0.0	False		,,,				2504	0.0				p.T202T		Atlas-SNP	.											MCHR2,NS,carcinoma,-1,1	MCHR2	97	.	1	Substitution - coding silent(1)	skin(1)	c.G606T						.						73.0	72.0	72.0					6																	100382375		2203	4298	6501	SO:0001819	synonymous_variant	84539	exon5			TGTTATCGTCAAA	AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"""GPCR / Class A : MCH receptors"""	20867	protein-coding gene	gene with protein product		606111	"""G protein-coupled receptor 145"""	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.606G>T	chr6.hg19:g.100382375C>A		42.0	0.0		58.0	3.0	NM_001040179	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Silent	SNP	ENST00000281806.2	hg19	CCDS5044.1																																																																																			.	.		0.333	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503	
DSE	29940	hgsc.bcm.edu	37	6	116757465	116757465	+	Missense_Mutation	SNP	G	G	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:116757465G>C	ENST00000331677.3	+	7	2278	c.1834G>C	c.(1834-1836)Ggt>Cgt	p.G612R	DSE_ENST00000452085.3_Missense_Mutation_p.G612R|DSE_ENST00000537543.1_Missense_Mutation_p.G631R|DSE_ENST00000359564.2_Missense_Mutation_p.G612R			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	612					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GCAGAGAGATGGTCTCTATAA	0.488																																					p.G612R		Atlas-SNP	.											.	DSE	98	.	0			c.G1834C						.						123.0	110.0	115.0					6																	116757465		2203	4300	6503	SO:0001583	missense	29940	exon6			AGAGATGGTCTCT	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.1834G>C	chr6.hg19:g.116757465G>C	ENSP00000332151:p.Gly612Arg	52.0	0.0		135.0	6.0	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370207	0.61624	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	6.01	6.01	0.97437	.	0.250132	0.47455	D	0.000228	T	0.61825	0.2378	L	0.56769	1.78	0.54753	D	0.999989	P;P	0.49635	0.926;0.926	P;B	0.47626	0.552;0.413	T	0.64833	-0.6314	10	0.62326	D	0.03	-16.2979	20.5211	0.99222	0.0:0.0:1.0:0.0	.	631;612	B7Z765;Q9UL01	.;DSE_HUMAN	R	612;631;612;612	ENSP00000404049:G612R;ENSP00000441152:G631R;ENSP00000332151:G612R;ENSP00000352567:G612R	ENSP00000332151:G612R	G	+	1	0	DSE	116864158	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	7.935000	0.87658	2.861000	0.98227	0.650000	0.86243	GGT	.	.		0.488	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
LTV1	84946	hgsc.bcm.edu	37	6	144184607	144184607	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:144184607A>G	ENST00000367576.5	+	11	1505	c.1371A>G	c.(1369-1371)agA>agG	p.R457R	ZC2HC1B_ENST00000237275.6_5'Flank|ZC2HC1B_ENST00000539295.1_5'Flank	NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	457						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		TGGAGAAAAGAAGGCAAGAAA	0.378																																					p.R457R		Atlas-SNP	.											.	LTV1	48	.	0			c.A1371G						.						99.0	98.0	99.0					6																	144184607		2203	4300	6503	SO:0001819	synonymous_variant	84946	exon11			GAAAAGAAGGCAA	BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 93"", ""LTV1 homolog (S. cerevisiae)"""	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.1371A>G	chr6.hg19:g.144184607A>G		201.0	0.0		260.0	77.0	NM_032860	Q96JX8	Silent	SNP	ENST00000367576.5	hg19	CCDS5201.1																																																																																			.	.		0.378	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860	
UTRN	7402	hgsc.bcm.edu	37	6	145021342	145021342	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:145021342A>G	ENST00000367545.3	+	52	7772	c.7772A>G	c.(7771-7773)gAt>gGt	p.D2591G	UTRN_ENST00000367526.4_Missense_Mutation_p.D146G	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2591					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATTGGAGGAGATGTTCCAGCC	0.388																																					p.D2591G		Atlas-SNP	.											.	UTRN	327	.	0			c.A7772G						.						119.0	112.0	114.0					6																	145021342		2203	4300	6503	SO:0001583	missense	7402	exon52			GAGGAGATGTTCC	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7772A>G	chr6.hg19:g.145021342A>G	ENSP00000356515:p.Asp2591Gly	62.0	0.0		94.0	4.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577040	0.86645	.	.	ENSG00000152818	ENST00000367545;ENST00000367526	T;T	0.48522	0.81;0.81	5.64	5.64	0.86602	.	0.000000	0.48767	D	0.000177	T	0.54663	0.1872	M	0.72894	2.215	0.58432	D	0.999996	P	0.43094	0.799	P	0.53518	0.728	T	0.60796	-0.7192	10	0.87932	D	0	.	15.8735	0.79141	1.0:0.0:0.0:0.0	.	2591	P46939	UTRO_HUMAN	G	2591;146	ENSP00000356515:D2591G;ENSP00000356496:D146G	ENSP00000356496:D146G	D	+	2	0	UTRN	145063035	1.000000	0.71417	0.824000	0.32777	0.978000	0.69477	8.671000	0.91174	2.149000	0.67028	0.533000	0.62120	GAT	.	.		0.388	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
SASH1	23328	hgsc.bcm.edu	37	6	148846461	148846461	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:148846461A>G	ENST00000367467.3	+	11	1719	c.1244A>G	c.(1243-1245)aAt>aGt	p.N415S	AL033378.1_ENST00000411390.2_RNA	NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	415					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GACTTGACGAATCGCTCTCTG	0.453																																					p.N415S		Atlas-SNP	.											.	SASH1	123	.	0			c.A1244G						.						216.0	198.0	204.0					6																	148846461		2203	4300	6503	SO:0001583	missense	23328	exon11			TGACGAATCGCTC	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1244A>G	chr6.hg19:g.148846461A>G	ENSP00000356437:p.Asn415Ser	61.0	0.0		67.0	17.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735475	0.69189	.	.	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.43688	0.94	5.63	5.63	0.86233	.	0.196718	0.53938	D	0.000057	T	0.48150	0.1484	L	0.43152	1.355	0.51767	D	0.999932	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.42849	-0.9427	10	0.40728	T	0.16	-33.4466	16.1339	0.81465	1.0:0.0:0.0:0.0	.	396;415	Q6P4R9;O94885	.;SASH1_HUMAN	S	415;176	ENSP00000356437:N415S	ENSP00000356437:N415S	N	+	2	0	SASH1	148888154	1.000000	0.71417	0.384000	0.26145	0.821000	0.46438	7.102000	0.77005	2.271000	0.75665	0.533000	0.62120	AAT	.	.		0.453	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
ARID1B	57492	hgsc.bcm.edu	37	6	157522125	157522125	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:157522125C>A	ENST00000350026.5	+	17	4359	c.4358C>A	c.(4357-4359)gCa>gAa	p.A1453E	ARID1B_ENST00000346085.5_Missense_Mutation_p.A1466E|ARID1B_ENST00000367148.1_Missense_Mutation_p.A1506E|ARID1B_ENST00000275248.4_Missense_Mutation_p.A1448E	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1453					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		AATATGTGGGCAGCACGCAAT	0.632																																					p.A1466E		Atlas-SNP	.											.	ARID1B	320	.	0			c.C4397A						.						43.0	47.0	45.0					6																	157522125		2203	4296	6499	SO:0001583	missense	57492	exon18			TGTGGGCAGCACG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4358C>A	chr6.hg19:g.157522125C>A	ENSP00000055163:p.Ala1453Glu	69.0	0.0		126.0	16.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	11.91	1.778375	0.31502	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02032	4.82;4.83;4.82;4.82;4.49	5.08	5.08	0.68730	.	0.175751	0.50627	D	0.000120	T	0.00845	0.0028	N	0.08118	0	0.36525	D	0.870411	B;B;B	0.19200	0.02;0.034;0.034	B;B;B	0.21708	0.016;0.036;0.036	T	0.61564	-0.7037	10	0.27785	T	0.31	.	18.8669	0.92296	0.0:1.0:0.0:0.0	.	1453;1466;1448	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	E	1466;1453;1506;1448;975	ENSP00000344546:A1466E;ENSP00000055163:A1453E;ENSP00000356116:A1506E;ENSP00000275248:A1448E;ENSP00000412835:A975E	ENSP00000275248:A1448E	A	+	2	0	ARID1B	157563817	0.931000	0.31567	0.957000	0.39632	0.958000	0.62258	2.049000	0.41288	2.528000	0.85240	0.591000	0.81541	GCA	.	.		0.632	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
MRPL18	29074	hgsc.bcm.edu	37	6	160212008	160212008	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr6:160212008C>T	ENST00000367034.4	+	2	211	c.89C>T	c.(88-90)cCg>cTg	p.P30L	TCP1_ENST00000420894.2_5'Flank|TCP1_ENST00000321394.7_5'Flank|TCP1_ENST00000544255.1_5'Flank|MRPL18_ENST00000480842.1_3'UTR|TCP1_ENST00000546023.1_5'Flank|TCP1_ENST00000392168.2_5'Flank	NM_014161.3	NP_054880.2	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18	30					rRNA import into mitochondrion (GO:0035928)|translation (GO:0006412)	extracellular space (GO:0005615)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	11		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		AGCTCCGAGCCGGCAGCGAAA	0.582																																					p.P30L		Atlas-SNP	.											MRPL18,NS,malignant_melanoma,0,1	MRPL18	25	.	0			c.C89T						.						28.0	31.0	30.0					6																	160212008		2203	4300	6503	SO:0001583	missense	29074	exon2			CCGAGCCGGCAGC	AF161556	CCDS5270.1	6q25.3	2012-09-13			ENSG00000112110	ENSG00000112110		"""Mitochondrial ribosomal proteins / large subunits"""	14477	protein-coding gene	gene with protein product		611831				11042152, 11551941	Standard	NM_014161		Approved	HSPC071	uc003qsw.4	Q9H0U6	OTTHUMG00000015942	ENST00000367034.4:c.89C>T	chr6.hg19:g.160212008C>T	ENSP00000356001:p.Pro30Leu	52.0	0.0		68.0	3.0	NM_014161	Q5TAP9|Q9NZW8	Missense_Mutation	SNP	ENST00000367034.4	hg19	CCDS5270.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802409	0.31869	.	.	ENSG00000112110	ENST00000367034	T	0.42513	0.97	5.32	4.45	0.53987	.	0.391638	0.26635	N	0.023282	T	0.20981	0.0505	M	0.65975	2.015	0.19575	N	0.999968	P	0.36768	0.569	B	0.30495	0.116	T	0.12915	-1.0529	10	0.20046	T	0.44	-8.8481	15.0244	0.71656	0.0:0.8567:0.1433:0.0	.	30	Q9H0U6	RM18_HUMAN	L	30	ENSP00000356001:P30L	ENSP00000356001:P30L	P	+	2	0	MRPL18	160131998	0.009000	0.17119	0.000000	0.03702	0.002000	0.02628	2.472000	0.45136	1.458000	0.47871	-0.176000	0.13171	CCG	.	.		0.582	MRPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042925.1		
SUN1	23353	hgsc.bcm.edu	37	7	882841	882841	+	Splice_Site	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:882841A>G	ENST00000405266.1	+	4	475		c.e4-1		SUN1_ENST00000425407.2_Splice_Site|SUN1_ENST00000401592.1_Splice_Site|SUN1_ENST00000457378.2_Splice_Site|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000456758.2_Splice_Site|SUN1_ENST00000389574.3_Splice_Site|SUN1_ENST00000403868.1_Splice_Site			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1						cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTTTTTTTTTAGGTCTTGATG	0.284																																					.		Atlas-SNP	.											.	SUN1	157	.	0			c.452-2A>G						.						90.0	89.0	89.0					7																	882841		1826	4091	5917	SO:0001630	splice_region_variant	23353	exon5			TTTTTTAGGTCTT	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.452-1A>G	chr7.hg19:g.882841A>G		78.0	0.0		90.0	5.0	NM_001171946	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Splice_Site	SNP	ENST00000405266.1	hg19		.	.	.	.	.	.	.	.	.	.	a	7.211	0.595337	0.13875	.	.	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000435699;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9403	0.64050	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUN1	849367	1.000000	0.71417	0.975000	0.42487	0.731000	0.41821	6.498000	0.73679	1.839000	0.53478	0.482000	0.46254	.	.	.		0.284	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	Intron
LFNG	3955	hgsc.bcm.edu	37	7	2552880	2552880	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:2552880C>T	ENST00000402506.1	+	2	263	c.137C>T	c.(136-138)aCa>aTa	p.T46I		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		gacagatggacagatggatgg	0.562																																					p.T46I		Atlas-SNP	.											.	LFNG	57	.	0			c.C137T						.						133.0	125.0	127.0					7																	2552880		1568	3582	5150	SO:0001583	missense	3955	exon2			GATGGACAGATGG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"""Beta 3-glycosyltransferases"""	6560	protein-coding gene	gene with protein product		602576	"""lunatic fringe (Drosophila) homolog"", ""lunatic fringe homolog (Drosophila)"""			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.137C>T	chr7.hg19:g.2552880C>T	ENSP00000385764:p.Thr46Ile	53.0	0.0		75.0	7.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000402506.1	hg19	CCDS55081.1	.	.	.	.	.	.	.	.	.	.	C	7.077	0.569507	0.13560	.	.	ENSG00000106003	ENST00000402506	T	0.73258	-0.73	2.36	1.47	0.22746	.	.	.	.	.	T	0.49047	0.1534	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.46133	-0.9213	7	0.87932	D	0	.	4.9157	0.13844	0.0:0.8209:0.0:0.1791	.	.	.	.	I	46	ENSP00000385764:T46I	ENSP00000385764:T46I	T	+	2	0	LFNG	2519406	0.000000	0.05858	0.003000	0.11579	0.032000	0.12392	-0.432000	0.06956	0.564000	0.29238	0.491000	0.48974	ACA	.	.		0.562	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304	
SP4	6671	hgsc.bcm.edu	37	7	21469601	21469601	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:21469601A>G	ENST00000222584.3	+	3	1036	c.818A>G	c.(817-819)aAc>aGc	p.N273S		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	273					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						GTGATAAACAACGTGGCTGCC	0.512																																					p.N273S		Atlas-SNP	.											.	SP4	91	.	0			c.A818G						.						71.0	65.0	67.0					7																	21469601		2203	4300	6503	SO:0001583	missense	6671	exon3			TAAACAACGTGGC		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.818A>G	chr7.hg19:g.21469601A>G	ENSP00000222584:p.Asn273Ser	130.0	0.0		174.0	44.0	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	A	0.398	-0.919762	0.02396	.	.	ENSG00000105866	ENST00000222584	T	0.07021	3.23	4.94	1.24	0.21308	.	0.132837	0.64402	N	0.000002	T	0.02767	0.0083	N	0.04090	-0.28	0.44234	D	0.997076	B	0.06786	0.001	B	0.04013	0.001	T	0.46456	-0.9190	10	0.02654	T	1	.	8.1388	0.31071	0.6845:0.0:0.3155:0.0	.	273	Q02446	SP4_HUMAN	S	273	ENSP00000222584:N273S	ENSP00000222584:N273S	N	+	2	0	SP4	21436126	0.950000	0.32346	0.930000	0.37139	0.996000	0.88848	2.331000	0.43894	0.057000	0.16193	0.533000	0.62120	AAC	.	.		0.512	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112	
HOXA5	3202	hgsc.bcm.edu	37	7	27181672	27181672	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:27181672G>A	ENST00000222726.3	-	2	655	c.595C>T	c.(595-597)Cgg>Tgg	p.R199W	HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA3_ENST00000521401.1_5'Flank|HOXA5_ENST00000520854.1_5'UTR	NM_019102.3	NP_061975.2	P20719	HXA5_HUMAN	homeobox A5	199					anterior/posterior pattern specification (GO:0009952)|bronchiole development (GO:0060435)|cell migration (GO:0016477)|cell-cell signaling involved in mammary gland development (GO:0060764)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|intestinal epithelial cell maturation (GO:0060574)|lung alveolus development (GO:0048286)|lung goblet cell differentiation (GO:0060480)|lung-associated mesenchyme development (GO:0060484)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal-epithelial cell signaling (GO:0060638)|multicellular organism growth (GO:0035264)|negative regulation of angiogenesis (GO:0016525)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of apoptotic process (GO:0043065)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|respiratory system process (GO:0003016)|thyroid gland development (GO:0030878)|trachea cartilage morphogenesis (GO:0060535)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(12)|skin(1)	16						TAGGCCGTCCGGGCCCTTTTG	0.562											OREG0017911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R199W	Colon(119;75 2200 7557 42868)	Atlas-SNP	.											HOXA5,NS,carcinoma,0,1	HOXA5	43	.	0			c.C595T						.						69.0	67.0	68.0					7																	27181672		2203	4300	6503	SO:0001583	missense	3202	exon2			CCGTCCGGGCCCT		CCDS5406.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106004	ENSG00000106004		"""Homeoboxes / ANTP class : HOXL subclass"""	5106	protein-coding gene	gene with protein product		142952	"""homeo box A5"""	HOX1C, HOX1		1973146, 1358459	Standard	NM_019102		Approved		uc003syn.2	P20719	OTTHUMG00000023214	ENST00000222726.3:c.595C>T	chr7.hg19:g.27181672G>A	ENSP00000222726:p.Arg199Trp	56.0	0.0	792	79.0	4.0	NM_019102	A4D179|O43367|Q96CY6	Missense_Mutation	SNP	ENST00000222726.3	hg19	CCDS5406.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.906675	0.52333	.	.	ENSG00000106004	ENST00000222726	D	0.99186	-5.53	4.76	2.83	0.33086	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	H	0.99682	4.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97771	1.0226	10	0.87932	D	0	.	13.2228	0.59899	0.0:0.0:0.7094:0.2906	.	199	P20719	HXA5_HUMAN	W	199	ENSP00000222726:R199W	ENSP00000222726:R199W	R	-	1	2	HOXA5	27148197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.944000	0.49034	0.470000	0.27294	0.543000	0.68304	CGG	.	.		0.562	HOXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358705.1		
DDX56	54606	hgsc.bcm.edu	37	7	44612257	44612257	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:44612257C>A	ENST00000258772.5	-	4	576	c.470G>T	c.(469-471)cGt>cTt	p.R157L	DDX56_ENST00000485367.1_5'UTR|DDX56_ENST00000431640.1_Missense_Mutation_p.R157L	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	157	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						CAGGGAGTCACGAAGTTTCAG	0.517																																					p.R157L		Atlas-SNP	.											.	DDX56	36	.	0			c.G470T						.						143.0	139.0	140.0					7																	44612257		2203	4300	6503	SO:0001583	missense	54606	exon4			GAGTCACGAAGTT	AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"""DEAD-boxes"""	18193	protein-coding gene	gene with protein product	"""nucleolar helicase of 61 kDa"""	608023	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"""			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.470G>T	chr7.hg19:g.44612257C>A	ENSP00000258772:p.Arg157Leu	133.0	0.0		209.0	51.0	NM_001257189	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	hg19	CCDS5492.1	.	.	.	.	.	.	.	.	.	.	.	11.51	1.660906	0.29515	.	.	ENSG00000136271	ENST00000258772;ENST00000431640	T;T	0.32753	1.44;1.44	5.48	1.7	0.24286	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.245391	0.41097	D	0.000958	T	0.19604	0.0471	L	0.28400	0.85	0.35968	D	0.835132	B;B	0.13145	0.006;0.007	B;B	0.17979	0.02;0.01	T	0.15838	-1.0423	10	0.22109	T	0.4	-2.929	9.567	0.39405	0.0:0.7103:0.0:0.2897	.	157;157	C9JV95;Q9NY93	.;DDX56_HUMAN	L	157	ENSP00000258772:R157L;ENSP00000393488:R157L	ENSP00000258772:R157L	R	-	2	0	DDX56	44578782	0.196000	0.23350	0.038000	0.18304	0.964000	0.63967	0.585000	0.23879	0.105000	0.17753	-0.140000	0.14226	CGT	.	.		0.517	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082	
POMZP3	22932	hgsc.bcm.edu	37	7	76240786	76240786	+	Missense_Mutation	SNP	A	A	C	rs71819724	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:76240786A>C	ENST00000310842.4	-	6	1244	c.560T>G	c.(559-561)cTg>cGg	p.L187R	UPK3B_ENST00000443097.2_Intron|POMZP3_ENST00000275569.4_Intron|AC004980.7_ENST00000418663.1_RNA|UPK3B_ENST00000419923.2_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	187										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CTGCGGTTACAGGGAAGCAGA	0.517																																					p.L187R		Atlas-SNP	.											.	POMZP3	19	.	0			c.T560G						.						51.0	55.0	54.0					7																	76240786		1684	3181	4865	SO:0001583	missense	22932	exon6			GGTTACAGGGAAG	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"""POM-ZP3 fusion protein"", ""POM121/ZP3 fusion protein"""	600587	"""POM (POM121 rat homolog) and ZP3 fusion"", ""POM (POM121 homolog, rat) and ZP3 fusion"""			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.560T>G	chr7.hg19:g.76240786A>C	ENSP00000309233:p.Leu187Arg	92.0	0.0		137.0	8.0	NM_012230	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	hg19	CCDS43606.1	.	.	.	.	.	.	.	.	.	.	N	12.82	2.052691	0.36181	.	.	ENSG00000146707	ENST00000310842	T	0.27256	1.68	.	.	.	.	48.261100	0.00760	U	0.001131	T	0.23926	0.0579	N	0.08118	0	0.09310	N	1	P	0.51240	0.943	P	0.55011	0.766	T	0.19745	-1.0296	8	0.87932	D	0	.	.	.	.	.	187	Q6PJE2	POZP3_HUMAN	R	187	ENSP00000309233:L187R	ENSP00000309233:L187R	L	-	2	0	POMZP3	76078722	0.049000	0.20398	0.276000	0.24689	0.537000	0.34900	-0.663000	0.05299	0.000000	0.14550	0.000000	0.15137	CTG	.	.		0.517	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230	
PCLO	27445	hgsc.bcm.edu	37	7	82389961	82389961	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:82389961A>G	ENST00000333891.9	-	24	15619	c.15282T>C	c.(15280-15282)tcT>tcC	p.S5094S		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTACCTGAAGAGAATGTCCTG	0.308																																					p.S5094S		Atlas-SNP	.											.	PCLO	1506	.	0			c.T15282C						.						118.0	117.0	118.0					7																	82389961		1823	4072	5895	SO:0001819	synonymous_variant	27445	exon24			CTGAAGAGAATGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.15282T>C	chr7.hg19:g.82389961A>G		390.0	0.0		508.0	113.0	NM_033026		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.308	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
FZD1	8321	hgsc.bcm.edu	37	7	90894459	90894459	+	Silent	SNP	A	A	G	rs71292991|rs139480179	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:90894459A>G	ENST00000287934.2	+	1	677	c.264A>G	c.(262-264)caA>caG	p.Q88Q		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	88					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q88_P89insP(2)|p.Q88_P89insA(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			cggggcAGCAACCGCCGCCGC	0.741																																					p.Q88Q		Atlas-SNP	.											.,4	FZD1	64	.	3	Insertion - In frame(3)	breast(2)|liver(1)	c.A264G						.						10.0	11.0	11.0					7																	90894459		2176	4257	6433	SO:0001819	synonymous_variant	8321	exon1			GCAGCAACCGCCG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"""GPCR / Class F : Frizzled receptors"""	4038	protein-coding gene	gene with protein product	"""Wnt receptor"", ""frizzled, Drosophila, homolog of, 1"""	603408	"""frizzled (Drosophila) homolog 1"", ""frizzled homolog 1 (Drosophila)"", ""frizzled 1, seven transmembrane spanning receptor"", ""frizzled family receptor 1"""			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.264A>G	chr7.hg19:g.90894459A>G		2.0	0.0		4.0	2.0	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	hg19	CCDS5620.1																																																																																			.	.		0.741	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505	
BUD31	8896	hgsc.bcm.edu	37	7	99017026	99017026	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:99017026G>A	ENST00000403633.2	+	6	926	c.397G>A	c.(397-399)Gag>Aag	p.E133K	PTCD1_ENST00000292478.4_3'UTR|BUD31_ENST00000222969.5_Missense_Mutation_p.E133K|BUD31_ENST00000431419.1_Missense_Mutation_p.E104K|BUD31_ENST00000456893.1_Missense_Mutation_p.E92K			P41223	BUD31_HUMAN	BUD31 homolog (S. cerevisiae)	133					regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	4	all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CCGCATCATCGAGTGCACACA	0.647																																					p.E133K		Atlas-SNP	.											BUD31,NS,carcinoma,0,1	BUD31	12	.	0			c.G397A						.						138.0	105.0	116.0					7																	99017026		2203	4300	6503	SO:0001583	missense	8896	exon6			ATCATCGAGTGCA	BC022821	CCDS5663.1	7q22.1	2012-06-07	2007-01-12	2006-03-16	ENSG00000106245	ENSG00000106245			29629	protein-coding gene	gene with protein product	"""G10 maternal transcript homolog (Xenopus laevis)"", ""functional spliceosome-associated protein 17"""	603477	"""BUD31 homolog (yeast)"""			7841202	Standard	NM_003910		Approved	YCR063W, EDG-2, EDG2, G10, fSAP17, Cwc14	uc003uqg.4	P41223	OTTHUMG00000154602	ENST00000403633.2:c.397G>A	chr7.hg19:g.99017026G>A	ENSP00000386023:p.Glu133Lys	57.0	0.0		71.0	3.0	NM_003910	A4D274|B7Z4S9|D6W5S6|Q6IB53|Q9UDV1	Missense_Mutation	SNP	ENST00000403633.2	hg19	CCDS5663.1	.	.	.	.	.	.	.	.	.	.	G	36	5.685340	0.96784	.	.	ENSG00000106245	ENST00000403633;ENST00000222969;ENST00000456893;ENST00000431419	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.82962	0.5151	M	0.83852	2.665	0.80722	D	1	D	0.69078	0.997	D	0.68353	0.957	D	0.85445	0.1157	9	0.72032	D	0.01	-24.6234	18.2539	0.90012	0.0:0.0:1.0:0.0	.	133	P41223	BUD31_HUMAN	K	133;133;92;104	.	ENSP00000222969:E133K	E	+	1	0	BUD31	98854962	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.986000	0.93492	2.625000	0.88918	0.655000	0.94253	GAG	.	.		0.647	BUD31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336275.1	NM_003910	
CNPY4	245812	hgsc.bcm.edu	37	7	99722425	99722425	+	Missense_Mutation	SNP	G	G	C	rs373606882|rs141457365	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:99722425G>C	ENST00000262932.3	+	6	793	c.661G>C	c.(661-663)Gag>Cag	p.E221Q	CNPY4_ENST00000480692.1_3'UTR|MBLAC1_ENST00000398075.2_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	221	Glu-rich.					extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					agagcaggaggaggaggagga	0.502																																					p.E221Q		Atlas-SNP	.											.	CNPY4	18	.	0			c.G661C						.						115.0	123.0	120.0					7																	99722425		2203	4300	6503	SO:0001583	missense	245812	exon6			CAGGAGGAGGAGG	AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"""protein associated with TLR4"""	610047	"""canopy 4 homolog (zebrafish)"""			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.661G>C	chr7.hg19:g.99722425G>C	ENSP00000262932:p.Glu221Gln	24.0	0.0		38.0	5.0	NM_152755	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	hg19	CCDS34701.1	.	.	.	.	.	.	.	.	.	.	G	5.539	0.284285	0.10513	.	.	ENSG00000166997	ENST00000262932	T	0.32988	1.43	4.51	-0.822	0.10819	.	0.852017	0.10394	N	0.680049	T	0.13457	0.0326	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33701	-0.9858	10	0.19147	T	0.46	.	8.1283	0.31012	0.1925:0.1573:0.6502:0.0	.	221	Q8N129	CNPY4_HUMAN	Q	221	ENSP00000262932:E221Q	ENSP00000262932:E221Q	E	+	1	0	CNPY4	99560361	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.091000	0.11146	-0.071000	0.12886	0.561000	0.74099	GAG	.	.		0.502	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755	
STAG3	10734	hgsc.bcm.edu	37	7	99787154	99787154	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:99787154A>G	ENST00000426455.1	+	8	1209	c.802A>G	c.(802-804)Aga>Gga	p.R268G	STAG3_ENST00000317296.5_Missense_Mutation_p.R268G|STAG3_ENST00000394018.2_Missense_Mutation_p.R210G	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	268					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGAGGCTGAAAGAAACAAGGG	0.507																																					p.R268G		Atlas-SNP	.											.	STAG3	121	.	0			c.A802G						.						123.0	132.0	129.0					7																	99787154		2203	4300	6503	SO:0001583	missense	10734	exon8			GCTGAAAGAAACA	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.802A>G	chr7.hg19:g.99787154A>G	ENSP00000400359:p.Arg268Gly	63.0	0.0		96.0	4.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.951549	0.73787	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000317296	T;T;T	0.47528	0.84;0.84;0.84	5.23	1.09	0.20402	STAG (1);	0.201076	0.24592	N	0.037210	T	0.64450	0.2599	M	0.73598	2.24	0.35792	D	0.822449	D;B	0.67145	0.996;0.153	D;B	0.67900	0.954;0.18	T	0.73232	-0.4048	10	0.87932	D	0	-8.616	13.1012	0.59219	0.5532:0.4468:0.0:0.0	.	210;268	B4DZ10;Q9UJ98	.;STAG3_HUMAN	G	268;210;226;268	ENSP00000400359:R268G;ENSP00000377586:R210G;ENSP00000319318:R268G	ENSP00000319318:R268G	R	+	1	2	STAG3	99625090	0.920000	0.31207	0.996000	0.52242	0.996000	0.88848	0.533000	0.23082	0.017000	0.15025	-0.173000	0.13275	AGA	.	.		0.507	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
LRRC17	10234	hgsc.bcm.edu	37	7	102575002	102575002	+	Missense_Mutation	SNP	A	A	T	rs3832497|rs77576273|rs531650613	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:102575002A>T	ENST00000339431.4	+	2	937	c.642A>T	c.(640-642)gaA>gaT	p.E214D	FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.E214D|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000393772.2_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	214	LRRCT 1.			Missing (in Ref. 2; AAQ89248). {ECO:0000305}.	bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TGTGTAATGAAGAAGAAAAGG	0.438																																					p.E214D		Atlas-SNP	.											.	LRRC17	45	.	0			c.A642T						.						19.0	11.0	14.0					7																	102575002		1944	3733	5677	SO:0001583	missense	10234	exon2			TAATGAAGAAGAA	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.642A>T	chr7.hg19:g.102575002A>T	ENSP00000344242:p.Glu214Asp	8.0	0.0		25.0	5.0	NM_005824	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419589	0.25552	.	.	ENSG00000128606	ENST00000339431;ENST00000249377	T;T	0.62639	0.22;0.01	5.28	2.92	0.33932	.	0.000000	0.56097	D	0.000026	T	0.46190	0.1380	L	0.37850	1.14	0.37180	D	0.903456	B;B	0.18013	0.015;0.025	B;B	0.20184	0.012;0.028	T	0.36648	-0.9739	10	0.34782	T	0.22	-31.8822	4.9104	0.13820	0.7178:0.0:0.1465:0.1357	.	214;214	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	D	214	ENSP00000344242:E214D;ENSP00000249377:E214D	ENSP00000249377:E214D	E	+	3	2	LRRC17	102362238	1.000000	0.71417	0.874000	0.34290	0.990000	0.78478	2.097000	0.41748	0.416000	0.25844	0.460000	0.39030	GAA	.	.		0.438	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824	
DOCK4	9732	hgsc.bcm.edu	37	7	111381259	111381259	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:111381259T>C	ENST00000437633.1	-	46	5160	c.4904A>G	c.(4903-4905)tAc>tGc	p.Y1635C	DOCK4_ENST00000428084.1_Missense_Mutation_p.Y1644C|DOCK4_ENST00000494651.2_Missense_Mutation_p.Y518C	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1635					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GACAGCTGGGTAACTTAACGG	0.423																																					p.Y1635C		Atlas-SNP	.											.	DOCK4	365	.	0			c.A4904G						.						204.0	201.0	202.0					7																	111381259		1862	4108	5970	SO:0001583	missense	9732	exon46			GCTGGGTAACTTA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4904A>G	chr7.hg19:g.111381259T>C	ENSP00000404179:p.Tyr1635Cys	71.0	0.0		95.0	4.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.73|17.73	3.462103|3.462103	0.63513|0.63513	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000423057;ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	.|T;T;T	.|0.05996	.|4.1;3.36;4.1	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.19046|0.19046	0.0457|0.0457	L|L	0.51422|0.51422	1.61|1.61	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D;D;D;D	.|0.67145	.|0.994;0.994;0.989;0.989;0.996	.|P;P;P;P;D	.|0.66847	.|0.783;0.892;0.887;0.887;0.947	T|T	0.00196|0.00196	-1.1931|-1.1931	5|10	.|0.51188	.|T	.|0.08	.|.	15.5536|15.5536	0.76173|0.76173	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|542;518;1680;1635;1644	.|B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2	.|.;.;.;DOCK4_HUMAN;.	A|C	1096;1668|1623;1644;518;1635;1632	.|ENSP00000410746:Y1644C;ENSP00000440944:Y518C;ENSP00000404179:Y1635C	.|ENSP00000345432:Y1632C	T|Y	-|-	1|2	0|0	DOCK4|DOCK4	111168495|111168495	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.694000|4.694000	0.61760|0.61760	2.260000|2.260000	0.74910|0.74910	0.533000|0.533000	0.62120|0.62120	ACC|TAC	.	.		0.423	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
METTL2B	55798	hgsc.bcm.edu	37	7	128117152	128117152	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:128117152T>C	ENST00000262432.8	+	2	164	c.127T>C	c.(127-129)Tcg>Ccg	p.S43P	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Intron	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	43					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TGTGGAGTGGTCGGAAGAGCA	0.587											OREG0018295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S43P		Atlas-SNP	.											.	METTL2B	34	.	0			c.T127C						.						37.0	50.0	46.0					7																	128117152		2203	4297	6500	SO:0001583	missense	55798	exon2			GAGTGGTCGGAAG	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.127T>C	chr7.hg19:g.128117152T>C	ENSP00000262432:p.Ser43Pro	92.0	0.0	1562	116.0	5.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	T	13.27	2.186819	0.38609	.	.	ENSG00000165055	ENST00000262432	D	0.83075	-1.68	2.52	-0.338	0.12651	.	0.171024	0.53938	D	0.000057	T	0.70360	0.3215	L	0.41710	1.295	0.80722	D	1	B	0.15719	0.014	B	0.19946	0.027	T	0.56786	-0.7921	10	0.62326	D	0.03	0.0689	3.0759	0.06246	0.2097:0.1354:0.0:0.6549	.	43	Q6P1Q9	MTL2B_HUMAN	P	43	ENSP00000262432:S43P	ENSP00000262432:S43P	S	+	1	0	METTL2B	127904388	1.000000	0.71417	0.844000	0.33320	0.161000	0.22273	3.519000	0.53458	-0.186000	0.10533	0.163000	0.16589	TCG	.	.		0.587	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
SCARA5	286133	hgsc.bcm.edu	37	8	27779159	27779159	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:27779159G>A	ENST00000354914.3	-	4	1330	c.845C>T	c.(844-846)gCg>gTg	p.A282V	SCARA5_ENST00000301906.4_Missense_Mutation_p.A239V|SCARA5_ENST00000518030.1_Missense_Mutation_p.A239V|SCARA5_ENST00000524352.1_Missense_Mutation_p.A282V|SCARA5_ENST00000380385.2_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	282					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		CTCGGTGACCGCGTTGAGCAT	0.677																																					p.A282V		Atlas-SNP	.											SCARA5,NS,lymphoid_neoplasm,0,1	SCARA5	53	.	0			c.C845T						.						73.0	53.0	60.0					8																	27779159		2203	4300	6503	SO:0001583	missense	286133	exon4			GTGACCGCGTTGA	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.845C>T	chr8.hg19:g.27779159G>A	ENSP00000346990:p.Ala282Val	45.0	0.0		30.0	3.0	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	hg19	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	G	8.161	0.789615	0.16258	.	.	ENSG00000168079	ENST00000354914;ENST00000517320;ENST00000524352;ENST00000518030;ENST00000301906	D;D;D;D	0.90385	-2.29;-2.66;-2.58;-2.58	4.52	-0.912	0.10504	.	1.061850	0.07302	N	0.874184	T	0.67249	0.2873	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.59974	-0.7353	10	0.10902	T	0.67	.	0.1936	0.00137	0.2933:0.144:0.2588:0.3039	.	282;239;282	Q6ZMJ2-2;Q6ZMJ2-3;Q6ZMJ2	.;.;SCAR5_HUMAN	V	282;82;282;239;239	ENSP00000346990:A282V;ENSP00000428663:A282V;ENSP00000430713:A239V;ENSP00000301906:A239V	ENSP00000301906:A239V	A	-	2	0	SCARA5	27835078	0.003000	0.15002	0.001000	0.08648	0.923000	0.55619	0.950000	0.29122	-0.048000	0.13401	0.456000	0.33151	GCG	.	.		0.677	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
TEX15	56154	hgsc.bcm.edu	37	8	30701385	30701385	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:30701385G>A	ENST00000256246.2	-	1	5223	c.5149C>T	c.(5149-5151)Cga>Tga	p.R1717*		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1717					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.R1717*(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGCAAGCTTCGCAATGTTGGT	0.388																																					p.R1717X		Atlas-SNP	.											TEX15,rectum,carcinoma,0,1	TEX15	350	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C5149T						.						142.0	133.0	136.0					8																	30701385		2203	4300	6503	SO:0001587	stop_gained	56154	exon1			AGCTTCGCAATGT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5149C>T	chr8.hg19:g.30701385G>A	ENSP00000256246:p.Arg1717*	99.0	1.0		91.0	30.0	NM_031271		Nonsense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	G	44	11.233117	0.99534	.	.	ENSG00000133863	ENST00000256246	.	.	.	5.69	4.79	0.61399	.	0.000000	0.48767	D	0.000161	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.4557	0.55702	0.0:0.0:0.6716:0.3283	.	.	.	.	X	1717	.	ENSP00000256246:R1717X	R	-	1	2	TEX15	30820927	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.381000	0.52455	1.323000	0.45263	0.563000	0.77884	CGA	.	.		0.388	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
IKBKB	3551	hgsc.bcm.edu	37	8	42176090	42176090	+	Missense_Mutation	SNP	C	C	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:42176090C>G	ENST00000520810.1	+	13	1447	c.1261C>G	c.(1261-1263)Ctc>Gtc	p.L421V	IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000416505.2_Missense_Mutation_p.L362V|IKBKB_ENST00000520835.1_Missense_Mutation_p.L419V|IKBKB_ENST00000379708.3_Missense_Mutation_p.L198V	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	421					B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAAGAGGAATCTCGCCTTCTT	0.527																																					p.L421V		Atlas-SNP	.											.	IKBKB	88	.	0			c.C1261G						.						87.0	84.0	85.0					8																	42176090		2203	4300	6503	SO:0001583	missense	3551	exon13			AGGAATCTCGCCT	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1261C>G	chr8.hg19:g.42176090C>G	ENSP00000430684:p.Leu421Val	100.0	0.0		77.0	12.0	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736000	0.69189	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	D;D;D;T	0.83755	-1.62;-1.76;-1.58;1.89	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	M	0.79258	2.445	0.58432	D	0.999999	D;D;D;D;D	0.76494	0.999;0.997;0.997;0.995;0.995	D;D;D;P;D	0.78314	0.991;0.966;0.991;0.831;0.953	D	0.89706	0.3908	10	0.44086	T	0.13	-24.9799	14.2701	0.66147	0.0:0.927:0.0:0.073	.	362;419;198;372;421	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920	.;.;.;.;IKKB_HUMAN	V	421;362;419;198	ENSP00000430684:L421V;ENSP00000404920:L362V;ENSP00000430868:L419V;ENSP00000369030:L198V	ENSP00000369030:L198V	L	+	1	0	IKBKB	42295247	0.992000	0.36948	0.180000	0.23079	0.606000	0.37113	3.446000	0.52928	2.740000	0.93945	0.555000	0.69702	CTC	.	.		0.527	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1		
COPS5	10987	hgsc.bcm.edu	37	8	67974167	67974167	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:67974167G>A	ENST00000357849.4	-	1	385	c.65C>T	c.(64-66)gCt>gTt	p.A22V	COPS5_ENST00000519963.1_5'UTR|AC109335.1_ENST00000578628.1_RNA|CSPP1_ENST00000412460.1_5'Flank|COPS5_ENST00000517736.1_Intron|CSPP1_ENST00000262210.5_5'Flank	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	22					cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GATACTCTGAGCTTCCTGCAT	0.557																																					p.A22V		Atlas-SNP	.											.	COPS5	29	.	0			c.C65T						.						149.0	135.0	139.0					8																	67974167		2203	4300	6503	SO:0001583	missense	10987	exon1			CTCTGAGCTTCCT	U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5"", ""COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"""			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563	ENST00000357849.4:c.65C>T	chr8.hg19:g.67974167G>A	ENSP00000350512:p.Ala22Val	71.0	0.0		92.0	7.0	NM_006837	O15386|Q6AW95|Q86WQ4|Q9BQ17	Missense_Mutation	SNP	ENST00000357849.4	hg19	CCDS6198.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559240	0.27827	.	.	ENSG00000121022	ENST00000357849	.	.	.	5.68	5.68	0.88126	.	0.102356	0.64402	D	0.000001	T	0.13586	0.0329	N	0.00358	-1.6	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38520	-0.9657	9	0.02654	T	1	-11.8083	12.4651	0.55753	0.0764:0.0:0.9236:0.0	.	22	Q92905	CSN5_HUMAN	V	22	.	ENSP00000350512:A22V	A	-	2	0	COPS5	68136721	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.806000	0.75195	2.838000	0.97847	0.655000	0.94253	GCT	.	.		0.557	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2		
PREX2	80243	hgsc.bcm.edu	37	8	68972975	68972975	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:68972975T>C	ENST00000288368.4	+	11	1577	c.1300T>C	c.(1300-1302)Ttg>Ctg	p.L434L	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	434	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGGCGTGCACTTGGGACAAGC	0.358																																					p.L434L		Atlas-SNP	.											.	PREX2	614	.	0			c.T1300C						.						113.0	115.0	114.0					8																	68972975		2203	4300	6503	SO:0001819	synonymous_variant	80243	exon11			GTGCACTTGGGAC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1300T>C	chr8.hg19:g.68972975T>C		109.0	0.0		97.0	4.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.358	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
CRISPLD1	83690	hgsc.bcm.edu	37	8	75927121	75927121	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:75927121G>A	ENST00000262207.4	+	6	1169	c.701G>A	c.(700-702)gGc>gAc	p.G234D	CRISPLD1_ENST00000523524.1_Missense_Mutation_p.G46D|CRISPLD1_ENST00000517786.1_Missense_Mutation_p.G48D	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	234					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			TTTGGAGGGGGCTGTAGAGAA	0.428																																					p.G234D		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.G701A						.						57.0	52.0	53.0					8																	75927121		2203	4300	6503	SO:0001583	missense	83690	exon6			GAGGGGGCTGTAG	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"""LCCL domain containing cysteine-rich secretory protein 1"""	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.701G>A	chr8.hg19:g.75927121G>A	ENSP00000262207:p.Gly234Asp	141.0	0.0		143.0	31.0	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.381005	0.82792	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	T;T;D	0.82711	0.27;-1.23;-1.64	4.69	4.69	0.59074	.	0.112857	0.64402	D	0.000010	D	0.82346	0.5017	M	0.67397	2.05	0.53005	D	0.999963	P;P	0.52577	0.954;0.514	B;B	0.41412	0.356;0.159	D	0.84987	0.0892	10	0.49607	T	0.09	.	17.8197	0.88647	0.0:0.0:1.0:0.0	.	48;234	B7Z929;Q9H336	.;CRLD1_HUMAN	D	234;46;48	ENSP00000262207:G234D;ENSP00000430105:G46D;ENSP00000429746:G48D	ENSP00000262207:G234D	G	+	2	0	CRISPLD1	76089676	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.604000	0.82830	2.429000	0.82318	0.460000	0.39030	GGC	.	.		0.428	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461	
ZFHX4	79776	hgsc.bcm.edu	37	8	77762578	77762578	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:77762578A>G	ENST00000521891.2	+	9	4392	c.3944A>G	c.(3943-3945)gAg>gGg	p.E1315G	ZFHX4_ENST00000518282.1_Missense_Mutation_p.E1289G|ZFHX4_ENST00000455469.2_Missense_Mutation_p.E1270G|ZFHX4_ENST00000050961.6_Missense_Mutation_p.E1270G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTGACAGCTGAGGGGTCTGGG	0.493										HNSCC(33;0.089)																											p.E1315G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A3944G						.						48.0	52.0	50.0					8																	77762578		1921	4133	6054	SO:0001583	missense	79776	exon9			CAGCTGAGGGGTC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.3944A>G	chr8.hg19:g.77762578A>G	ENSP00000430497:p.Glu1315Gly	78.0	0.0		92.0	5.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	9.876	1.200222	0.22121	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.54675	0.56;0.62;0.59;0.57	5.17	3.99	0.46301	.	0.196425	0.24750	U	0.035906	T	0.45438	0.1342	L	0.47716	1.5	0.48830	D	0.99971	B;B;B	0.13594	0.005;0.008;0.008	B;B;B	0.18561	0.01;0.022;0.022	T	0.30563	-0.9974	10	0.31617	T	0.26	.	12.4307	0.55573	0.8601:0.1399:0.0:0.0	.	1270;1270;1315	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	G	1315;1315;1270;1270;1289	ENSP00000430497:E1315G;ENSP00000399605:E1270G;ENSP00000050961:E1270G;ENSP00000430848:E1289G	ENSP00000050961:E1270G	E	+	2	0	ZFHX4	77925133	1.000000	0.71417	0.340000	0.25575	0.517000	0.34286	5.421000	0.66447	0.953000	0.37825	0.459000	0.35465	GAG	.	.		0.493	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
VPS13B	157680	hgsc.bcm.edu	37	8	100829851	100829851	+	Missense_Mutation	SNP	A	A	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:100829851A>C	ENST00000358544.2	+	45	8367	c.8256A>C	c.(8254-8256)caA>caC	p.Q2752H	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.Q2727H	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2752					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ACATTGGTCAAGATGGACAAG	0.398																																					p.Q2752H	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A8256C						.						110.0	104.0	106.0					8																	100829851		2203	4300	6503	SO:0001583	missense	157680	exon45			TGGTCAAGATGGA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.8256A>C	chr8.hg19:g.100829851A>C	ENSP00000351346:p.Gln2752His	147.0	0.0		232.0	49.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.237867	0.39598	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70045	-0.45;-0.45	5.61	-1.03	0.10102	.	0.398694	0.25759	N	0.028484	T	0.36386	0.0965	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.003	T	0.03818	-1.1001	10	0.48119	T	0.1	.	2.745	0.05264	0.5313:0.1103:0.2513:0.1071	.	2727;2752	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	H	2727;2752	ENSP00000349685:Q2727H;ENSP00000351346:Q2752H	ENSP00000349685:Q2727H	Q	+	3	2	VPS13B	100899027	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.661000	0.25023	0.143000	0.18926	0.533000	0.62120	CAA	.	.		0.398	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
ATAD2	29028	hgsc.bcm.edu	37	8	124382155	124382155	+	Missense_Mutation	SNP	A	A	T	rs373904648		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:124382155A>T	ENST00000287394.5	-	7	944	c.837T>A	c.(835-837)gaT>gaA	p.D279E	ATAD2_ENST00000534257.1_5'Flank|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	279	Asp-rich.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			catcttcatcatcttcatcat	0.373																																					p.D279E		Atlas-SNP	.											.	ATAD2	160	.	0			c.T837A						.						270.0	209.0	230.0					8																	124382155		2203	4300	6503	SO:0001583	missense	29028	exon7			TTCATCATCTTCA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.837T>A	chr8.hg19:g.124382155A>T	ENSP00000287394:p.Asp279Glu	135.0	0.0		210.0	20.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	A	0.804	-0.754275	0.03041	.	.	ENSG00000156802	ENST00000287394	T	0.15718	2.4	3.43	-6.86	0.01676	.	1.759450	0.01899	N	0.039043	T	0.08358	0.0208	L	0.27053	0.805	0.58432	D	0.999999	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.0	T	0.45702	-0.9243	10	0.02654	T	1	-1.7868	4.1656	0.10305	0.2875:0.0:0.1907:0.5219	.	109;279	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	E	279	ENSP00000287394:D279E	ENSP00000287394:D279E	D	-	3	2	ATAD2	124451336	0.679000	0.27596	0.008000	0.14137	0.002000	0.02628	-0.320000	0.08028	-2.138000	0.00808	-1.800000	0.00619	GAT	.	.		0.373	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
ATAD2	29028	hgsc.bcm.edu	37	8	124382158	124382158	+	Missense_Mutation	SNP	T	T	A	rs373904648|rs374184884|rs145137934|rs112640031|rs371096883|rs373069275|rs113064839	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:124382158T>A	ENST00000287394.5	-	7	941	c.834A>T	c.(832-834)gaA>gaT	p.E278D	ATAD2_ENST00000534257.1_5'Flank|ATAD2_ENST00000521903.1_De_novo_Start_OutOfFrame	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	278	Asp-rich.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			cttcatcatcttcatcatcat	0.378																																					p.E278D		Atlas-SNP	.											.	ATAD2	160	.	0			c.A834T						.						260.0	205.0	224.0					8																	124382158		2203	4300	6503	SO:0001583	missense	29028	exon7			ATCATCTTCATCA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.834A>T	chr8.hg19:g.124382158T>A	ENSP00000287394:p.Glu278Asp	133.0	0.0		204.0	19.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	t	0.007	-1.995361	0.00435	.	.	ENSG00000156802	ENST00000287394	T	0.05786	3.39	3.43	-2.99	0.05497	.	1.396170	0.03921	N	0.283542	T	0.02929	0.0087	N	0.03608	-0.345	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.0	T	0.49133	-0.8971	10	0.10902	T	0.67	-2.6732	9.3965	0.38406	0.5472:0.0:0.0:0.4528	.	108;278	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	D	278	ENSP00000287394:E278D	ENSP00000287394:E278D	E	-	3	2	ATAD2	124451339	0.007000	0.16637	0.018000	0.16275	0.001000	0.01503	-1.836000	0.01690	-0.689000	0.05149	-4.187000	0.00009	GAA	.	.		0.378	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
ANXA13	312	hgsc.bcm.edu	37	8	124705521	124705521	+	Nonsense_Mutation	SNP	C	C	T	rs146521013		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:124705521C>T	ENST00000419625.1	-	8	630	c.558G>A	c.(556-558)tgG>tgA	p.W186*	ANXA13_ENST00000262219.6_Nonsense_Mutation_p.W227*	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	186					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			CATCAGTGCCCCAGCGGCCTT	0.463																																					p.W227X		Atlas-SNP	.											.	ANXA13	38	.	0			c.G681A						.						142.0	143.0	142.0					8																	124705521		2203	4300	6503	SO:0001587	stop_gained	312	exon9			AGTGCCCCAGCGG	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.558G>A	chr8.hg19:g.124705521C>T	ENSP00000390809:p.Trp186*	90.0	0.0		166.0	9.0	NM_001003954	Q9BQR5	Nonsense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1	.	.	.	.	.	.	.	.	.	.	C	36	5.644737	0.96704	.	.	ENSG00000104537	ENST00000262219;ENST00000419625	.	.	.	5.41	5.41	0.78517	.	0.314542	0.39909	N	0.001227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.3145	0.90215	0.0:1.0:0.0:0.0	.	.	.	.	X	227;186	.	ENSP00000262219:W227X	W	-	3	0	ANXA13	124774702	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.234000	0.43035	2.701000	0.92244	0.650000	0.86243	TGG	.	C|1.000;A|0.000		0.463	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
EPPK1	83481	hgsc.bcm.edu	37	8	144940354	144940354	+	Silent	SNP	G	G	A	rs375604799		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:144940354G>A	ENST00000525985.1	-	2	7139	c.7068C>T	c.(7066-7068)cgC>cgT	p.R2356R				P58107	EPIPL_HUMAN	epiplakin 1	2356						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCACGGGCACGCGGTGGCTGT	0.692																																					p.R2356R		Atlas-SNP	.											.	EPPK1	199	.	0			c.C7068T						.	G		2,4332		0,2,2165	195.0	189.0	191.0		7068	1.3	1.0	8		191	0,8472		0,0,4236	no	coding-synonymous	EPPK1	NM_031308.1		0,2,6401	AA,AG,GG		0.0,0.0461,0.0156		2356/2420	144940354	2,12804	2167	4236	6403	SO:0001819	synonymous_variant	83481	exon1			GGGCACGCGGTGG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7068C>T	chr8.hg19:g.144940354G>A		23.0	0.0		22.0	10.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.692	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
OPLAH	26873	hgsc.bcm.edu	37	8	145112137	145112137	+	Silent	SNP	C	C	T	rs546232581		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:145112137C>T	ENST00000426825.1	-	11	1590	c.1509G>A	c.(1507-1509)ctG>ctA	p.L503L	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	503					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGTCCATGCCCAGGGCCCGGG	0.657																																					p.L503L		Atlas-SNP	.											.	OPLAH	78	.	0			c.G1509A						.						20.0	25.0	23.0					8																	145112137		2128	4227	6355	SO:0001819	synonymous_variant	26873	exon11			CATGCCCAGGGCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1509G>A	chr8.hg19:g.145112137C>T		77.0	0.0		43.0	9.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	hg19																																																																																				.	.		0.657	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
OPLAH	26873	hgsc.bcm.edu	37	8	145112386	145112386	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:145112386C>T	ENST00000426825.1	-	10	1468	c.1387G>A	c.(1387-1389)Gag>Aag	p.E463K	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	463					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CACATGGCCTCGTTGGCCACG	0.701																																					p.E463K		Atlas-SNP	.											OPLAH,NS,carcinoma,0,1	OPLAH	78	.	0			c.G1387A						.						13.0	17.0	16.0					8																	145112386		2080	4210	6290	SO:0001583	missense	26873	exon10			TGGCCTCGTTGGC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1387G>A	chr8.hg19:g.145112386C>T	ENSP00000475943:p.Glu463Lys	62.0	0.0		14.0	2.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.51	2.556270	0.45487	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.78528	0.4297	.	.	.	0.50813	D	0.999898	D	0.89917	1.0	D	0.97110	1.0	D	0.84723	0.0741	7	0.87932	D	0	.	14.2922	0.66286	0.0:1.0:0.0:0.0	.	463	O14841	OPLA_HUMAN	K	463	.	ENSP00000412071:E463K	E	-	1	0	OPLAH	145184374	1.000000	0.71417	0.998000	0.56505	0.913000	0.54294	7.100000	0.76989	2.025000	0.59659	0.467000	0.42956	GAG	.	.		0.701	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
CPSF1	29894	hgsc.bcm.edu	37	8	145634528	145634528	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr8:145634528G>T	ENST00000349769.3	-	2	109	c.15C>A	c.(13-15)taC>taA	p.Y5*	GS1-393G12.14_ENST00000607491.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	5					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GCGCCTGTTTGTACACGGCGT	0.677																																					p.Y5X	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C15A						.						91.0	84.0	86.0					8																	145634528		2203	4300	6503	SO:0001587	stop_gained	29894	exon2			CTGTTTGTACACG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.15C>A	chr8.hg19:g.145634528G>T	ENSP00000339353:p.Tyr5*	42.0	0.0		30.0	8.0	NM_013291	Q96AF0	Nonsense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	G	38	6.704147	0.97776	.	.	ENSG00000071894	ENST00000349769;ENST00000531042	.	.	.	5.14	3.3	0.37823	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.0503	8.4787	0.33030	0.0846:0.0:0.7636:0.1518	.	.	.	.	X	5	.	ENSP00000339353:Y5X	Y	-	3	2	CPSF1	145605336	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.793000	0.69060	1.162000	0.42619	0.556000	0.70494	TAC	.	.		0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
TEK	7010	hgsc.bcm.edu	37	9	27190548	27190548	+	Missense_Mutation	SNP	C	C	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:27190548C>G	ENST00000380036.4	+	10	1791	c.1349C>G	c.(1348-1350)gCc>gGc	p.A450G	TEK_ENST00000406359.4_Missense_Mutation_p.A407G|TEK_ENST00000519097.1_Missense_Mutation_p.A303G	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	450	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CCCCTGAATGCCCCAAACGTG	0.418																																					p.A450G		Atlas-SNP	.											.	TEK	250	.	0			c.C1349G						.						186.0	179.0	182.0					9																	27190548		2203	4300	6503	SO:0001583	missense	7010	exon10			TGAATGCCCCAAA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.1349C>G	chr9.hg19:g.27190548C>G	ENSP00000369375:p.Ala450Gly	184.0	0.0		183.0	17.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490725	0.64074	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.55	5.55	0.83447	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.43919	U	0.000513	T	0.69043	0.3067	L	0.53249	1.67	0.46149	D	0.998891	P;P;D;P	0.69078	0.611;0.866;0.997;0.801	B;P;D;B	0.80764	0.253;0.61;0.994;0.334	T	0.69109	-0.5232	10	0.54805	T	0.06	.	17.6716	0.88220	0.0:1.0:0.0:0.0	.	303;483;407;450	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	G	303;450;407;407;260	ENSP00000430686:A303G;ENSP00000369375:A450G;ENSP00000383977:A407G;ENSP00000428337:A260G	ENSP00000343716:A407G	A	+	2	0	TEK	27180548	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.702000	0.61817	2.610000	0.88304	0.591000	0.81541	GCC	.	.		0.418	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
NAA35	60560	hgsc.bcm.edu	37	9	88631506	88631506	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:88631506G>A	ENST00000361671.5	+	18	1754	c.1621G>A	c.(1621-1623)Gat>Aat	p.D541N		NM_024635.3	NP_078911.3	Q5VZE5	NAA35_HUMAN	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	541					negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						GAGTCGTGCCGATGGCTCTCA	0.378																																					p.D541N		Atlas-SNP	.											.	NAA35	50	.	0			c.G1621A						.						102.0	96.0	98.0					9																	88631506		2203	4300	6503	SO:0001583	missense	60560	exon18			CGTGCCGATGGCT	AK025266	CCDS6673.1	9q22.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000135040	ENSG00000135040		"""N(alpha)-acetyltransferase subunits"""	24340	protein-coding gene	gene with protein product			"""MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)"""	MAK10		14702039, 19660095	Standard	NM_024635		Approved	FLJ21613, FLJ22643, bA379P1.1	uc004aoi.4	Q5VZE5	OTTHUMG00000020131	ENST00000361671.5:c.1621G>A	chr9.hg19:g.88631506G>A	ENSP00000354972:p.Asp541Asn	81.0	0.0		69.0	4.0	NM_024635	Q5VZE6|Q9H631|Q9H703	Missense_Mutation	SNP	ENST00000361671.5	hg19	CCDS6673.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055047	0.75960	.	.	ENSG00000135040	ENST00000361671	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.44117	0.1278	L	0.34521	1.04	0.80722	D	1	P	0.37398	0.593	B	0.26202	0.067	T	0.37478	-0.9704	9	0.19590	T	0.45	-14.8571	19.169	0.93569	0.0:0.0:1.0:0.0	.	541	Q5VZE5	NAA35_HUMAN	N	541	.	ENSP00000354972:D541N	D	+	1	0	NAA35	87821326	1.000000	0.71417	0.990000	0.47175	0.880000	0.50808	9.544000	0.98092	2.527000	0.85204	0.491000	0.48974	GAT	.	.		0.378	NAA35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052906.1	NM_024635	
FGD3	89846	hgsc.bcm.edu	37	9	95768397	95768397	+	Missense_Mutation	SNP	G	G	A	rs371917520		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:95768397G>A	ENST00000375482.3	+	6	1268	c.772G>A	c.(772-774)Gta>Ata	p.V258I	FGD3_ENST00000337352.6_Missense_Mutation_p.V258I|FGD3_ENST00000416701.2_Missense_Mutation_p.V258I	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	258	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.V258I(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TGACCGAGCCGTAGGGCTGGT	0.582																																					p.V258I		Atlas-SNP	.											FGD3_ENST00000375482,colon,carcinoma,0,4	FGD3	116	.	2	Substitution - Missense(2)	endometrium(2)	c.G772A						.	G	ILE/VAL,ILE/VAL	0,4332		0,0,2166	64.0	70.0	68.0		772,772	-6.4	0.0	9		68	1,8571		0,1,4285	no	missense,missense	FGD3	NM_033086.2,NM_001083536.1	29,29	0,1,6451	AA,AG,GG		0.0117,0.0,0.0077	benign,benign	258/726,258/726	95768397	1,12903	2166	4286	6452	SO:0001583	missense	89846	exon6			CGAGCCGTAGGGC	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.772G>A	chr9.hg19:g.95768397G>A	ENSP00000364631:p.Val258Ile	45.0	0.0		50.0	2.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758422	0.49468	0.0	1.17E-4	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352	T;T;T	0.62941	-0.01;-0.01;-0.01	4.54	-6.4	0.01944	Dbl homology (DH) domain (5);	0.689202	0.12020	N	0.507040	T	0.38799	0.1054	N	0.11651	0.15	0.80722	D	1	B;P;B	0.45240	0.194;0.854;0.381	B;B;B	0.40256	0.146;0.324;0.163	T	0.44097	-0.9350	10	0.30854	T	0.27	.	16.6006	0.84815	0.8497:0.0:0.1503:0.0	.	258;258;258	Q5JSP0-2;F8W7P2;Q5JSP0	.;.;FGD3_HUMAN	I	258	ENSP00000364631:V258I;ENSP00000413833:V258I;ENSP00000336914:V258I	ENSP00000336914:V258I	V	+	1	0	FGD3	94808218	0.316000	0.24580	0.005000	0.12908	0.975000	0.68041	1.023000	0.30065	-1.330000	0.02255	0.655000	0.94253	GTA	.	.		0.582	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
WNK2	65268	hgsc.bcm.edu	37	9	96021717	96021717	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:96021717C>A	ENST00000297954.4	+	11	2887	c.2887C>A	c.(2887-2889)Ccc>Acc	p.P963T	WNK2_ENST00000395477.2_Missense_Mutation_p.P963T|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.P575T|WNK2_ENST00000349097.3_Missense_Mutation_p.P575T	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	963					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						ACCCACGCTGCCCCCTCAACC	0.692																																					p.P963T		Atlas-SNP	.											.	WNK2	277	.	0			c.C2887A						.						45.0	42.0	43.0					9																	96021717		2177	4250	6427	SO:0001583	missense	65268	exon11			ACGCTGCCCCCTC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.2887C>A	chr9.hg19:g.96021717C>A	ENSP00000297954:p.Pro963Thr	31.0	0.0		21.0	4.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	1.974|1.974|1.974	-0.435765|-0.435765|-0.435765	0.04636|0.04636|0.04636	.|.|.	.|.|.	ENSG00000165238|ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	.|.|T;T;T;T	.|.|0.70045	.|.|-0.45;-0.4;0.12;0.12	1.82|1.82|1.82	-1.72|-1.72|-1.72	0.08107|0.08107|0.08107	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|.|T	0.34745|.|0.34745	0.0908|.|0.0908	N|N|N	0.08118|0.08118|0.08118	0|0|0	0.09310|0.09310|0.09310	N|N|N	0.999991|0.999991|0.999991	.|.|B;B;B;B;B	.|.|0.24317	.|.|0.101;0.038;0.061;0.101;0.061	.|.|B;B;B;B;B	.|.|0.12837	.|.|0.008;0.008;0.006;0.008;0.006	T|.|T	0.17623|.|0.17623	-1.0363|.|-1.0363	5|.|8	.|.|.	.|.|.	.|.|.	.|.|.	1.4464|1.4464|1.4464	0.02365|0.02365|0.02365	0.3453:0.3433:0.0:0.3115|0.3453:0.3433:0.0:0.3115|0.3453:0.3433:0.0:0.3115	.|.|.	.|.|963;963;566;963;963	.|.|Q9Y3S1-2;Q9Y3S1-4;A6PVR4;F8W9F9;Q9Y3S1	.|.|.;.;.;.;WNK2_HUMAN	D|X|T	566|958|963;963;575;575	.|.|ENSP00000297954:P963T;ENSP00000378860:P963T;ENSP00000297876:P575T;ENSP00000411181:P575T	.|.|.	A|C|P	+|+|+	2|3|1	0|2|0	WNK2|WNK2|WNK2	95061538|95061538|95061538	0.023000|0.023000|0.023000	0.18921|0.18921|0.18921	0.038000|0.038000|0.038000	0.18304|0.18304|0.18304	0.040000|0.040000|0.040000	0.13550|0.13550|0.13550	1.441000|1.441000|1.441000	0.35035|0.35035|0.35035	0.478000|0.478000|0.478000	0.27488|0.27488|0.27488	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	GCC|TGC|CCC	.	.		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
ZNF618	114991	hgsc.bcm.edu	37	9	116812389	116812389	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:116812389G>A	ENST00000374126.5	+	15	2906	c.2807G>A	c.(2806-2808)cGg>cAg	p.R936Q	ZNF618_ENST00000288466.7_Missense_Mutation_p.R843Q|ZNF618_ENST00000470105.1_3'UTR			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	936					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R843Q(1)|p.R936Q(1)		breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						AAACGGAGGCGGCTGCTCAGT	0.483																																					p.R843Q		Atlas-SNP	.											ZNF618_ENST00000374126,NS,NS,0,2	ZNF618	184	.	2	Substitution - Missense(2)	NS(2)	c.G2528A						.						71.0	78.0	76.0					9																	116812389		1865	4103	5968	SO:0001583	missense	114991	exon14			GGAGGCGGCTGCT	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.2807G>A	chr9.hg19:g.116812389G>A	ENSP00000363241:p.Arg936Gln	39.0	0.0		36.0	2.0	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.95	2.090912	0.36855	.	.	ENSG00000157657	ENST00000374126;ENST00000288466	T;T	0.21543	2.0;2.0	5.93	5.93	0.95920	Ribonuclease H-like (1);	0.063525	0.64402	D	0.000005	T	0.40670	0.1126	.	.	.	0.53005	D	0.999963	D;P;B	0.71674	0.998;0.499;0.144	D;B;B	0.66602	0.945;0.013;0.013	T	0.01819	-1.1267	9	0.17832	T	0.49	-3.1706	19.3319	0.94293	0.0:0.0:1.0:0.0	.	903;936;843	B9EG82;Q5T7W0;Q5T7W0-2	.;ZN618_HUMAN;.	Q	936;843	ENSP00000363241:R936Q;ENSP00000288466:R843Q	ENSP00000288466:R843Q	R	+	2	0	ZNF618	115852210	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	5.957000	0.70323	2.815000	0.96918	0.561000	0.74099	CGG	.	.		0.483	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
COL27A1	85301	hgsc.bcm.edu	37	9	117068878	117068878	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:117068878A>G	ENST00000356083.3	+	58	5408	c.5017A>G	c.(5017-5019)Atc>Gtc	p.I1673V		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1673	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CAGCAACCTCATCCAGAGCAT	0.567											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I1673V		Atlas-SNP	.											COL27A1,colon,carcinoma,0,1	COL27A1	200	.	0			c.A5017G						.						76.0	77.0	77.0					9																	117068878		2203	4300	6503	SO:0001583	missense	85301	exon58			AACCTCATCCAGA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.5017A>G	chr9.hg19:g.117068878A>G	ENSP00000348385:p.Ile1673Val	56.0	0.0	1478	50.0	2.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.749458	0.49257	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.90900	-2.75	5.2	4.06	0.47325	Fibrillar collagen, C-terminal (2);	.	.	.	.	D	0.85881	0.5800	L	0.56340	1.77	0.52501	D	0.999953	B	0.32781	0.384	B	0.33196	0.159	T	0.78602	-0.2140	9	0.16896	T	0.51	.	8.8977	0.35474	0.91:0.0:0.09:0.0	.	1673	Q8IZC6	CORA1_HUMAN	V	1673;1680	ENSP00000348385:I1673V	ENSP00000348385:I1673V	I	+	1	0	COL27A1	116108699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.131000	0.77243	0.807000	0.34208	0.460000	0.39030	ATC	.	.		0.567	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
TNC	3371	hgsc.bcm.edu	37	9	117848274	117848274	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:117848274A>G	ENST00000350763.4	-	3	2147	c.1736T>C	c.(1735-1737)aTc>aCc	p.I579T	TNC_ENST00000423613.2_Missense_Mutation_p.I579T|TNC_ENST00000346706.3_Missense_Mutation_p.I579T|TNC_ENST00000542877.1_Missense_Mutation_p.I579T|TNC_ENST00000535648.1_Missense_Mutation_p.I579T|TNC_ENST00000537320.1_Missense_Mutation_p.I579T|TNC_ENST00000345230.3_Missense_Mutation_p.I579T|TNC_ENST00000341037.4_Missense_Mutation_p.I579T|TNC_ENST00000340094.3_Missense_Mutation_p.I579T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	579	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CTCGTGGCAGATGCACTGGCC	0.597																																					p.I579T		Atlas-SNP	.											.	TNC	282	.	0			c.T1736C						.						85.0	61.0	69.0					9																	117848274		2203	4300	6503	SO:0001583	missense	3371	exon3			TGGCAGATGCACT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.1736T>C	chr9.hg19:g.117848274A>G	ENSP00000265131:p.Ile579Thr	77.0	0.0		110.0	6.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457564	0.26161	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.03607	3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87;3.87	5.95	3.61	0.41365	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.879489	0.10084	N	0.717986	T	0.04634	0.0126	L	0.39020	1.185	0.29269	N	0.870809	B;B	0.13594	0.008;0.0	B;B	0.10450	0.005;0.001	T	0.27640	-1.0068	10	0.48119	T	0.1	.	10.3075	0.43689	0.8667:0.0:0.1333:0.0	.	579;579	E9PC84;P24821	.;TENA_HUMAN	T	579	ENSP00000344400:I579T;ENSP00000438152:I579T;ENSP00000344555:I579T;ENSP00000345861:I579T;ENSP00000265131:I579T;ENSP00000339553:I579T;ENSP00000411406:I579T;ENSP00000443478:I579T;ENSP00000442242:I579T	ENSP00000344400:I579T	I	-	2	0	TNC	116888095	0.987000	0.35691	0.582000	0.28627	0.715000	0.41141	4.481000	0.60250	0.501000	0.28013	0.460000	0.39030	ATC	.	.		0.597	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
SETX	23064	hgsc.bcm.edu	37	9	135204112	135204112	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:135204112A>G	ENST00000224140.5	-	10	3055	c.2873T>C	c.(2872-2874)aTa>aCa	p.I958T	SETX_ENST00000372169.2_Missense_Mutation_p.I958T|SETX_ENST00000393220.1_Missense_Mutation_p.I958T	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	958					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GTCTCTGTCTATCTGAGAATC	0.423																																					p.I958T		Atlas-SNP	.											.	SETX	234	.	0			c.T2873C						.						99.0	95.0	96.0					9																	135204112		2203	4300	6503	SO:0001583	missense	23064	exon10			CTGTCTATCTGAG	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.2873T>C	chr9.hg19:g.135204112A>G	ENSP00000224140:p.Ile958Thr	173.0	0.0		206.0	29.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997014	0.54147	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87887	-2.21;-2.31;-1.92	5.63	5.63	0.86233	.	7739.210000	0.00166	N	0.000000	D	0.84683	0.5526	N	0.24115	0.695	0.33344	D	0.570162	B;B;B	0.30361	0.277;0.181;0.277	B;B;B	0.30495	0.116;0.054;0.116	T	0.68659	-0.5350	10	0.87932	D	0	.	15.329	0.74190	1.0:0.0:0.0:0.0	.	958;958;958	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	T	958	ENSP00000224140:I958T;ENSP00000361242:I958T;ENSP00000376913:I958T	ENSP00000224140:I958T	I	-	2	0	SETX	134193933	0.844000	0.29557	0.974000	0.42286	0.954000	0.61252	3.164000	0.50770	2.281000	0.76405	0.533000	0.62120	ATA	.	.		0.423	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
COL5A1	1289	hgsc.bcm.edu	37	9	137593180	137593180	+	Splice_Site	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:137593180G>A	ENST00000371817.3	+	4	1068		c.e4+1		COL5A1_ENST00000464187.1_Splice_Site	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1						axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGTGTTTGAGGTGAGCAGGAG	0.617																																					.		Atlas-SNP	.											.	COL5A1	323	.	0			c.654+1G>A						.						112.0	89.0	96.0					9																	137593180		2202	4298	6500	SO:0001630	splice_region_variant	1289	exon4			TTTGAGGTGAGCA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.654+1G>A	chr9.hg19:g.137593180G>A		68.0	0.0		91.0	4.0	NM_000093	Q15094|Q5SUX4	Splice_Site	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149789	0.78001	.	.	ENSG00000130635	ENST00000371817	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5036	0.90890	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL5A1	136733001	1.000000	0.71417	0.994000	0.49952	0.754000	0.42855	9.489000	0.97949	2.428000	0.82296	0.491000	0.48974	.	.	.		0.617	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Intron
GPSM1	26086	hgsc.bcm.edu	37	9	139250948	139250948	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:139250948C>T	ENST00000440944.1	+	13	1987	c.1767C>T	c.(1765-1767)caC>caT	p.H589H	GPSM1_ENST00000392944.1_Silent_p.H80H|GPSM1_ENST00000429455.1_Silent_p.H80H	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	589					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)	p.H566H(1)		biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		TCCGAGGCCACGGCGAGCCCC	0.711																																					p.H589H		Atlas-SNP	.											GPSM1,NS,carcinoma,0,1	GPSM1	50	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1767T						.						24.0	32.0	29.0					9																	139250948		2199	4298	6497	SO:0001819	synonymous_variant	26086	exon13			AGGCCACGGCGAG	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1767C>T	chr9.hg19:g.139250948C>T		44.0	1.0		16.0	3.0	NM_001145638	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Silent	SNP	ENST00000440944.1	hg19	CCDS48055.1																																																																																			.	.		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
CARD9	64170	hgsc.bcm.edu	37	9	139265325	139265325	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:139265325C>T	ENST00000371732.5	-	4	760	c.595G>A	c.(595-597)Gcg>Acg	p.A199T	CARD9_ENST00000315908.7_Missense_Mutation_p.A199T|CARD9_ENST00000371734.3_Missense_Mutation_p.A199T	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	199					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CGCATGAGCGCGGCGCCCTTC	0.726																																					p.A199T		Atlas-SNP	.											CARD9,colon,carcinoma,0,1	CARD9	47	.	0			c.G595A						.						23.0	25.0	24.0					9																	139265325		2196	4296	6492	SO:0001583	missense	64170	exon4			TGAGCGCGGCGCC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.595G>A	chr9.hg19:g.139265325C>T	ENSP00000360797:p.Ala199Thr	56.0	0.0		28.0	3.0	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	hg19	CCDS6997.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992165	0.93167	.	.	ENSG00000187796	ENST00000371734;ENST00000371732;ENST00000315908	T;T;T	0.37584	1.19;1.19;1.19	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.996;0.996	T	0.63804	-0.6554	10	0.49607	T	0.09	-34.6344	16.9898	0.86350	0.0:1.0:0.0:0.0	.	95;199;199;199	B4DIK5;Q9H257-2;Q5SXM5;Q9H257	.;.;.;CARD9_HUMAN	T	199	ENSP00000360799:A199T;ENSP00000360797:A199T;ENSP00000323719:A199T	ENSP00000323719:A199T	A	-	1	0	CARD9	138385146	1.000000	0.71417	0.494000	0.27515	0.743000	0.42351	4.453000	0.60061	2.251000	0.74343	0.563000	0.77884	GCG	.	.		0.726	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
PITRM1	10531	hgsc.bcm.edu	37	10	3208566	3208567	+	Missense_Mutation	DNP	CT	CT	TG	rs28416720|rs33996077|rs4266975|rs148472807|rs114690446	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:3208566_3208567CT>TG	ENST00000224949.4	-	4	306_307	c.272_273AG>CA	c.(271-273)cAG>cCA	p.Q91P	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.Q59P|PITRM1_ENST00000380989.2_Missense_Mutation_p.Q91P|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAGTACGGAACTGCACGCTAGG	0.49																																					p.Q91Q|p.Q91P		Atlas-SNP	.											PITRM1,colon,carcinoma,-1,3|PITRM1,colon,carcinoma,0,3	PITRM1	109	.	0			c.G273A|c.A272C						.																																			SO:0001583	missense	10531	exon4			ACGGAACTGCACG|CGGAACTGCACGC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.272_273delinsTG	chr10.hg19:g.3208566_3208567delinsTG	ENSP00000224949:p.Gln91Pro	14.0|13.0	0.0		31.0|30.0	9.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent|Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.		0.490	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
MSRB2	22921	hgsc.bcm.edu	37	10	23393130	23393130	+	Missense_Mutation	SNP	C	C	G	rs201493683		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:23393130C>G	ENST00000376510.3	+	2	279	c.176C>G	c.(175-177)aCc>aGc	p.T59S		NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	59					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	AAGAAACTAACCCCGGAGCAG	0.443																																					p.T59S	Esophageal Squamous(89;1240 1363 4973 30188 42299)	Atlas-SNP	.											.	MSRB2	21	.	0			c.C176G						.						83.0	81.0	82.0					10																	23393130		1908	4129	6037	SO:0001583	missense	22921	exon2			AACTAACCCCGGA	AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"""methionine sulfoxide reductase B"""	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.176C>G	chr10.hg19:g.23393130C>G	ENSP00000365693:p.Thr59Ser	101.0	0.0		117.0	25.0	NM_012228	Q17R44|Q4G1C7|Q9Y5W6	Missense_Mutation	SNP	ENST00000376510.3	hg19	CCDS41495.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.097652	0.56075	.	.	ENSG00000148450	ENST00000376510	T	0.78003	-1.14	4.79	3.88	0.44766	Mss4-like (1);Methionine sulphoxide reductase B (3);	0.053873	0.64402	D	0.000001	T	0.69450	0.3112	L	0.33710	1.025	0.36486	D	0.868135	B	0.25235	0.121	B	0.34590	0.186	T	0.71567	-0.4554	10	0.51188	T	0.08	-1.569	9.252	0.37560	0.0:0.897:0.0:0.103	.	59	Q9Y3D2	MSRB2_HUMAN	S	59	ENSP00000365693:T59S	ENSP00000365693:T59S	T	+	2	0	MSRB2	23433136	0.993000	0.37304	0.997000	0.53966	0.869000	0.49853	2.713000	0.47194	1.325000	0.45301	0.557000	0.71058	ACC	.	C|0.999;T|0.001		0.443	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047205.1	NM_012228	
MICU1	10367	hgsc.bcm.edu	37	10	74293540	74293540	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:74293540A>G	ENST00000361114.5	-	5	597	c.501T>C	c.(499-501)ggT>ggC	p.G167G	MICU1_ENST00000398761.4_Silent_p.G167G|MICU1_ENST00000401998.3_Silent_p.G167G	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	167					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										ATTGATCCAGACCCAAGTCTG	0.303																																					p.G167G		Atlas-SNP	.											.	.	.	.	0			c.T501C						.						62.0	61.0	61.0					10																	74293540		1800	4063	5863	SO:0001819	synonymous_variant	10367	exon5			ATCCAGACCCAAG	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"""EF-hand domain containing"""	1530	protein-coding gene	gene with protein product		605084	"""calcium binding atopy-related autoantigen 1"""	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.501T>C	chr10.hg19:g.74293540A>G		45.0	0.0		54.0	4.0	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Silent	SNP	ENST00000361114.5	hg19	CCDS55715.1																																																																																			.	.		0.303	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077	
KAT6B	23522	hgsc.bcm.edu	37	10	76781899	76781899	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:76781899A>G	ENST00000287239.4	+	16	3771	c.3282A>G	c.(3280-3282)gaA>gaG	p.E1094E	KAT6B_ENST00000490365.1_3'UTR|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372714.1_Silent_p.E802E|KAT6B_ENST00000372711.1_Silent_p.E911E|KAT6B_ENST00000372724.1_Silent_p.E802E|KAT6B_ENST00000372725.1_Silent_p.E802E|RP11-77G23.2_ENST00000413431.1_RNA	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1094	Poly-Glu.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										aagaggaggaagaagaggaag	0.463											OREG0020273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E1094E		Atlas-SNP	.											.	.	.	.	0			c.A3282G						.						42.0	38.0	39.0					10																	76781899		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon16			GGAGGAAGAAGAG	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3282A>G	chr10.hg19:g.76781899A>G		90.0	0.0	1170	108.0	14.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.463	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
PLAC9	219348	hgsc.bcm.edu	37	10	81901931	81901931	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:81901931A>G	ENST00000372263.3	+	2	200	c.158A>G	c.(157-159)gAg>gGg	p.E53G	PLAC9_ENST00000372267.2_Missense_Mutation_p.E53G|PLAC9_ENST00000372270.2_Missense_Mutation_p.E11G	NM_001012973.1	NP_001012991.1	Q5JTB6	PLAC9_HUMAN	placenta-specific 9	53						extracellular region (GO:0005576)				kidney(1)|ovary(1)	2	Prostate(51;0.0095)|all_epithelial(25;0.175)		Colorectal(32;0.109)			GATGTCATGGAGGAGGTAACA	0.552																																					p.E53G		Atlas-SNP	.											.	PLAC9	9	.	0			c.A158G						.						135.0	93.0	107.0					10																	81901931		2203	4300	6503	SO:0001583	missense	219348	exon2			TCATGGAGGAGGT		CCDS31232.1	10q23.2	2008-02-04			ENSG00000189129	ENSG00000189129			19255	protein-coding gene	gene with protein product		612857					Standard	NM_001012973		Approved		uc001kbp.1	Q5JTB6	OTTHUMG00000018596	ENST00000372263.3:c.158A>G	chr10.hg19:g.81901931A>G	ENSP00000361337:p.Glu53Gly	40.0	0.0		52.0	4.0	NM_001012973		Missense_Mutation	SNP	ENST00000372263.3	hg19	CCDS31232.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.336328	0.24253	.	.	ENSG00000189129	ENST00000372270;ENST00000372267;ENST00000372263	.	.	.	3.74	2.62	0.31277	.	0.179151	0.26935	N	0.021756	T	0.40423	0.1116	.	.	.	0.35800	D	0.823069	B	0.23058	0.079	B	0.21546	0.035	T	0.47100	-0.9143	8	0.87932	D	0	.	5.6218	0.17461	0.877:0.0:0.123:0.0	.	53	Q5JTB6	PLAC9_HUMAN	G	11;53;53	.	ENSP00000361337:E53G	E	+	2	0	PLAC9	81891911	1.000000	0.71417	0.759000	0.31340	0.440000	0.31957	1.994000	0.40757	0.817000	0.34445	0.439000	0.28862	GAG	.	.		0.552	PLAC9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049019.1	NM_001012973	
LDB3	11155	hgsc.bcm.edu	37	10	88466389	88466389	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:88466389C>T	ENST00000361373.4	+	7	1019	c.998C>T	c.(997-999)tCg>tTg	p.S333L	LDB3_ENST00000429277.2_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000263066.6_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						AGTGCGGCTTCGCCACCCCTG	0.687																																					p.S333L		Atlas-SNP	.											LDB3,right_upper_lobe,carcinoma,-1,1	LDB3	164	.	0			c.C998T						.						51.0	50.0	50.0					10																	88466389		2203	4299	6502	SO:0001583	missense	11155	exon7			CGGCTTCGCCACC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"""cypher"", ""oracle"", ""Z-band alternatively spliced PDZ motif protein"""	605906	"""cardiomyopathy, dilated 1C (autosomal dominant)"""	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.998C>T	chr10.hg19:g.88466389C>T	ENSP00000355296:p.Ser333Leu	82.0	0.0		27.0	3.0	NM_007078		Missense_Mutation	SNP	ENST00000361373.4	hg19	CCDS7377.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256973	0.39896	.	.	ENSG00000122367	ENST00000361373	T	0.53423	0.62	5.52	3.03	0.35002	.	0.331826	0.17113	N	0.186533	T	0.30759	0.0775	N	0.25647	0.755	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.08764	-1.0706	10	0.28530	T	0.3	.	7.6515	0.28350	0.0:0.7206:0.17:0.1094	.	333	O75112	LDB3_HUMAN	L	333	ENSP00000355296:S333L	ENSP00000355296:S333L	S	+	2	0	LDB3	88456369	0.997000	0.39634	1.000000	0.80357	0.844000	0.47949	1.197000	0.32211	1.368000	0.46115	0.655000	0.94253	TCG	.	.		0.687	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2		
C10orf12	26148	hgsc.bcm.edu	37	10	98742889	98742889	+	Missense_Mutation	SNP	G	G	A	rs141178994		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:98742889G>A	ENST00000286067.2	+	1	1849	c.1742G>A	c.(1741-1743)cGc>cAc	p.R581H		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	581								p.R581H(1)		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)		GTCAATGAACGCCCCTCTGAG	0.522																																					p.R581H		Atlas-SNP	.											C10orf12,colon,carcinoma,0,1	C10orf12	94	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1742A						.	G	HIS/ARG	0,4406		0,0,2203	48.0	55.0	53.0		1742	-3.3	0.0	10	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	no	missense	C10orf12	NM_015652.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	581/1248	98742889	1,13005	2203	4300	6503	SO:0001583	missense	26148	exon1			ATGAACGCCCCTC	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.1742G>A	chr10.hg19:g.98742889G>A	ENSP00000286067:p.Arg581His	83.0	1.0		71.0	4.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182323	0.01633	0.0	1.16E-4	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.06528	3.29	4.94	-3.26	0.05064	.	1.241240	0.05944	N	0.637619	T	0.02888	0.0086	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	10	0.35671	T	0.21	0.7721	10.8904	0.46992	0.4179:0.0:0.5821:0.0	.	581	Q8N655	CJ012_HUMAN	H	581;415	ENSP00000286067:R581H	ENSP00000286067:R581H	R	+	2	0	C10orf12	98732879	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.007000	0.13174	-0.439000	0.07222	-1.267000	0.01435	CGC	.	G|1.000;A|0.000		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
LOXL4	84171	hgsc.bcm.edu	37	10	100013493	100013493	+	Missense_Mutation	SNP	C	C	T	rs375427147		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:100013493C>T	ENST00000260702.3	-	11	1802	c.1652G>A	c.(1651-1653)cGc>cAc	p.R551H	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	551	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GCTGAGCGGGCGGTCCTCCAA	0.627																																					p.R551H		Atlas-SNP	.											.	LOXL4	60	.	0			c.G1652A						.	C	HIS/ARG	0,4406		0,0,2203	76.0	73.0	74.0		1652	4.9	1.0	10		74	1,8599	1.2+/-3.3	0,1,4299	no	missense	LOXL4	NM_032211.6	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	551/757	100013493	1,13005	2203	4300	6503	SO:0001583	missense	84171	exon11			AGCGGGCGGTCCT	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1652G>A	chr10.hg19:g.100013493C>T	ENSP00000260702:p.Arg551His	39.0	0.0		37.0	5.0	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	hg19	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	C	34	5.348214	0.95807	0.0	1.16E-4	ENSG00000138131	ENST00000260702	T	0.32753	1.44	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.64670	0.2619	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73401	-0.3994	10	0.66056	D	0.02	.	16.9772	0.86316	0.0:1.0:0.0:0.0	.	551	Q96JB6	LOXL4_HUMAN	H	551	ENSP00000260702:R551H	ENSP00000260702:R551H	R	-	2	0	LOXL4	100003483	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	7.651000	0.83577	2.536000	0.85505	0.491000	0.48974	CGC	.	.		0.627	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
HPS1	3257	hgsc.bcm.edu	37	10	100179909	100179909	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:100179909A>G	ENST00000325103.6	-	18	1983	c.1750T>C	c.(1750-1752)Tct>Cct	p.S584P	HPS1_ENST00000361490.4_Missense_Mutation_p.S584P|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	584					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGGATCAGAGACCAGACCTGG	0.582									Hermansky-Pudlak syndrome																												p.S584P		Atlas-SNP	.											.	HPS1	65	.	0			c.T1750C						.						134.0	116.0	122.0					10																	100179909		2203	4300	6503	SO:0001583	missense	3257	exon18	Familial Cancer Database	HPS, HPS1-8	TCAGAGACCAGAC	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1750T>C	chr10.hg19:g.100179909A>G	ENSP00000326649:p.Ser584Pro	69.0	0.0		75.0	4.0	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	hg19	CCDS7475.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.843616	0.71488	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891	T;T	0.47528	0.84;0.84	5.45	0.523	0.17060	.	0.576373	0.19226	N	0.119539	T	0.61274	0.2334	M	0.79475	2.455	0.80722	D	1	D;D;D	0.53312	0.959;0.959;0.959	P;P;P	0.54100	0.742;0.742;0.742	T	0.69752	-0.5060	10	0.62326	D	0.03	.	16.0411	0.80683	0.4704:0.5296:0.0:0.0	.	551;584;585	Q92902-2;Q8WXE5;D3DR62	.;.;.	P	584;584;551	ENSP00000326649:S584P;ENSP00000355310:S584P	ENSP00000326649:S584P	S	-	1	0	HPS1	100169899	0.995000	0.38212	1.000000	0.80357	0.929000	0.56500	0.362000	0.20284	0.082000	0.17018	0.459000	0.35465	TCT	.	.		0.582	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
GBF1	8729	hgsc.bcm.edu	37	10	104118303	104118303	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:104118303T>C	ENST00000369983.3	+	10	1088	c.828T>C	c.(826-828)tcT>tcC	p.S276S		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	276					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCATCTCCTCTGCAAGTTCAG	0.512																																					p.S276S		Atlas-SNP	.											.	GBF1	142	.	0			c.T828C						.						118.0	110.0	113.0					10																	104118303		2203	4300	6503	SO:0001819	synonymous_variant	8729	exon10			CTCCTCTGCAAGT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.828T>C	chr10.hg19:g.104118303T>C		74.0	0.0		74.0	4.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	hg19	CCDS7533.1																																																																																			.	.		0.512	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
GBF1	8729	hgsc.bcm.edu	37	10	104125298	104125298	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:104125298A>G	ENST00000369983.3	+	18	2508	c.2248A>G	c.(2248-2250)Atg>Gtg	p.M750V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	750	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GGACAAGAAGATGATTGGAGA	0.498																																					p.M751V		Atlas-SNP	.											.	GBF1	142	.	0			c.A2251G						.						115.0	111.0	112.0					10																	104125298		2203	4300	6503	SO:0001583	missense	8729	exon18			AAGAAGATGATTG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2248A>G	chr10.hg19:g.104125298A>G	ENSP00000359000:p.Met750Val	131.0	0.0		117.0	6.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.892879	0.91889	.	.	ENSG00000107862	ENST00000369983	T	0.53206	0.63	5.79	5.79	0.91817	SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.59783	0.2219	L	0.45581	1.43	0.80722	D	1	D;D;P	0.67145	0.996;0.991;0.906	P;D;P	0.63033	0.904;0.91;0.626	T	0.56643	-0.7945	10	0.35671	T	0.21	-19.3013	16.1303	0.81428	1.0:0.0:0.0:0.0	.	750;750;750	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	V	750	ENSP00000359000:M750V	ENSP00000359000:M750V	M	+	1	0	GBF1	104115288	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.094000	0.94168	2.218000	0.71995	0.533000	0.62120	ATG	.	.		0.498	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
PDCD11	22984	hgsc.bcm.edu	37	10	105202983	105202983	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:105202983T>C	ENST00000369797.3	+	33	5111	c.5017T>C	c.(5017-5019)Tct>Cct	p.S1673P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1673					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CATGTACGGCTCTCAGGAGTC	0.552																																					p.S1673P		Atlas-SNP	.											.	PDCD11	160	.	0			c.T5017C						.						94.0	80.0	85.0					10																	105202983		2203	4300	6503	SO:0001583	missense	22984	exon33			TACGGCTCTCAGG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5017T>C	chr10.hg19:g.105202983T>C	ENSP00000358812:p.Ser1673Pro	63.0	0.0		92.0	4.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.819707	0.71028	.	.	ENSG00000148843	ENST00000369797	T	0.36520	1.25	5.51	4.33	0.51752	Tetratricopeptide-like helical (1);	0.101091	0.64402	D	0.000003	T	0.34745	0.0908	L	0.33245	0.995	0.39191	D	0.962966	D	0.56968	0.978	P	0.50192	0.634	T	0.28267	-1.0049	10	0.72032	D	0.01	-11.5805	10.0005	0.41927	0.3219:0.0:0.0:0.6781	.	1673	Q14690	RRP5_HUMAN	P	1673	ENSP00000358812:S1673P	ENSP00000358812:S1673P	S	+	1	0	PDCD11	105192973	1.000000	0.71417	0.993000	0.49108	0.837000	0.47467	3.161000	0.50747	2.088000	0.63022	0.454000	0.30748	TCT	.	.		0.552	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
CALHM2	51063	hgsc.bcm.edu	37	10	105209279	105209279	+	Silent	SNP	T	T	C	rs201668640		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:105209279T>C	ENST00000260743.5	-	3	943	c.420A>G	c.(418-420)tcA>tcG	p.S140S	CALHM2_ENST00000369788.3_Silent_p.S140S|CALHM2_ENST00000494180.1_5'Flank|CALHM2_ENST00000393235.1_Silent_p.S140S|RP11-225H22.7_ENST00000608063.1_RNA	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	140					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|skin(1)	11						TGGCCGTGAGTGAGGAAGGGT	0.607																																					p.S140S		Atlas-SNP	.											.	CALHM2	30	.	0			c.A420G						.						78.0	68.0	71.0					10																	105209279		2203	4300	6503	SO:0001819	synonymous_variant	51063	exon3			CGTGAGTGAGGAA	BC000039	CCDS7549.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000138172	ENSG00000138172			23493	protein-coding gene	gene with protein product		612235	"""family with sequence similarity 26, member B"""	FAM26B		18585350	Standard	NM_015916		Approved		uc001kxa.3	Q9HA72	OTTHUMG00000018990	ENST00000260743.5:c.420A>G	chr10.hg19:g.105209279T>C		60.0	0.0		55.0	4.0	NM_015916	D3DR94|O95893|Q6ZUV9	Silent	SNP	ENST00000260743.5	hg19	CCDS7549.1																																																																																			.	T|0.999;C|0.001		0.607	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916	
PDCD4	27250	hgsc.bcm.edu	37	10	112641040	112641040	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:112641040T>C	ENST00000280154.7	+	3	367	c.93T>C	c.(91-93)gcT>gcC	p.A31A	PDCD4_ENST00000393104.2_Silent_p.A20A	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	31					apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		AAGAAAATGCTGGGACTGAGG	0.338																																					p.A31A	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.T93C						.						82.0	92.0	88.0					10																	112641040		2203	4300	6503	SO:0001819	synonymous_variant	27250	exon3			AAATGCTGGGACT	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"""nuclear antigen H731"""	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.93T>C	chr10.hg19:g.112641040T>C		92.0	0.0		91.0	4.0	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	hg19	CCDS7567.1																																																																																			.	.		0.338	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456	
NHLRC2	374354	hgsc.bcm.edu	37	10	115644138	115644138	+	Splice_Site	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:115644138A>G	ENST00000369301.3	+	5	1250	c.1038A>G	c.(1036-1038)tcA>tcG	p.S346S		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	346										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		TTGGAACATCAGGTATGTGAA	0.338																																					p.S346S		Atlas-SNP	.											.	NHLRC2	56	.	0			c.A1038G						.						108.0	100.0	103.0					10																	115644138		2203	4300	6503	SO:0001630	splice_region_variant	374354	exon5			AACATCAGGTATG	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1039+1A>G	chr10.hg19:g.115644138A>G		90.0	0.0		87.0	4.0	NM_198514	Q8N1H1|Q8N5A6	Silent	SNP	ENST00000369301.3	hg19	CCDS7585.1																																																																																			.	.		0.338	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	Silent
DOCK1	1793	hgsc.bcm.edu	37	10	129172467	129172467	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:129172467G>A	ENST00000280333.6	+	35	3710	c.3601G>A	c.(3601-3603)Gtc>Atc	p.V1201I		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1201					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.V1201I(2)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GAGCTGCACCGTCAATGTGCT	0.443																																					p.V1201I		Atlas-SNP	.											DOCK1,colon,carcinoma,-1,2	DOCK1	188	.	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	c.G3601A						.						56.0	56.0	56.0					10																	129172467		1964	4167	6131	SO:0001583	missense	1793	exon35			TGCACCGTCAATG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.3601G>A	chr10.hg19:g.129172467G>A	ENSP00000280333:p.Val1201Ile	70.0	0.0		66.0	3.0	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	G	28.1	4.894732	0.91962	.	.	ENSG00000150760	ENST00000280333	T	0.38240	1.15	5.52	5.52	0.82312	.	0.071608	0.56097	D	0.000037	T	0.60932	0.2307	M	0.87097	2.86	0.80722	D	1	D;D;D	0.69078	0.994;0.995;0.997	P;P;P	0.54544	0.755;0.559;0.693	T	0.67654	-0.5615	10	0.72032	D	0.01	.	19.2287	0.93829	0.0:0.0:1.0:0.0	.	1201;1267;1201	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	I	1201	ENSP00000280333:V1201I	ENSP00000280333:V1201I	V	+	1	0	DOCK1	129062457	1.000000	0.71417	0.961000	0.40146	0.795000	0.44927	9.575000	0.98187	2.878000	0.98634	0.650000	0.86243	GTC	.	.		0.443	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
CALY	50632	hgsc.bcm.edu	37	10	135140482	135140482	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr10:135140482C>A	ENST00000252939.4	-	4	353	c.260G>T	c.(259-261)cGg>cTg	p.R87L	CALY_ENST00000368556.2_Missense_Mutation_p.R87L|CALY_ENST00000368558.1_Missense_Mutation_p.R87L|RP11-122K13.14_ENST00000605518.1_lincRNA|CALY_ENST00000467611.1_5'Flank|ZNF511_ENST00000368554.4_Intron	NM_015722.3	NP_056537.1	Q9NYX4	CALY_HUMAN	calcyon neuron-specific vesicular protein	87					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)|endocytosis (GO:0006897)|positive regulation of endocytosis (GO:0045807)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)	clathrin light chain binding (GO:0032051)			kidney(1)|lung(2)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;6.94e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)	Apomorphine(DB00714)|Clozapine(DB00363)|Trifluoperazine(DB00831)	GGCGATCATCCGTGCGGTGGG	0.672																																					p.R87L		Atlas-SNP	.											CALY,colon,carcinoma,0,1	CALY	19	.	0			c.G260T						.						49.0	39.0	42.0					10																	135140482		2200	4292	6492	SO:0001583	missense	50632	exon4			ATCATCCGTGCGG	AF225903	CCDS7678.1	10q26.3	2008-07-02	2008-01-16	2008-01-16	ENSG00000130643	ENSG00000130643			17938	protein-coding gene	gene with protein product		604647	"""dopamine receptor D1 interacting protein"""	DRD1IP		10698743, 17623072	Standard	NM_015722		Approved	CALCYON, NSG3	uc001lmo.2	Q9NYX4	OTTHUMG00000019310	ENST00000252939.4:c.260G>T	chr10.hg19:g.135140482C>A	ENSP00000252939:p.Arg87Leu	82.0	1.0		39.0	2.0	NM_015722	Q5VWX3|Q5VWY5|Q5VWY6	Missense_Mutation	SNP	ENST00000252939.4	hg19	CCDS7678.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257847	0.39896	.	.	ENSG00000130643	ENST00000252939;ENST00000368558;ENST00000368556	.	.	.	4.27	4.27	0.50696	.	0.072991	0.53938	D	0.000050	T	0.61400	0.2344	L	0.48877	1.53	0.34212	D	0.674436	D	0.89917	1.0	D	0.85130	0.997	T	0.63102	-0.6712	9	0.15952	T	0.53	-7.0591	12.414	0.55483	0.0:1.0:0.0:0.0	.	87	Q9NYX4	CALY_HUMAN	L	87	.	ENSP00000252939:R87L	R	-	2	0	CALY	134990472	0.902000	0.30710	0.918000	0.36340	0.421000	0.31385	3.111000	0.50360	2.371000	0.80710	0.643000	0.83706	CGG	.	.		0.672	CALY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051122.1	NM_015722	
RRM1	6240	hgsc.bcm.edu	37	11	4153626	4153626	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:4153626G>A	ENST00000300738.5	+	16	2084	c.1880G>A	c.(1879-1881)cGc>cAc	p.R627H	RRM1_ENST00000537197.1_Missense_Mutation_p.R289H|RRM1_ENST00000423050.2_Missense_Mutation_p.R530H|RRM1_ENST00000534285.1_Missense_Mutation_p.R405H	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	627					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ATCTATACTCGCAGAGTCTTG	0.453																																					p.R627H	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.G1880A						.						140.0	132.0	134.0					11																	4153626		2201	4298	6499	SO:0001583	missense	6240	exon16			ATACTCGCAGAGT	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"""ribonucleotide reductase M1 polypeptide"""			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1880G>A	chr11.hg19:g.4153626G>A	ENSP00000300738:p.Arg627His	75.0	0.0		93.0	4.0	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	G	30	5.055544	0.93793	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.07	5.07	0.68467	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75583	0.3869	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.63033	0.91	T	0.81346	-0.0974	10	0.87932	D	0	-6.0041	17.39	0.87427	0.0:0.0:1.0:0.0	.	627	P23921	RIR1_HUMAN	H	627;530;540;405;405;289	ENSP00000300738:R627H;ENSP00000390539:R530H;ENSP00000431464:R405H;ENSP00000442148:R289H	ENSP00000300738:R627H	R	+	2	0	RRM1	4110202	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.379000	0.97198	2.515000	0.84797	0.650000	0.86243	CGC	.	.		0.453	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
OR51G2	81282	hgsc.bcm.edu	37	11	4936238	4936238	+	Missense_Mutation	SNP	A	A	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:4936238A>C	ENST00000322013.3	-	1	684	c.656T>G	c.(655-657)aTc>aGc	p.I219S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGAGAAGAGGATGAGCAGTGA	0.517																																					p.I219S		Atlas-SNP	.											.	OR51G2	70	.	0			c.T656G						.						144.0	113.0	123.0					11																	4936238		2201	4298	6499	SO:0001583	missense	81282	exon1			AAGAGGATGAGCA	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"""GPCR / Class A : Olfactory receptors"""	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.656T>G	chr11.hg19:g.4936238A>C	ENSP00000322593:p.Ile219Ser	101.0	0.0		116.0	32.0	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	hg19	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.160945	0.78226	.	.	ENSG00000176893	ENST00000322013	T	0.00333	8.07	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000092	T	0.01661	0.0053	H	0.98199	4.17	0.53688	D	0.999978	D	0.89917	1.0	D	0.91635	0.999	T	0.08066	-1.0740	10	0.87932	D	0	.	14.7226	0.69317	1.0:0.0:0.0:0.0	.	219	Q8NGK0	O51G2_HUMAN	S	219	ENSP00000322593:I219S	ENSP00000322593:I219S	I	-	2	0	OR51G2	4892814	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	5.806000	0.69150	2.343000	0.79666	0.533000	0.62120	ATC	.	.		0.517	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
OR51I1	390063	hgsc.bcm.edu	37	11	5462447	5462447	+	Missense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:5462447G>T	ENST00000380211.1	-	1	297	c.298C>A	c.(298-300)Ctg>Atg	p.L100M	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	100					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L100L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCTGGACCAGGCAAGCATTA	0.453																																					p.L100M		Atlas-SNP	.											OR51I1,NS,carcinoma,0,1	OR51I1	66	.	1	Substitution - coding silent(1)	lung(1)	c.C298A						.						140.0	123.0	129.0					11																	5462447		2201	4297	6498	SO:0001583	missense	390063	exon1			GGACCAGGCAAGC	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"""GPCR / Class A : Olfactory receptors"""	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.298C>A	chr11.hg19:g.5462447G>T	ENSP00000369559:p.Leu100Met	89.0	0.0		139.0	37.0	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	hg19	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.378082	0.24944	.	.	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.21543	2.0	5.78	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	D	0.000565	T	0.32466	0.0830	L	0.54323	1.7	0.09310	N	1	D	0.76494	0.999	D	0.83275	0.996	T	0.06734	-1.0810	10	0.49607	T	0.09	.	3.7444	0.08542	0.3241:0.0:0.5063:0.1696	.	100	Q9H343	O51I1_HUMAN	M	85;97;100	ENSP00000369559:L100M	ENSP00000348350:L85M	L	-	1	2	OR51I1	5419023	0.000000	0.05858	0.976000	0.42696	0.329000	0.28539	-2.635000	0.00868	0.266000	0.21894	-0.290000	0.09829	CTG	.	.		0.453	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
APBB1	322	hgsc.bcm.edu	37	11	6413367	6413367	+	IGR	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:6413367G>A	ENST00000609360.1	-	0	2642				SMPD1_ENST00000342245.4_Missense_Mutation_p.E358K|SMPD1_ENST00000299397.3_Missense_Mutation_p.E358K|SMPD1_ENST00000356761.2_Missense_Mutation_p.E358K|SMPD1_ENST00000527275.1_Missense_Mutation_p.E357K|APBB1_ENST00000526240.1_5'Flank	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GCTGCCTGCCGAAGCCCTGCG	0.577																																					p.E358K	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											SMPD1_ENST00000342245,NS,carcinoma,0,2	SMPD1	108	.	0			c.G1072A						.						52.0	50.0	51.0					11																	6413367		2201	4296	6497	SO:0001628	intergenic_variant	6609	exon2			CCTGCCGAAGCCC	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			chr11.hg19:g.6413367G>A		76.0	0.0		95.0	4.0	NM_000543	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.18	2.159477	0.38119	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.94650	-3.48;-1.97;-3.03;-3.03	5.01	3.01	0.34805	Metallophosphoesterase domain (1);	0.556195	0.18471	N	0.140212	D	0.87842	0.6279	L	0.46885	1.475	0.09310	N	1	P;B;P	0.41624	0.757;0.451;0.507	B;B;B	0.31495	0.131;0.08;0.131	T	0.80585	-0.1317	10	0.37606	T	0.19	-22.1764	5.2868	0.15706	0.084:0.1428:0.6264:0.1468	.	357;358;356	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	K	358;358;358;357	ENSP00000299397:E358K;ENSP00000349203:E358K;ENSP00000340409:E358K;ENSP00000435350:E357K	ENSP00000299397:E358K	E	+	1	0	SMPD1	6369943	0.697000	0.27767	0.996000	0.52242	0.992000	0.81027	3.175000	0.50855	2.336000	0.79503	0.561000	0.74099	GAA	.	.		0.577	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
ZNF143	7702	hgsc.bcm.edu	37	11	9537864	9537864	+	Silent	SNP	G	G	A	rs572827042		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:9537864G>A	ENST00000396602.2	+	14	1760	c.1641G>A	c.(1639-1641)acG>acA	p.T547T	ZNF143_ENST00000530463.1_Silent_p.T546T|ZNF143_ENST00000299606.2_Silent_p.T519T|ZNF143_ENST00000396597.3_Silent_p.T516T|ZNF143_ENST00000396604.1_Silent_p.T546T	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	547					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T547T(1)		endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		CAGCAGGAACGCACTCTGTTG	0.473																																					p.T547T		Atlas-SNP	.											ZNF143,NS,carcinoma,0,1	ZNF143	38	.	1	Substitution - coding silent(1)	lung(1)	c.G1641A						.						101.0	75.0	84.0					11																	9537864		2201	4294	6495	SO:0001819	synonymous_variant	7702	exon14			AGGAACGCACTCT	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"""Zinc fingers, C2H2-type"""	12928	protein-coding gene	gene with protein product		603433	"""zinc finger protein 143 (clone pHZ-1)"""				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1641G>A	chr11.hg19:g.9537864G>A		42.0	0.0		34.0	2.0	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	hg19	CCDS7799.2	.	.	.	.	.	.	.	.	.	.	A	9.521	1.108420	0.20714	.	.	ENSG00000166478	ENST00000447186	.	.	.	5.82	3.48	0.39840	.	.	.	.	.	T	0.59376	0.2189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53143	-0.8480	4	.	.	.	.	9.5411	0.39252	0.7316:0.0:0.2684:0.0	.	.	.	.	T	73	.	.	A	+	1	0	ZNF143	9494440	0.991000	0.36638	1.000000	0.80357	0.981000	0.71138	0.407000	0.21049	0.467000	0.27218	-0.254000	0.11334	GCA	.	.		0.473	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442	
AMPD3	272	hgsc.bcm.edu	37	11	10503698	10503698	+	Missense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:10503698G>T	ENST00000396554.3	+	4	883	c.542G>T	c.(541-543)cGc>cTc	p.R181L	AMPD3_ENST00000444303.2_Missense_Mutation_p.R13L	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	172					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GCCTACCACCGCTTCCCGCGG	0.612																																					p.R181L		Atlas-SNP	.											.	AMPD3	68	.	0			c.G542T						.						85.0	91.0	89.0					11																	10503698		2201	4294	6495	SO:0001583	missense	272	exon4			ACCACCGCTTCCC	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.542G>T	chr11.hg19:g.10503698G>T	ENSP00000379802:p.Arg181Leu	51.0	0.0		69.0	10.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Missense_Mutation	SNP	ENST00000396554.3	hg19	CCDS7802.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004679	0.93287	.	.	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000524866;ENST00000396553;ENST00000528723;ENST00000529507	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.88	4.97	0.65823	.	0.097493	0.64402	D	0.000001	T	0.60157	0.2247	M	0.84683	2.71	0.54753	D	0.999986	D;B;D	0.54397	0.966;0.447;0.966	P;B;P	0.52514	0.701;0.242;0.701	T	0.67530	-0.5647	10	0.52906	T	0.07	-14.7447	15.134	0.72549	0.0676:0.0:0.9324:0.0	.	179;172;181	B7Z763;Q01432;A0AUX0	.;AMPD3_HUMAN;.	L	13;181;172;172;179;172	ENSP00000396000:R13L;ENSP00000379802:R181L;ENSP00000433284:R172L;ENSP00000379801:R172L;ENSP00000436987:R179L;ENSP00000431648:R172L	ENSP00000379801:R172L	R	+	2	0	AMPD3	10460274	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.666000	0.74446	1.489000	0.48450	0.655000	0.94253	CGC	.	.		0.612	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
CCDC34	91057	hgsc.bcm.edu	37	11	27384473	27384473	+	Missense_Mutation	SNP	A	A	C	rs77142757		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:27384473A>C	ENST00000328697.6	-	1	942	c.269T>G	c.(268-270)gTg>gGg	p.V90G	CCDC34_ENST00000317945.6_Missense_Mutation_p.V90G	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	90	Asp-rich.									endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						CTCATCATCCACGTCTTCCTC	0.572																																					p.V90G		Atlas-SNP	.											.	CCDC34	48	.	0			c.T269G						.						198.0	172.0	181.0					11																	27384473		2202	4299	6501	SO:0001583	missense	91057	exon1			TCATCCACGTCTT	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.269T>G	chr11.hg19:g.27384473A>C	ENSP00000330240:p.Val90Gly	116.0	0.0		98.0	13.0	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	hg19	CCDS31448.1	.	.	.	.	.	.	.	.	.	.	-	0.162	-1.080247	0.01888	.	.	ENSG00000109881	ENST00000328697;ENST00000317945	T;T	0.25579	1.79;1.79	.	.	.	.	0.390690	0.08080	U	1.000000	T	0.11196	0.0273	N	0.08118	0	0.24817	N	0.99261	.	.	.	.	.	.	T	0.35822	-0.9773	6	0.22109	T	0.4	.	.	.	.	.	90;90	Q96HJ3-2;Q96HJ3	.;CCD34_HUMAN	G	90	ENSP00000330240:V90G;ENSP00000321563:V90G	ENSP00000321563:V90G	V	-	2	0	CCDC34	27341049	0.021000	0.18746	0.328000	0.25416	0.257000	0.26127	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GTG	.	A|1.000;C|0.000		0.572	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
C11orf74	119710	hgsc.bcm.edu	37	11	36631742	36631742	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:36631742A>G	ENST00000334307.5	+	2	204	c.89A>G	c.(88-90)cAa>cGa	p.Q30R	C11orf74_ENST00000446510.2_Missense_Mutation_p.Q30R|C11orf74_ENST00000534635.1_Missense_Mutation_p.Q30R|C11orf74_ENST00000347206.4_Missense_Mutation_p.Q30R	NM_138787.2	NP_620142.2	Q86VG3	CK074_HUMAN	chromosome 11 open reading frame 74	30										breast(1)|kidney(1)|large_intestine(1)|lung(5)	8	all_lung(20;0.226)	all_hematologic(20;0.0118)				TGTCATGAGCAAACATATGAT	0.313																																					p.G30G		Atlas-SNP	.											.	C11orf74	22	.	0			c.G89G						.						83.0	83.0	83.0					11																	36631742		2202	4298	6500	SO:0001583	missense	119710	exon2			ATGAGCAAACATA	AK095997, BC009561	CCDS7904.1, CCDS60762.1	11p12	2012-08-10			ENSG00000166352	ENSG00000166352			25142	protein-coding gene	gene with protein product						12477932	Standard	NM_001276722		Approved	FLJ38678, HEPIS	uc031pzr.1	Q86VG3	OTTHUMG00000166397	ENST00000334307.5:c.89A>G	chr11.hg19:g.36631742A>G	ENSP00000334848:p.Gln30Arg	57.0	0.0		81.0	4.0	NM_138787	D3DR18|Q96DD6	Silent	SNP	ENST00000334307.5	hg19	CCDS7904.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.268274	0.80469	.	.	ENSG00000166352	ENST00000334307;ENST00000531554;ENST00000347206;ENST00000534635;ENST00000446510;ENST00000530697;ENST00000527108;ENST00000532470	.	.	.	6.17	6.17	0.99709	.	0.208574	0.34932	N	0.003563	T	0.79540	0.4463	M	0.78801	2.425	0.45580	D	0.998528	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.81922	-0.0711	9	0.87932	D	0	-21.2486	14.5632	0.68156	1.0:0.0:0.0:0.0	.	30;30	Q86VG3;Q86VG3-2	CK074_HUMAN;.	R	30	.	ENSP00000334848:Q30R	Q	+	2	0	C11orf74	36588318	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	2.766000	0.47629	2.371000	0.80710	0.533000	0.62120	CAA	.	.		0.313	C11orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389567.1	NM_138787	
OR4C46	119749	hgsc.bcm.edu	37	11	51515417	51515417	+	Missense_Mutation	SNP	A	A	C	rs372979385|rs148928414|rs545486160	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:51515417A>C	ENST00000328188.1	+	1	136	c.136A>C	c.(136-138)Acc>Ccc	p.T46P		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	46						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						CATTGTGGTCACCATCACTGC	0.463																																					p.T46P		Atlas-SNP	.											.	OR4C46	96	.	0			c.A136C						.						233.0	233.0	233.0					11																	51515417		2198	4296	6494	SO:0001583	missense	119749	exon1			GTGGTCACCATCA		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.136A>C	chr11.hg19:g.51515417A>C	ENSP00000329056:p.Thr46Pro	78.0	0.0		117.0	26.0	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	hg19	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	14.40	2.523554	0.44866	.	.	ENSG00000185926	ENST00000328188	T	0.03094	4.05	2.63	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	D	0.000862	T	0.19644	0.0472	H	0.95437	3.67	0.09310	N	0.999999	D	0.58620	0.983	D	0.65233	0.933	T	0.07654	-1.0761	10	0.87932	D	0	.	5.0922	0.14713	0.7359:0.0:0.0:0.264	.	46	A6NHA9	O4C46_HUMAN	P	46	ENSP00000329056:T46P	ENSP00000329056:T46P	T	+	1	0	OR4C46	51371993	0.000000	0.05858	0.022000	0.16811	0.119000	0.20118	-0.272000	0.08560	1.239000	0.43787	0.113000	0.15668	ACC	.	.		0.463	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798847	55798847	+	Missense_Mutation	SNP	G	G	A	rs201114315		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:55798847G>A	ENST00000313555.1	+	1	953	c.953G>A	c.(952-954)cGt>cAt	p.R318H		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	318						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					TATTTAAATCGTTTAAGAATA	0.259																																					p.R318H		Atlas-SNP	.											OR5AS1,NS,carcinoma,0,1	OR5AS1	121	.	0			c.G953A						.	G	HIS/ARG	0,4370		0,0,2185	43.0	53.0	50.0		953	-3.4	0.0	11		50	2,8570		0,2,4284	yes	missense	OR5AS1	NM_001001921.1	29	0,2,6469	AA,AG,GG		0.0233,0.0,0.0155	benign	318/325	55798847	2,12940	2185	4286	6471	SO:0001583	missense	219447	exon1			TAAATCGTTTAAG	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.953G>A	chr11.hg19:g.55798847G>A	ENSP00000324111:p.Arg318His	26.0	0.0		35.0	2.0	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	hg19	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	G	8.970	0.972697	0.18736	0.0	2.33E-4	ENSG00000181785	ENST00000313555	T	0.00364	7.81	4.07	-3.43	0.04810	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09596	-1.0667	9	0.32370	T	0.25	.	5.4905	0.16773	0.3208:0.2938:0.3854:0.0	.	318	Q8N127	O5AS1_HUMAN	H	318	ENSP00000324111:R318H	ENSP00000324111:R318H	R	+	2	0	OR5AS1	55555423	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.250000	0.08830	-0.563000	0.06078	-0.333000	0.08304	CGT	.	.		0.259	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
MS4A6A	64231	hgsc.bcm.edu	37	11	59947379	59947379	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:59947379A>G	ENST00000530839.1	-	4	699	c.207T>C	c.(205-207)gcT>gcC	p.A69A	MS4A6A_ENST00000532169.1_Silent_p.A69A|MS4A6A_ENST00000529054.1_Silent_p.A97A|MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000420732.2_Silent_p.A69A|MS4A6A_ENST00000412309.2_Silent_p.A97A|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000528851.1_Silent_p.A69A|MS4A6A_ENST00000426738.2_Intron|MS4A6A_ENST00000323961.3_Silent_p.A69A	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	69						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAGAGAAGGAAGCAGATGCCA	0.438																																					p.A97A		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T291C						.						100.0	92.0	95.0					11																	59947379		2201	4295	6496	SO:0001819	synonymous_variant	64231	exon4			GAAGGAAGCAGAT	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.207T>C	chr11.hg19:g.59947379A>G		95.0	0.0		121.0	5.0	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	hg19	CCDS7981.1																																																																																			.	.		0.438	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
TMEM138	51524	hgsc.bcm.edu	37	11	61131933	61131933	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:61131933T>C	ENST00000278826.6	+	2	630	c.71T>C	c.(70-72)gTc>gCc	p.V24A	TMEM138_ENST00000540194.1_3'UTR|CYB561A3_ENST00000544118.1_5'Flank|CYB561A3_ENST00000447532.2_5'Flank|CYB561A3_ENST00000426130.2_5'Flank|TMEM138_ENST00000381787.2_5'Flank|CYB561A3_ENST00000294072.4_5'Flank|CYB561A3_ENST00000540317.1_5'Flank|CYB561A3_ENST00000546151.1_5'Flank|TMEM138_ENST00000542946.1_Missense_Mutation_p.V24A	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	24					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						GACCTCTTTGTCAATTCCTTC	0.517																																					p.V24A		Atlas-SNP	.											.	TMEM138	16	.	0			c.T71C						.						185.0	156.0	166.0					11																	61131933		2203	4299	6502	SO:0001583	missense	51524	exon2			TCTTTGTCAATTC	AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.71T>C	chr11.hg19:g.61131933T>C	ENSP00000278826:p.Val24Ala	68.0	0.0		99.0	4.0	NM_016464	A6NGA7|B4E044|Q5JPE1	Missense_Mutation	SNP	ENST00000278826.6	hg19	CCDS8005.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395067	0.62066	.	.	ENSG00000149483	ENST00000278826;ENST00000542946	D;T	0.89681	-2.55;-1.25	5.32	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.86456	0.5937	M	0.61703	1.905	0.80722	D	1	P;B;B	0.41450	0.75;0.054;0.031	B;B;B	0.39152	0.292;0.043;0.043	D	0.85489	0.1184	10	0.87932	D	0	-18.1327	10.5792	0.45246	0.0:0.0759:0.0:0.9241	.	24;24;24	B4E044;Q9NPI0-2;Q9NPI0	.;.;TM138_HUMAN	A	24	ENSP00000278826:V24A;ENSP00000445792:V24A	ENSP00000278826:V24A	V	+	2	0	TMEM138	60888509	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.986000	0.70563	0.872000	0.35775	0.460000	0.39030	GTC	.	.		0.517	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65357652	65357652	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:65357652A>G	ENST00000309295.4	+	15	4419	c.4154A>G	c.(4153-4155)gAg>gGg	p.E1385G	EHBP1L1_ENST00000533364.1_5'Flank	NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	1385						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GCTGAGGTGGAGATGCAGCTG	0.602																																					p.E1385G		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A4154G						.						64.0	76.0	72.0					11																	65357652		2149	4257	6406	SO:0001583	missense	254102	exon15			AGGTGGAGATGCA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.4154A>G	chr11.hg19:g.65357652A>G	ENSP00000312671:p.Glu1385Gly	53.0	0.0		90.0	5.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.203325	0.58234	.	.	ENSG00000173442	ENST00000309295	T	0.58652	0.32	4.36	4.36	0.52297	Domain of unknown function DUF3585 (1);	0.000000	0.64402	D	0.000006	T	0.78394	0.4276	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81604	-0.0857	10	0.59425	D	0.04	.	9.903	0.41359	1.0:0.0:0.0:0.0	.	1385	Q8N3D4	EH1L1_HUMAN	G	1385	ENSP00000312671:E1385G	ENSP00000312671:E1385G	E	+	2	0	EHBP1L1	65114228	1.000000	0.71417	0.997000	0.53966	0.204000	0.24138	5.838000	0.69388	1.849000	0.53698	0.460000	0.39030	GAG	.	.		0.602	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
OVOL1	5017	hgsc.bcm.edu	37	11	65561586	65561586	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:65561586A>G	ENST00000335987.3	+	2	537	c.185A>G	c.(184-186)aAc>aGc	p.N62S	OVOL1_ENST00000532448.1_5'UTR|RP11-770G2.5_ENST00000531155.1_RNA	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1	62					cytoskeleton organization (GO:0007010)|epidermal cell differentiation (GO:0009913)|germline cell cycle switching, mitotic to meiotic cell cycle (GO:0051729)|kidney development (GO:0001822)|mesoderm development (GO:0007498)|negative regulation of meiotic cell cycle phase transition (GO:1901994)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6				READ - Rectum adenocarcinoma(159;0.17)		CTGGCTTTGAACATGAGCCTT	0.647																																					p.N62S		Atlas-SNP	.											.	OVOL1	15	.	0			c.A185G						.						82.0	85.0	84.0					11																	65561586		2201	4297	6498	SO:0001583	missense	5017	exon2			CTTTGAACATGAG	BC059408	CCDS8112.1	11q13	2013-10-17	2013-10-17		ENSG00000172818	ENSG00000172818		"""Zinc fingers, C2H2-type"""	8525	protein-coding gene	gene with protein product		602313	"""ovo (Drosophila) homolog-like 1"", ""ovo-like 1(Drosophila)"""			9383297	Standard	NM_004561		Approved	HOVO1	uc001ofp.3	O14753	OTTHUMG00000166600	ENST00000335987.3:c.185A>G	chr11.hg19:g.65561586A>G	ENSP00000337862:p.Asn62Ser	81.0	0.0		92.0	4.0	NM_004561	Q6PCB1	Missense_Mutation	SNP	ENST00000335987.3	hg19	CCDS8112.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.289065	0.23478	.	.	ENSG00000172818	ENST00000335987	T	0.07567	3.18	4.65	4.65	0.58169	.	0.693200	0.13231	N	0.403679	T	0.05318	0.0141	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35126	-0.9801	10	0.52906	T	0.07	-23.0656	10.7778	0.46361	1.0:0.0:0.0:0.0	.	62	O14753	OVOL1_HUMAN	S	62	ENSP00000337862:N62S	ENSP00000337862:N62S	N	+	2	0	OVOL1	65318162	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.701000	0.37825	1.863000	0.54032	0.533000	0.62120	AAC	.	.		0.647	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	NM_004561	
KDM2A	22992	hgsc.bcm.edu	37	11	66982895	66982895	+	Missense_Mutation	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:66982895A>T	ENST00000529006.2	+	7	1017	c.571A>T	c.(571-573)Atg>Ttg	p.M191L	KDM2A_ENST00000398645.2_Missense_Mutation_p.M191L|KDM2A_ENST00000526258.1_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	191	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						CATCTTGGAGATGCAGTACCC	0.478																																					p.M191L		Atlas-SNP	.											.	KDM2A	80	.	0			c.A571T						.						101.0	98.0	99.0					11																	66982895		2001	4168	6169	SO:0001583	missense	22992	exon7			TTGGAGATGCAGT	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.571A>T	chr11.hg19:g.66982895A>T	ENSP00000432786:p.Met191Leu	66.0	0.0		81.0	18.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390848	0.82902	.	.	ENSG00000173120	ENST00000398645;ENST00000529006	T;T	0.69435	-0.4;-0.4	5.76	5.76	0.90799	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.60958	0.2309	L	0.55103	1.725	0.80722	D	1	B	0.30455	0.28	B	0.25987	0.065	T	0.58160	-0.7685	10	0.24483	T	0.36	-3.2157	15.2488	0.73526	1.0:0.0:0.0:0.0	.	191	Q9Y2K7	KDM2A_HUMAN	L	191	ENSP00000381640:M191L;ENSP00000432786:M191L	ENSP00000381640:M191L	M	+	1	0	KDM2A	66739471	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.942000	0.92970	2.201000	0.70794	0.533000	0.62120	ATG	.	.		0.478	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308	
MTL5	9633	hgsc.bcm.edu	37	11	68475846	68475846	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:68475846T>C	ENST00000255087.5	-	10	1640	c.1457A>G	c.(1456-1458)gAg>gGg	p.E486G		NM_004923.3	NP_004914.2	Q9Y4I5	MTL5_HUMAN	metallothionein-like 5, testis-specific (tesmin)	486					cell differentiation (GO:0030154)|cellular metal ion homeostasis (GO:0006875)|multicellular organismal development (GO:0007275)|response to metal ion (GO:0010038)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	15	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)			TCCAAATTCCTCCAGGATCAT	0.483																																					p.E486G		Atlas-SNP	.											.	MTL5	37	.	0			c.A1457G						.						124.0	120.0	122.0					11																	68475846		2200	4294	6494	SO:0001583	missense	9633	exon10			AATTCCTCCAGGA	U86074	CCDS8184.1, CCDS44661.1	11q13.2-q13.3	2007-01-03			ENSG00000132749	ENSG00000132749			7446	protein-coding gene	gene with protein product	"""CXC domain containing 2"""	604374				1091092	Standard	XR_428932		Approved	CXCDC2	uc001ooc.3	Q9Y4I5	OTTHUMG00000167891	ENST00000255087.5:c.1457A>G	chr11.hg19:g.68475846T>C	ENSP00000255087:p.Glu486Gly	132.0	0.0		149.0	6.0	NM_004923	A8K8J3|Q4G182|Q6P2E2|Q8NCC8	Missense_Mutation	SNP	ENST00000255087.5	hg19	CCDS8184.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582750	0.86748	.	.	ENSG00000132749	ENST00000255087	T	0.37235	1.21	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.61426	0.2346	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.67417	-0.5676	10	0.87932	D	0	-24.7053	14.256	0.66053	0.0:0.0:0.0:1.0	.	486	Q9Y4I5	MTL5_HUMAN	G	486	ENSP00000255087:E486G	ENSP00000255087:E486G	E	-	2	0	MTL5	68232422	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.074000	0.76791	2.016000	0.59253	0.329000	0.21502	GAG	.	.		0.483	MTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396844.1	NM_004923	
TENM4	26011	hgsc.bcm.edu	37	11	78775891	78775891	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:78775891C>T	ENST00000278550.7	-	6	847	c.385G>A	c.(385-387)Gtg>Atg	p.V129M		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	129	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CACAGACGCACGGGGTGCTCA	0.647																																					p.V129M		Atlas-SNP	.											.	.	.	.	0			c.G385A						.						31.0	31.0	31.0					11																	78775891		692	1591	2283	SO:0001583	missense	26011	exon6			GACGCACGGGGTG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.385G>A	chr11.hg19:g.78775891C>T	ENSP00000278550:p.Val129Met	45.0	0.0		48.0	12.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.009528	0.54361	.	.	ENSG00000149256	ENST00000278550	T	0.39229	1.09	4.69	3.78	0.43462	Teneurin intracellular, N-terminal (2);	0.078666	0.49916	N	0.000135	T	0.19644	0.0472	N	0.04203	-0.255	0.46927	D	0.99925	B;B	0.29085	0.232;0.028	B;B	0.24269	0.052;0.018	T	0.06463	-1.0825	9	.	.	.	.	13.1	0.59214	0.0:0.9217:0.0:0.0783	.	129;129	G3CAT1;Q6N022	.;TEN4_HUMAN	M	129	ENSP00000278550:V129M	.	V	-	1	0	ODZ4	78453539	0.998000	0.40836	0.867000	0.34043	0.986000	0.74619	3.884000	0.56175	1.325000	0.45301	0.563000	0.77884	GTG	.	.		0.647	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
CTSC	1075	hgsc.bcm.edu	37	11	88070831	88070831	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:88070831C>A	ENST00000227266.5	-	1	124	c.10G>T	c.(10-12)Ggg>Tgg	p.G4W	CTSC_ENST00000524463.1_Missense_Mutation_p.G4W|CTSC_ENST00000393301.4_5'UTR|CTSC_ENST00000529974.1_Missense_Mutation_p.G4W	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	4					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)	p.G4W(1)		large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAGGAGGGCCCAGCACCCATG	0.657																																					p.G4W		Atlas-SNP	.											CTSC,NS,carcinoma,0,1	CTSC	46	.	1	Substitution - Missense(1)	ovary(1)	c.G10T						.						10.0	11.0	11.0					11																	88070831		2189	4282	6471	SO:0001583	missense	1075	exon1			AGGGCCCAGCACC	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.10G>T	chr11.hg19:g.88070831C>A	ENSP00000227266:p.Gly4Trp	85.0	0.0		43.0	3.0	NM_148170	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	hg19	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	C	5.816	0.334889	0.11013	.	.	ENSG00000109861	ENST00000393302;ENST00000227266;ENST00000524463;ENST00000529974	T	0.70986	-0.53	4.71	-9.42	0.00610	.	10.698900	0.00166	N	0.000002	T	0.36580	0.0972	N	0.01800	-0.715	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42137	-0.9469	9	.	.	.	.	5.3711	0.16140	0.115:0.4781:0.2502:0.1567	.	4;4;4	Q2HIY8;P53634-2;P53634	.;.;CATC_HUMAN	W	4	ENSP00000227266:G4W	.	G	-	1	0	CTSC	87710479	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.846000	0.01676	-3.971000	0.00086	-1.157000	0.01802	GGG	.	.		0.657	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
FAT3	120114	hgsc.bcm.edu	37	11	92616495	92616495	+	Silent	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:92616495C>A	ENST00000298047.6	+	23	12890	c.12873C>A	c.(12871-12873)gcC>gcA	p.A4291A	FAT3_ENST00000533797.1_Silent_p.A626A|FAT3_ENST00000525166.1_Silent_p.A4141A|FAT3_ENST00000489716.1_3'UTR|FAT3_ENST00000409404.2_Silent_p.A4291A			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4291					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ACCTCCCCGCCGTGTCACCCT	0.652										TCGA Ovarian(4;0.039)																											p.A4291A		Atlas-SNP	.											.	FAT3	1822	.	0			c.C12873A						.						22.0	28.0	26.0					11																	92616495		2021	4085	6106	SO:0001819	synonymous_variant	120114	exon23			CCCCGCCGTGTCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12873C>A	chr11.hg19:g.92616495C>A		36.0	0.0		25.0	10.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.652	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103027464	103027464	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:103027464A>G	ENST00000375735.2	+	26	4236	c.4092A>G	c.(4090-4092)gaA>gaG	p.E1364E	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.E1364E	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1364	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGCCAAAAGAACAGACACGCT	0.348																																					p.E1364E		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A4092G						.						56.0	56.0	56.0					11																	103027464		1847	4090	5937	SO:0001819	synonymous_variant	79659	exon26			AAAAGAACAGACA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.4092A>G	chr11.hg19:g.103027464A>G		67.0	0.0		81.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.348	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
NCAM1	4684	hgsc.bcm.edu	37	11	113085206	113085206	+	Silent	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:113085206T>A	ENST00000533760.1	+	8	1277	c.678T>A	c.(676-678)tcT>tcA	p.S226S	NCAM1_ENST00000401611.2_Silent_p.S343S|NCAM1_ENST00000316851.7_Silent_p.S334S|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	344	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GGAGGACTTCTACCCGGAACA	0.522																																					p.S344S		Atlas-SNP	.											.	NCAM1	372	.	0			c.T1032A						.						60.0	62.0	61.0					11																	113085206		1914	4123	6037	SO:0001819	synonymous_variant	4684	exon9			GACTTCTACCCGG		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.678T>A	chr11.hg19:g.113085206T>A		81.0	0.0		112.0	11.0	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Silent	SNP	ENST00000533760.1	hg19																																																																																				.	.		0.522	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615	
TECTA	7007	hgsc.bcm.edu	37	11	121058616	121058616	+	Silent	SNP	C	C	T	rs559874132		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:121058616C>T	ENST00000392793.1	+	21	6346	c.6075C>T	c.(6073-6075)acC>acT	p.T2025T	TECTA_ENST00000264037.2_Silent_p.T2025T			O75443	TECTA_HUMAN	tectorin alpha	2025	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TTCACGTCACCGTCTTTAAAT	0.438													C|||	1	0.000199681	0.0	0.0	5008	,	,		22638	0.0		0.0	False		,,,				2504	0.001				p.T2025T		Atlas-SNP	.											.	TECTA	329	.	0			c.C6075T						.						183.0	159.0	167.0					11																	121058616		2203	4299	6502	SO:0001819	synonymous_variant	7007	exon20			CGTCACCGTCTTT	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.6075C>T	chr11.hg19:g.121058616C>T		93.0	0.0		89.0	24.0	NM_005422		Silent	SNP	ENST00000392793.1	hg19	CCDS8434.1																																																																																			.	.		0.438	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
ACRV1	56	hgsc.bcm.edu	37	11	125542541	125542541	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:125542541T>C	ENST00000533904.1	-	4	1087	c.745A>G	c.(745-747)Acg>Gcg	p.T249A	ACRV1_ENST00000345274.1_Missense_Mutation_p.T139A|ACRV1_ENST00000527795.1_Missense_Mutation_p.T179A|CHEK1_ENST00000428830.2_Intron|ACRV1_ENST00000425431.1_Missense_Mutation_p.T105A|ACRV1_ENST00000353070.1_Missense_Mutation_p.T65A|ACRV1_ENST00000530048.1_Missense_Mutation_p.T194A|ACRV1_ENST00000348856.3_Missense_Mutation_p.T149A|ACRV1_ENST00000315608.3_Missense_Mutation_p.T230A|ACRV1_ENST00000445562.1_Missense_Mutation_p.T154A|ACRV1_ENST00000453509.1_Missense_Mutation_p.T160A			P26436	ASPX_HUMAN	acrosomal vesicle protein 1	249					multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				kidney(1)|large_intestine(3)|lung(2)	6	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		TGCATCCTCGTTCCATGGGAG	0.453																																					p.T249A		Atlas-SNP	.											.	ACRV1	21	.	0			c.A745G						.						189.0	163.0	172.0					11																	125542541		2201	4299	6500	SO:0001583	missense	56	exon4			TCCTCGTTCCATG	AK223335	CCDS8460.1, CCDS8461.1, CCDS44759.1, CCDS44761.1	11q24.2	2012-05-16			ENSG00000134940	ENSG00000134940			127	protein-coding gene	gene with protein product	"""sperm protein 10"""	102525				1693291, 8288254	Standard	NM_001612		Approved	SPACA2, SP-10, D11S4365	uc001qcs.3	P26436	OTTHUMG00000165854	ENST00000533904.1:c.745A>G	chr11.hg19:g.125542541T>C	ENSP00000432816:p.Thr249Ala	76.0	0.0		88.0	4.0	NM_001612	Q53FF4	Missense_Mutation	SNP	ENST00000533904.1	hg19	CCDS8460.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.646568	0.67358	.	.	ENSG00000134940	ENST00000533904;ENST00000433875;ENST00000257382;ENST00000426183;ENST00000453509;ENST00000445562;ENST00000348856;ENST00000345274;ENST00000425431;ENST00000353070;ENST00000315608;ENST00000530048;ENST00000527795	T;T;T;T;T;T;T;T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75	4.28	4.28	0.50868	.	0.374057	0.23483	N	0.047686	T	0.46946	0.1419	M	0.72118	2.19	0.34724	D	0.729022	D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;0.996;0.999;1.0;0.999;0.999;0.992	D;D;D;D;D;D;D;D;P	0.87578	0.996;0.979;0.998;0.99;0.997;0.998;0.963;0.995;0.85	T	0.60326	-0.7285	10	0.56958	D	0.05	-5.3828	10.1032	0.42517	0.0:0.0:0.0:1.0	.	249;230;139;65;154;194;105;179;160	P26436;P26436-2;P26436-8;P26436-11;P26436-6;P26436-3;P26436-10;P26436-4;P26436-5	ASPX_HUMAN;.;.;.;.;.;.;.;.	A	249;230;194;179;160;154;149;139;105;65;230;194;179	ENSP00000432816:T249A;ENSP00000407846:T230A;ENSP00000257382:T194A;ENSP00000411583:T179A;ENSP00000397448:T160A;ENSP00000412653:T154A;ENSP00000257385:T149A;ENSP00000257383:T139A;ENSP00000395453:T105A;ENSP00000257386:T65A;ENSP00000317684:T230A;ENSP00000433720:T194A;ENSP00000436819:T179A	ENSP00000257382:T194A	T	-	1	0	ACRV1	125047751	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.139000	0.50577	2.158000	0.67659	0.533000	0.62120	ACG	.	.		0.453	ACRV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386722.1	NM_001612	
APLP2	334	hgsc.bcm.edu	37	11	129991652	129991652	+	Missense_Mutation	SNP	T	T	G	rs3837393|rs71750553|rs1063201	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:129991652T>G	ENST00000263574.5	+	5	732	c.660T>G	c.(658-660)gaT>gaG	p.D220E	APLP2_ENST00000539648.1_Missense_Mutation_p.D64E|APLP2_ENST00000278756.7_Missense_Mutation_p.D230E|APLP2_ENST00000345598.5_Intron|APLP2_ENST00000543137.1_Missense_Mutation_p.D127E|APLP2_ENST00000528499.1_Missense_Mutation_p.D220E|APLP2_ENST00000338167.5_Missense_Mutation_p.D220E	NM_001642.2	NP_001633.1	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	220	Asp/Glu-rich (highly acidic).|Poly-Glu.				cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)		aagaggaagatgaagaggaag	0.418																																					p.D230E		Atlas-SNP	.											.	APLP2	71	.	0			c.T690G						.						91.0	89.0	90.0					11																	129991652		2201	4297	6498	SO:0001583	missense	334	exon5			GGAAGATGAAGAG	L19597	CCDS8486.1, CCDS44773.1, CCDS44774.1, CCDS44775.1, CCDS58196.1	11q24	2008-02-05			ENSG00000084234	ENSG00000084234			598	protein-coding gene	gene with protein product		104776		APPL2		10702673	Standard	NM_001642		Approved	APPH	uc021qsg.1	Q06481	OTTHUMG00000165767	ENST00000263574.5:c.660T>G	chr11.hg19:g.129991652T>G	ENSP00000263574:p.Asp220Glu	111.0	0.0		150.0	9.0	NM_001243299	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	ENST00000263574.5	hg19	CCDS8486.1	.	.	.	.	.	.	.	.	.	.	G	1.814	-0.473995	0.04414	.	.	ENSG00000084234	ENST00000528499;ENST00000539648;ENST00000263574;ENST00000338167;ENST00000278756;ENST00000543137	D;D;D;D;D;D	0.94457	-3.43;-3.36;-1.79;-1.9;-1.91;-1.9	4.5	-9.01	0.00744	.	0.365080	0.29806	N	0.011148	T	0.80839	0.4700	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.001;0.001	T	0.67106	-0.5754	10	0.12766	T	0.61	-1.3135	1.0637	0.01606	0.399:0.184:0.1083:0.3086	.	64;220;220;214;220;220	F5H845;Q06481;Q06481-2;B4E3I5;Q06481-4;Q06481-3	.;APLP2_HUMAN;.;.;.;.	E	220;64;220;220;230;127	ENSP00000435914:D220E;ENSP00000443728:D64E;ENSP00000263574:D220E;ENSP00000345444:D220E;ENSP00000278756:D230E;ENSP00000444122:D127E	ENSP00000263574:D220E	D	+	3	2	APLP2	129496862	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-2.113000	0.01331	-5.053000	0.00023	-1.251000	0.01509	GAT	.	.		0.418	APLP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386109.1	NM_001642	
OPCML	4978	hgsc.bcm.edu	37	11	132527021	132527021	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:132527021T>A	ENST00000331898.7	-	2	939	c.361A>T	c.(361-363)Aat>Tat	p.N121Y	OPCML_ENST00000524381.1_Missense_Mutation_p.N114Y|OPCML_ENST00000374778.4_Missense_Mutation_p.N80Y|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000541867.1_Missense_Mutation_p.N121Y	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	121	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TTGGGATGATTGTCTGTCTGC	0.502																																					p.N121Y		Atlas-SNP	.											.	OPCML	166	.	0			c.A361T						.						220.0	181.0	194.0					11																	132527021		2201	4297	6498	SO:0001583	missense	4978	exon2			GATGATTGTCTGT	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"""Immunoglobulin superfamily / I-set domain containing"""	8143	protein-coding gene	gene with protein product	"""IgLON family member 1"""	600632	"""opioid-binding protein/cell adhesion molecule-like"""			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.361A>T	chr11.hg19:g.132527021T>A	ENSP00000330862:p.Asn121Tyr	175.0	0.0		243.0	54.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	hg19	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795007	0.90453	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.83	5.83	0.93111	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.052133	0.85682	D	0.000000	T	0.77280	0.4107	M	0.70275	2.135	0.52099	D	0.999949	D;D;D;D	0.58620	0.966;0.983;0.966;0.966	D;P;P;P	0.64321	0.924;0.908;0.889;0.842	T	0.79713	-0.1688	10	0.72032	D	0.01	-20.5804	16.1846	0.81942	0.0:0.0:0.0:1.0	.	121;114;121;121	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	Y	121;114;80;88;121	ENSP00000330862:N121Y;ENSP00000434750:N114Y;ENSP00000363910:N80Y;ENSP00000445496:N121Y	ENSP00000330862:N121Y	N	-	1	0	OPCML	132032231	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.190000	0.72057	2.229000	0.72834	0.533000	0.62120	AAT	.	.		0.502	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393	
CCDC77	84318	hgsc.bcm.edu	37	12	520926	520926	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:520926T>C	ENST00000239830.4	+	4	231	c.52T>C	c.(52-54)Tcc>Ccc	p.S18P	CCDC77_ENST00000540344.1_3'UTR|CCDC77_ENST00000422000.1_5'UTR|CCDC77_ENST00000540180.1_5'UTR|CCDC77_ENST00000412006.2_5'UTR	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	18						centrosome (GO:0005813)|membrane (GO:0016020)				cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			AACAGTTGTCTCCAAACGTGG	0.468																																					p.S18P		Atlas-SNP	.											.	CCDC77	35	.	0			c.T52C						.						83.0	73.0	76.0					12																	520926		2203	4300	6503	SO:0001583	missense	84318	exon4			GTTGTCTCCAAAC	AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.52T>C	chr12.hg19:g.520926T>C	ENSP00000239830:p.Ser18Pro	56.0	0.0		77.0	4.0	NM_032358	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	hg19	CCDS8503.1	.	.	.	.	.	.	.	.	.	.	T	8.999	0.979608	0.18812	.	.	ENSG00000120647	ENST00000535052;ENST00000239830	T;T	0.56941	0.43;0.43	4.5	-8.91	0.00778	.	1.710740	0.02799	N	0.122922	T	0.32194	0.0821	N	0.17082	0.46	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.25433	-1.0132	10	0.51188	T	0.08	13.3553	8.0285	0.30451	0.0:0.4114:0.3232:0.2654	.	18	Q9BR77	CCD77_HUMAN	P	18	ENSP00000443209:S18P;ENSP00000239830:S18P	ENSP00000239830:S18P	S	+	1	0	CCDC77	391187	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.974000	0.03794	-1.814000	0.01224	-0.388000	0.06559	TCC	.	.		0.468	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358	
B4GALNT3	283358	hgsc.bcm.edu	37	12	653566	653566	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:653566T>C	ENST00000266383.5	+	4	426	c.413T>C	c.(412-414)cTc>cCc	p.L138P	B4GALNT3_ENST00000544638.1_3'UTR	NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	138					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ATCCAGCAGCTCAGGAGGAAC	0.617																																					p.L138P		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.T413C						.						131.0	114.0	120.0					12																	653566		2203	4300	6503	SO:0001583	missense	283358	exon4			AGCAGCTCAGGAG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.413T>C	chr12.hg19:g.653566T>C	ENSP00000266383:p.Leu138Pro	32.0	0.0		46.0	5.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.273531	0.80580	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.23950	1.88;1.88	4.73	4.73	0.59995	PA14 (2);	0.000000	0.64402	D	0.000001	T	0.51058	0.1652	M	0.79011	2.435	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.71870	0.975;0.951	T	0.57406	-0.7817	10	0.72032	D	0.01	-20.2878	14.2118	0.65769	0.0:0.0:0.0:1.0	.	40;138	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	P	138;40	ENSP00000266383:L138P;ENSP00000322953:L40P	ENSP00000266383:L138P	L	+	2	0	B4GALNT3	523827	1.000000	0.71417	0.984000	0.44739	0.944000	0.59088	7.609000	0.82925	1.757000	0.51966	0.402000	0.26972	CTC	.	.		0.617	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
SLC38A1	81539	hgsc.bcm.edu	37	12	46599923	46599923	+	Missense_Mutation	SNP	C	C	T	rs369346779		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:46599923C>T	ENST00000398637.5	-	9	1280	c.586G>A	c.(586-588)Gtt>Att	p.V196I	SLC38A1_ENST00000439706.1_Missense_Mutation_p.V196I|SLC38A1_ENST00000546893.1_Missense_Mutation_p.V196I|SLC38A1_ENST00000549049.1_Missense_Mutation_p.V196I|SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000552197.1_Missense_Mutation_p.V196I	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	196					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)			NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			ACCACCAGAACGCGGCCATCC	0.393																																					p.V196I		Atlas-SNP	.											SLC38A1,colon,carcinoma,0,1	SLC38A1	58	.	0			c.G586A						.	C	ILE/VAL,ILE/VAL	0,3836		0,0,1918	87.0	90.0	89.0		586,586	-5.6	0.0	12		89	1,8287		0,1,4143	no	missense,missense	SLC38A1	NM_001077484.1,NM_030674.3	29,29	0,1,6061	TT,TC,CC		0.0121,0.0,0.0082	benign,benign	196/488,196/488	46599923	1,12123	1918	4144	6062	SO:0001583	missense	81539	exon9			CCAGAACGCGGCC	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"""Solute carriers"""	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.586G>A	chr12.hg19:g.46599923C>T	ENSP00000381634:p.Val196Ile	34.0	0.0		39.0	2.0	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	hg19	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	C	9.492	1.100901	0.20552	0.0	1.21E-4	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197	T;T;T;T;T	0.02525	4.26;4.26;4.26;4.26;4.26	5.7	-5.61	0.02489	.	0.669277	0.13946	N	0.351847	T	0.00815	0.0027	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.12630	0.006;0.003;0.0	B;B;B	0.13407	0.009;0.005;0.003	T	0.44050	-0.9353	10	0.29301	T	0.29	-0.7853	2.2946	0.04147	0.2037:0.2101:0.3999:0.1863	.	196;196;196	B5MEC5;F8VX04;Q9H2H9	.;.;S38A1_HUMAN	I	196	ENSP00000449607:V196I;ENSP00000398142:V196I;ENSP00000381634:V196I;ENSP00000447853:V196I;ENSP00000449756:V196I	ENSP00000381634:V196I	V	-	1	0	SLC38A1	44886190	0.000000	0.05858	0.001000	0.08648	0.650000	0.38633	-0.721000	0.04963	-0.512000	0.06505	-0.463000	0.05309	GTT	.	.		0.393	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2		
SLC38A2	54407	hgsc.bcm.edu	37	12	46756927	46756927	+	Splice_Site	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:46756927T>C	ENST00000256689.5	-	13	1500	c.1056A>G	c.(1054-1056)gaA>gaG	p.E352E	SLC38A2_ENST00000551374.1_Splice_Site_p.E190E|SLC38A2_ENST00000547252.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	352					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		ACTCAACATGTTCTACAGGGA	0.393																																					p.E352E	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A1056G						.						137.0	128.0	131.0					12																	46756927		2203	4300	6503	SO:0001630	splice_region_variant	54407	exon13			AACATGTTCTACA	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"""Solute carriers"""	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.1055-1A>G	chr12.hg19:g.46756927T>C		64.0	0.0		75.0	4.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Silent	SNP	ENST00000256689.5	hg19	CCDS8749.1																																																																																			.	.		0.393	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1		Silent
LMBR1L	55716	hgsc.bcm.edu	37	12	49500745	49500745	+	Splice_Site	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:49500745T>C	ENST00000267102.8	-	2	498	c.156A>G	c.(154-156)acA>acG	p.T52T	LMBR1L_ENST00000547382.1_Splice_Site_p.T52T|LMBR1L_ENST00000395141.4_5'Flank|LMBR1L_ENST00000553204.1_5'UTR	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	52	LCN1-binding.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TCAAAGTACCTGTGGTGAACT	0.522																																					p.T52T		Atlas-SNP	.											.	LMBR1L	61	.	0			c.A156G						.						122.0	138.0	133.0					12																	49500745		2113	4236	6349	SO:0001630	splice_region_variant	55716	exon2			AGTACCTGTGGTG	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"""limb region 1 homolog (mouse)-like"""			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.157+1A>G	chr12.hg19:g.49500745T>C		97.0	0.0		119.0	5.0	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Silent	SNP	ENST00000267102.8	hg19	CCDS8780.2																																																																																			.	.		0.522	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113	Silent
FAIM2	23017	hgsc.bcm.edu	37	12	50281167	50281167	+	Splice_Site	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:50281167A>T	ENST00000320634.3	-	11	896		c.e11+1		FAIM2_ENST00000550890.1_Splice_Site	NM_012306.3	NP_036438.2	Q9BWQ8	LFG2_HUMAN	Fas apoptotic inhibitory molecule 2						apoptotic process (GO:0006915)|cerebellar granular layer development (GO:0021681)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum development (GO:0021549)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of neuron apoptotic process (GO:0043523)|response to ischemia (GO:0002931)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|postsynaptic membrane (GO:0045211)				endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|skin(2)	14						GACCACACTCACCAATGTAAA	0.577																																					.		Atlas-SNP	.											.	FAIM2	32	.	0			c.801+2T>A						.						129.0	95.0	106.0					12																	50281167		2203	4300	6503	SO:0001630	splice_region_variant	23017	exon12			ACACTCACCAATG	AB023167	CCDS8791.1	12q13	2010-03-18				ENSG00000135472			17067	protein-coding gene	gene with protein product	"""transmembrane BAX inhibitor motif containing 2"""	604306				10231032, 10535980	Standard	NM_012306		Approved	KIAA0950, LFG, NMP35, LIFEGUARD, TMBIM2, LFG2	uc001rvj.2	Q9BWQ8	OTTHUMG00000169808	ENST00000320634.3:c.801+1T>A	chr12.hg19:g.50281167A>T		32.0	0.0		47.0	10.0	NM_012306	A8K1W6|B3KR08|Q9UJY9|Q9Y2F7	Splice_Site	SNP	ENST00000320634.3	hg19	CCDS8791.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.449226	0.63178	.	.	ENSG00000135472	ENST00000320634;ENST00000550890;ENST00000550635;ENST00000552669	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8714	0.41177	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAIM2	48567434	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	5.056000	0.64287	1.841000	0.53522	0.379000	0.24179	.	.	.		0.577	FAIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405984.1	NM_012306	Intron
AQP5	362	hgsc.bcm.edu	37	12	50357929	50357929	+	Missense_Mutation	SNP	G	G	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:50357929G>C	ENST00000293599.6	+	3	731	c.583G>C	c.(583-585)Gtc>Ctc	p.V195L	RP11-469H8.6_ENST00000550214.1_RNA|RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA	NM_001651.2	NP_001642.1	P55064	AQP5_HUMAN	aquaporin 5	195					camera-type eye morphogenesis (GO:0048593)|carbon dioxide transport (GO:0015670)|excretion (GO:0007588)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			large_intestine(1)|lung(3)	4						CCCTGCGGTGGTCATGAATCG	0.607																																					p.V195L		Atlas-SNP	.											.	AQP5	19	.	0			c.G583C						.						126.0	105.0	112.0					12																	50357929		2203	4300	6503	SO:0001583	missense	362	exon3			GCGGTGGTCATGA	U46569	CCDS8793.1	12q13	2013-09-10				ENSG00000161798		"""Ion channels / Aquaporins"""	638	protein-coding gene	gene with protein product		600442				8621489, 23830519	Standard	NM_001651		Approved		uc001rvo.3	P55064	OTTHUMG00000169710	ENST00000293599.6:c.583G>C	chr12.hg19:g.50357929G>C	ENSP00000293599:p.Val195Leu	82.0	0.0		107.0	15.0	NM_001651	Q6FGW8	Missense_Mutation	SNP	ENST00000293599.6	hg19	CCDS8793.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.784050	0.31593	.	.	ENSG00000161798	ENST00000293599	D	0.86497	-2.13	5.07	0.489	0.16854	Aquaporin-like (2);	0.424918	0.19449	N	0.113991	T	0.74809	0.3765	N	0.25286	0.73	0.32061	N	0.595644	B	0.02656	0.0	B	0.08055	0.003	T	0.66448	-0.5921	10	0.31617	T	0.26	-36.1104	8.0666	0.30665	0.4327:0.0:0.5673:0.0	.	195	P55064	AQP5_HUMAN	L	195	ENSP00000293599:V195L	ENSP00000293599:V195L	V	+	1	0	AQP5	48644196	0.018000	0.18449	0.860000	0.33809	0.724000	0.41520	0.077000	0.14738	0.244000	0.21351	0.655000	0.94253	GTC	.	.		0.607	AQP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405542.2	NM_001651	
ATG101	60673	hgsc.bcm.edu	37	12	52470885	52470885	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:52470885T>C	ENST00000336854.4	+	4	1046	c.568T>C	c.(568-570)Tac>Cac	p.Y190H	OR7E47P_ENST00000546390.1_RNA|RP11-1100L3.7_ENST00000550301.1_RNA	NM_001098673.1|NM_021934.4	NP_001092143.1|NP_068753.2	Q9BSB4	ATGA1_HUMAN		190					autophagic vacuole assembly (GO:0000045)	pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein complex binding (GO:0032403)			endometrium(1)|lung(2)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(357;0.0978)		GCCCTACCTGTACAAGATCTC	0.572																																					p.Y190H		Atlas-SNP	.											.	C12orf44	14	.	0			c.T568C						.						105.0	92.0	96.0					12																	52470885		2203	4300	6503	SO:0001583	missense	60673	exon4			TACCTGTACAAGA																												ENST00000336854.4:c.568T>C	chr12.hg19:g.52470885T>C	ENSP00000338990:p.Tyr190His	72.0	0.0		97.0	4.0	NM_001098673	Q9HAE2|Q9HBN1	Missense_Mutation	SNP	ENST00000336854.4	hg19	CCDS8820.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.079662	0.55753	.	.	ENSG00000123395	ENST00000336854;ENST00000553049;ENST00000550984	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	N	0.11560	0.145	0.58432	D	0.999998	B	0.11235	0.004	B	0.09377	0.004	T	0.23261	-1.0193	9	0.41790	T	0.15	-26.5336	13.7571	0.62943	0.0:0.0:0.0:1.0	.	190	Q9BSB4	ATGA1_HUMAN	H	190	.	ENSP00000338990:Y190H	Y	+	1	0	C12orf44	50757152	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.455000	0.80726	2.145000	0.66743	0.533000	0.62120	TAC	.	.		0.572	C12orf44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405063.1		
ITGA7	3679	hgsc.bcm.edu	37	12	56088716	56088716	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:56088716C>T	ENST00000555728.1	-	16	2202	c.2174G>A	c.(2173-2175)gGg>gAg	p.G725E	ITGA7_ENST00000257880.7_Missense_Mutation_p.G725E|ITGA7_ENST00000452168.2_Missense_Mutation_p.G588E|ITGA7_ENST00000553804.1_Missense_Mutation_p.G685E|ITGA7_ENST00000394230.2_Missense_Mutation_p.G685E|ITGA7_ENST00000347027.6_Missense_Mutation_p.G675E|ITGA7_ENST00000394229.2_Missense_Mutation_p.G681E|ITGA7_ENST00000257879.6_Missense_Mutation_p.G681E			Q13683	ITA7_HUMAN	integrin, alpha 7	725					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GACTGGCTGCCCACTCAGTGC	0.612																																					p.G685E		Atlas-SNP	.											.	ITGA7	194	.	0			c.G2054A						.						52.0	52.0	52.0					12																	56088716		2203	4300	6503	SO:0001583	missense	3679	exon15			GGCTGCCCACTCA		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.2174G>A	chr12.hg19:g.56088716C>T	ENSP00000452387:p.Gly725Glu	49.0	0.0		61.0	6.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.89	2.371490	0.42003	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000555728	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	4.95	4.95	0.65309	Integrin alpha-2 (1);	0.201844	0.42294	N	0.000730	T	0.44912	0.1316	L	0.43152	1.355	0.48901	D	0.999723	B;B;B;P	0.39601	0.007;0.368;0.017;0.68	B;B;B;P	0.44860	0.018;0.329;0.051;0.462	T	0.40997	-0.9533	10	0.49607	T	0.09	.	9.6719	0.40017	0.0:0.9039:0.0:0.0961	.	588;725;685;744	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	E	685;681;675;588;725;685;681;725	ENSP00000452120:G685E;ENSP00000257879:G681E;ENSP00000343009:G675E;ENSP00000393844:G588E;ENSP00000257880:G725E;ENSP00000377777:G685E;ENSP00000377776:G681E;ENSP00000452387:G725E	ENSP00000257879:G681E	G	-	2	0	ITGA7	54374983	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.267000	0.58877	2.471000	0.83476	0.561000	0.74099	GGG	.	.		0.612	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
ORMDL2	29095	hgsc.bcm.edu	37	12	56212815	56212815	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:56212815A>G	ENST00000243045.5	+	2	227	c.32A>G	c.(31-33)aAc>aGc	p.N11S	SARNP_ENST00000336133.3_5'Flank|SARNP_ENST00000552080.1_5'Flank|ORMDL2_ENST00000550836.1_Intron|RP11-762I7.5_ENST00000546837.1_Intron|ORMDL2_ENST00000552672.1_Intron|SARNP_ENST00000444631.2_5'Flank|RP11-762I7.5_ENST00000552719.1_Intron|ORMDL2_ENST00000548974.1_Missense_Mutation_p.N11S	NM_014182.4	NP_054901.1	Q53FV1	ORML2_HUMAN	ORMDL sphingolipid biosynthesis regulator 2	11					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|lung(3)	4						AGCGAAGTAAACCCCAACACC	0.527																																					p.N11S		Atlas-SNP	.											.	ORMDL2	8	.	0			c.A32G						.						154.0	128.0	137.0					12																	56212815		2203	4300	6503	SO:0001583	missense	29095	exon2			AAGTAAACCCCAA	AF395707	CCDS8893.1	12q13.2	2014-06-16	2014-06-16			ENSG00000123353			16037	protein-coding gene	gene with protein product		610074	"""ORM1 (S. cerevisiae)-like 2"", ""ORM1-like 2 (S. cerevisiae)"""			12093374, 23066021	Standard	NM_014182		Approved	HSPC160, adoplin-2, MST095, MSTP095	uc001shw.1	Q53FV1		ENST00000243045.5:c.32A>G	chr12.hg19:g.56212815A>G	ENSP00000243045:p.Asn11Ser	81.0	0.0		81.0	4.0	NM_014182	B2RA58|Q7Z4E5|Q8NFX0|Q9P004	Missense_Mutation	SNP	ENST00000243045.5	hg19	CCDS8893.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.692480	0.48202	.	.	ENSG00000123353	ENST00000243045;ENST00000548974	.	.	.	5.05	3.91	0.45181	.	0.000000	0.85682	D	0.000000	T	0.81777	0.4894	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83198	-0.0080	9	0.56958	D	0.05	-16.2825	9.1752	0.37107	0.914:0.0:0.086:0.0	.	11	Q53FV1	ORML2_HUMAN	S	11	.	ENSP00000243045:N11S	N	+	2	0	ORMDL2	54499082	1.000000	0.71417	0.987000	0.45799	0.038000	0.13279	9.139000	0.94554	1.061000	0.40601	-0.256000	0.11100	AAC	.	.		0.527	ORMDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407934.1	NM_014182	
LRP1	4035	hgsc.bcm.edu	37	12	57577928	57577928	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:57577928C>T	ENST00000243077.3	+	37	6456	c.5990C>T	c.(5989-5991)tCc>tTc	p.S1997F		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1997					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTCAATGGCTCCTTCCGCTAC	0.592																																					p.S1997F		Atlas-SNP	.											.	LRP1	428	.	0			c.C5990T						.						74.0	58.0	64.0					12																	57577928		2203	4300	6503	SO:0001583	missense	4035	exon37			ATGGCTCCTTCCG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5990C>T	chr12.hg19:g.57577928C>T	ENSP00000243077:p.Ser1997Phe	74.0	0.0		104.0	12.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244038	0.95272	.	.	ENSG00000123384	ENST00000243077	D	0.96265	-3.96	4.84	4.84	0.62591	Six-bladed beta-propeller, TolB-like (1);	0.152639	0.43919	D	0.000507	D	0.98185	0.9400	M	0.86343	2.81	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.98316	1.0526	10	0.46703	T	0.11	.	16.9352	0.86201	0.0:1.0:0.0:0.0	.	1997	Q07954	LRP1_HUMAN	F	1997	ENSP00000243077:S1997F	ENSP00000243077:S1997F	S	+	2	0	LRP1	55864195	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.879000	0.69690	2.532000	0.85374	0.555000	0.69702	TCC	.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816822	75816822	+	Intron	SNP	A	A	G	rs75261424		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:75816822A>G	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000320460.4_Silent_p.K241K|GLIPR1L2_ENST00000441218.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TGGACAAGAAAAATAAGCGAT	0.313																																					p.K241K		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.A723G						.						109.0	111.0	110.0					12																	75816822		2203	4300	6503	SO:0001627	intron_variant	144321	exon4			CAAGAAAAATAAG	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+53A>G	chr12.hg19:g.75816822A>G		109.0	0.0		90.0	5.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	hg19	CCDS58258.1																																																																																			.	.		0.313	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
PTPRQ	374462	hgsc.bcm.edu	37	12	81014071	81014071	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:81014071T>A	ENST00000266688.5	+	37	5516	c.5516T>A	c.(5515-5517)aTc>aAc	p.I1839N				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1885					regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						GAAATCTACATCATAGGTGCT	0.348																																					p.I1671N		Atlas-SNP	.											.	PTPRQ	119	.	0			c.T5012A						.						170.0	133.0	144.0					12																	81014071		692	1590	2282	SO:0001583	missense	374462	exon29			TCTACATCATAGG	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.5516T>A	chr12.hg19:g.81014071T>A	ENSP00000266688:p.Ile1839Asn	165.0	0.0		177.0	35.0	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.24|15.24	2.775931|2.775931	0.49786|0.49786	.|.	.|.	ENSG00000139304|ENSG00000139304	ENST00000266688|ENST00000532722	T|.	0.36157|.	1.27|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	.|.	.|.	.|.	.|.	T|T	0.53449|0.53449	0.1797|0.1797	.|.	.|.	.|.	0.30508|0.30508	N|N	0.769704|0.769704	P|.	0.39624|.	0.681|.	B|.	0.34536|.	0.185|.	T|T	0.55774|0.55774	-0.8088|-0.8088	8|4	0.35671|.	T|.	0.21|.	.|.	15.5213|15.5213	0.75869|0.75869	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1885|.	Q9UMZ3|.	PTPRQ_HUMAN|.	N|T	1839|1540	ENSP00000266688:I1839N|.	ENSP00000266688:I1839N|.	I|S	+|+	2|1	0|0	PTPRQ|PTPRQ	79538202|79538202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.736000|0.736000	0.42039|0.42039	6.303000|6.303000	0.72794|0.72794	2.129000|2.129000	0.65627|0.65627	0.454000|0.454000	0.30748|0.30748	ATC|TCA	.	.		0.348	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
USP30	84749	hgsc.bcm.edu	37	12	109519740	109519740	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:109519740T>C	ENST00000257548.5	+	9	876	c.783T>C	c.(781-783)ggT>ggC	p.G261G	USP30_ENST00000392784.2_Silent_p.G230G	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	261	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						TGCTGTAGGGTCACCCATTGA	0.443																																					p.G261G		Atlas-SNP	.											.	USP30	48	.	0			c.T783C						.						215.0	189.0	198.0					12																	109519740		2203	4300	6503	SO:0001819	synonymous_variant	84749	exon9			GTAGGGTCACCCA	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"""Ubiquitin-specific peptidases"""	20065	protein-coding gene	gene with protein product		612492	"""ubiquitin specific protease 30"""			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.783T>C	chr12.hg19:g.109519740T>C		94.0	0.0		155.0	7.0	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Silent	SNP	ENST00000257548.5	hg19	CCDS9123.2																																																																																			.	.		0.443	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663	
NOS1	4842	hgsc.bcm.edu	37	12	117726019	117726019	+	Missense_Mutation	SNP	C	C	A	rs368611180	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr12:117726019C>A	ENST00000344089.3	-	6	1728	c.1043G>T	c.(1042-1044)cGg>cTg	p.R348L	NOS1_ENST00000338101.4_Silent_p.T329T|NOS1_ENST00000317775.6_Silent_p.T329T	NM_001204213.1|NM_001204214.1	NP_001191142.1|NP_001191143.1	Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.T329T(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CAGTGCATCCCGTTTCCTGGA	0.512																																					p.T329T	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,NS,carcinoma,0,1	NOS1	240	.	1	Substitution - coding silent(1)	lung(1)	c.G987T						.						111.0	108.0	109.0					12																	117726019		1955	4160	6115	SO:0001583	missense	4842	exon5			GCATCCCGTTTCC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000344089.3:c.1043G>T	chr12.hg19:g.117726019C>A	ENSP00000339862:p.Arg348Leu	35.0	0.0		44.0	2.0	NM_000620		Silent	SNP	ENST00000344089.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.39	1.924686	0.34002	.	.	ENSG00000089250	ENST00000344089	T	0.08282	3.11	5.93	-3.56	0.04626	.	.	.	.	.	T	0.08537	0.0212	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.36696	-0.9737	6	0.87932	D	0	-11.6477	4.4175	0.11463	0.0795:0.288:0.1693:0.4632	.	.	.	.	L	348	ENSP00000339862:R348L	ENSP00000339862:R348L	R	-	2	0	NOS1	116210402	0.000000	0.05858	0.890000	0.34922	0.487000	0.33371	-3.658000	0.00401	-0.588000	0.05882	-1.008000	0.02478	CGG	.	.		0.512	NOS1-201	KNOWN	basic	protein_coding	protein_coding			
XPO4	64328	hgsc.bcm.edu	37	13	21375110	21375110	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:21375110T>C	ENST00000255305.6	-	14	1908	c.1837A>G	c.(1837-1839)Aga>Gga	p.R613G	XPO4_ENST00000400602.2_Missense_Mutation_p.R613G			Q9C0E2	XPO4_HUMAN	exportin 4	613					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		TCTGAAACTCTGAGAATGGCA	0.358																																					p.R613G		Atlas-SNP	.											.	XPO4	153	.	0			c.A1837G						.						90.0	81.0	84.0					13																	21375110		1810	4073	5883	SO:0001583	missense	64328	exon14			AAACTCTGAGAAT	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"""Exportins"""	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.1837A>G	chr13.hg19:g.21375110T>C	ENSP00000255305:p.Arg613Gly	90.0	0.0		89.0	4.0	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Missense_Mutation	SNP	ENST00000255305.6	hg19	CCDS41872.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.054300	0.55218	.	.	ENSG00000132953	ENST00000400602;ENST00000456108;ENST00000255305	T;T	0.65178	-0.14;-0.14	5.65	3.12	0.35913	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55081	0.1898	L	0.55481	1.735	0.52099	D	0.999945	B	0.30146	0.27	B	0.27076	0.076	T	0.50268	-0.8848	10	0.40728	T	0.16	-9.1414	12.507	0.55987	0.0:0.0:0.2639:0.7361	.	613	Q9C0E2	XPO4_HUMAN	G	613;483;613	ENSP00000383444:R613G;ENSP00000255305:R613G	ENSP00000255305:R613G	R	-	1	2	XPO4	20273110	0.999000	0.42202	0.483000	0.27378	0.935000	0.57460	3.155000	0.50700	0.378000	0.24764	0.533000	0.62120	AGA	.	.		0.358	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459	
SKA3	221150	hgsc.bcm.edu	37	13	21750551	21750551	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:21750551C>T	ENST00000314759.5	-	1	190	c.66G>A	c.(64-66)acG>acA	p.T22T	SKA3_ENST00000400018.3_Silent_p.T22T|MRP63_ENST00000309594.4_5'Flank	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	22					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.T22T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GCAGCCGGGCCGTCTCGCAGT	0.731																																					p.T22T		Atlas-SNP	.											SKA3,NS,carcinoma,0,1	SKA3	76	.	1	Substitution - coding silent(1)	ovary(1)	c.G66A						.						7.0	8.0	8.0					13																	21750551		2140	4233	6373	SO:0001819	synonymous_variant	221150	exon1			CCGGGCCGTCTCG	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.66G>A	chr13.hg19:g.21750551C>T		22.0	0.0		16.0	2.0	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Silent	SNP	ENST00000314759.5	hg19	CCDS31946.1																																																																																			.	.		0.731	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
MICU2	221154	hgsc.bcm.edu	37	13	22140947	22140947	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:22140947T>C	ENST00000382374.4	-	2	412	c.347A>G	c.(346-348)gAg>gGg	p.E116G		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	116					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TTCCATTTGCTCAAACATCAC	0.383																																					p.E116G		Atlas-SNP	.											.	EFHA1	33	.	0			c.A347G						.						63.0	61.0	62.0					13																	22140947		2202	4300	6502	SO:0001583	missense	221154	exon2			ATTTGCTCAAACA	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"""EF-hand domain containing"""	31830	protein-coding gene	gene with protein product		610632	"""EF hand domain family A1"", ""EF-hand domain family, member A1"""	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.347A>G	chr13.hg19:g.22140947T>C	ENSP00000371811:p.Glu116Gly	57.0	0.0		80.0	4.0	NM_152726	Q8N0T6|Q8NAX8	Missense_Mutation	SNP	ENST00000382374.4	hg19	CCDS9297.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.169989	0.57584	.	.	ENSG00000165487	ENST00000382374	T	0.80566	-1.39	5.22	5.22	0.72569	.	0.151435	0.64402	D	0.000012	T	0.64271	0.2583	N	0.12182	0.205	0.58432	D	0.999996	P	0.42871	0.792	B	0.37650	0.255	T	0.65257	-0.6212	10	0.22706	T	0.39	-18.8093	14.091	0.64990	0.0:0.0:0.0:1.0	.	116	Q8IYU8	EFHA1_HUMAN	G	116	ENSP00000371811:E116G	ENSP00000371811:E116G	E	-	2	0	EFHA1	21038947	1.000000	0.71417	0.993000	0.49108	0.581000	0.36288	5.140000	0.64807	1.957000	0.56846	0.528000	0.53228	GAG	.	.		0.383	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726	
BRCA2	675	hgsc.bcm.edu	37	13	32937423	32937423	+	Missense_Mutation	SNP	C	C	T	rs80359048		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:32937423C>T	ENST00000380152.3	+	18	8317	c.8084C>T	c.(8083-8085)tCa>tTa	p.S2695L	BRCA2_ENST00000544455.1_Missense_Mutation_p.S2695L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2695					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.S2695*(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		GACATAATTTCATTGAGCGCA	0.368			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.S2695L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	BRCA2_ENST00000544455,NS,carcinoma,0,2	BRCA2	812	.	2	Substitution - Nonsense(2)	lung(2)	c.C8084T						.	C	LEU/SER	0,4406		0,0,2203	100.0	97.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8084	4.1	0.2	13	dbSNP_132	98	1,8599	1.2+/-3.3	0,1,4299	no	missense	BRCA2	NM_000059.3	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	2695/3419	32937423	1,13005	2203	4300	6503	SO:0001583	missense	675	exon18	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TAATTTCATTGAG	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8084C>T	chr13.hg19:g.32937423C>T	ENSP00000369497:p.Ser2695Leu	98.0	0.0		124.0	5.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180052	0.57800	0.0	1.16E-4	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.80909	-1.43;-1.43	4.94	4.1	0.47936	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 1 (1);	0.068240	0.64402	D	0.000013	T	0.79924	0.4530	M	0.79123	2.44	0.38522	D	0.948745	P	0.37636	0.603	B	0.35039	0.194	D	0.83490	0.0069	10	0.87932	D	0	.	13.655	0.62333	0.0:0.9243:0.0:0.0757	.	2695	P51587	BRCA2_HUMAN	L	2695	ENSP00000369497:S2695L;ENSP00000439902:S2695L	ENSP00000369497:S2695L	S	+	2	0	BRCA2	31835423	0.667000	0.27484	0.153000	0.22517	0.524000	0.34500	3.023000	0.49666	1.217000	0.43442	0.313000	0.20887	TCA	.	.		0.368	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
LHFP	10186	hgsc.bcm.edu	37	13	40175086	40175086	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:40175086C>T	ENST00000379589.3	-	2	730	c.268G>A	c.(268-270)Ggc>Agc	p.G90S	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	90						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		CAACCCAGGCCGGTCACTATG	0.607			T	HMGA2	lipoma																																p.G90S		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	LHFP,NS,carcinoma,0,1	LHFP	31	.	0			c.G268A						.						145.0	134.0	138.0					13																	40175086		2203	4300	6503	SO:0001583	missense	10186	exon2			CCAGGCCGGTCAC	AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.268G>A	chr13.hg19:g.40175086C>T	ENSP00000368908:p.Gly90Ser	56.0	0.0		71.0	3.0	NM_005780	B2R7M2|Q53FC0|Q96SH5	Missense_Mutation	SNP	ENST00000379589.3	hg19	CCDS9369.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.012607	0.93346	.	.	ENSG00000183722	ENST00000379589	T	0.72282	-0.64	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000001	T	0.80571	0.4648	M	0.67397	2.05	0.80722	D	1	D	0.76494	0.999	P	0.58391	0.838	T	0.80202	-0.1480	9	.	.	.	.	18.101	0.89505	0.0:1.0:0.0:0.0	.	90	Q9Y693	LHFP_HUMAN	S	90	ENSP00000368908:G90S	.	G	-	1	0	LHFP	39073086	1.000000	0.71417	0.956000	0.39512	0.541000	0.35023	7.409000	0.80053	2.522000	0.85027	0.655000	0.94253	GGC	.	.		0.607	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780	
PHF11	51131	hgsc.bcm.edu	37	13	50080776	50080776	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:50080776T>C	ENST00000378319.3	+	2	141	c.100T>C	c.(100-102)Ttt>Ctt	p.F34L	PHF11_ENST00000488958.1_5'UTR|PHF11_ENST00000357596.3_5'UTR	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	34					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		TATAGGTGTCTTTCAGGTTGC	0.418																																					p.F34L		Atlas-SNP	.											.	PHF11	20	.	0			c.T100C						.						95.0	89.0	91.0					13																	50080776		2203	4300	6503	SO:0001583	missense	51131	exon2			GGTGTCTTTCAGG	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"""Zinc fingers, PHD-type"""	17024	protein-coding gene	gene with protein product	"""IgE responsiveness (atopic)"""	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.100T>C	chr13.hg19:g.50080776T>C	ENSP00000367570:p.Phe34Leu	45.0	0.0		54.0	4.0	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Missense_Mutation	SNP	ENST00000378319.3	hg19	CCDS31975.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077362	0.36662	.	.	ENSG00000136147	ENST00000378319	T	0.72725	-0.68	4.78	4.78	0.61160	.	0.780292	0.11255	N	0.583203	T	0.61553	0.2356	L	0.48642	1.525	0.80722	D	1	B;B	0.16166	0.002;0.016	B;B	0.10450	0.003;0.005	T	0.51228	-0.8732	10	0.11182	T	0.66	-3.2169	10.8893	0.46986	0.0:0.0:0.0:1.0	.	34;34	B4DTX8;Q9UIL8	.;PHF11_HUMAN	L	34	ENSP00000367570:F34L	ENSP00000367570:F34L	F	+	1	0	PHF11	48978777	0.991000	0.36638	1.000000	0.80357	0.708000	0.40852	2.456000	0.44997	2.156000	0.67533	0.528000	0.53228	TTT	.	.		0.418	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119	
NEK3	4752	hgsc.bcm.edu	37	13	52718058	52718058	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:52718058C>T	ENST00000400357.2	-	9	2162	c.869G>A	c.(868-870)aGa>aAa	p.R290K	NEK3_ENST00000452082.2_Missense_Mutation_p.R311K|NEK3_ENST00000339406.3_Missense_Mutation_p.R290K|NEK3_ENST00000378101.2_Missense_Mutation_p.R290K			P51956	NEK3_HUMAN	NIMA-related kinase 3	290					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		TACTTTTTTTCTTGGTGTGTT	0.244																																					p.R290K		Atlas-SNP	.											.	NEK3	41	.	0			c.G869A						.						65.0	52.0	56.0					13																	52718058		1612	3644	5256	SO:0001583	missense	4752	exon10			TTTTTTCTTGGTG	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.869G>A	chr13.hg19:g.52718058C>T	ENSP00000383210:p.Arg290Lys	80.0	0.0		112.0	6.0	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	hg19	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	C	2.676	-0.276501	0.05679	.	.	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.70986	-0.36;-0.36;-0.53;-0.4;-0.37	5.78	2.6	0.31112	.	1.743130	0.02684	N	0.109966	T	0.47135	0.1429	.	.	.	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.45483	-0.9258	9	0.05833	T	0.94	.	6.2114	0.20631	0.0:0.5806:0.0:0.4194	rs3837575	311;284	Q6ZN64;F8VS47	.;.	K	290;290;290;311;284	ENSP00000339429:R290K;ENSP00000367341:R290K;ENSP00000383210:R290K;ENSP00000404197:R311K;ENSP00000448716:R284K	ENSP00000448782:R290K	R	-	2	0	NEK3	51616059	0.656000	0.27385	0.004000	0.12327	0.110000	0.19582	0.640000	0.24705	0.163000	0.19507	0.591000	0.81541	AGA	.	.		0.244	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
GPC5	2262	hgsc.bcm.edu	37	13	92380785	92380785	+	Splice_Site	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr13:92380785G>T	ENST00000377067.3	+	4	1392		c.e4-1		GPC5_ENST00000483422.1_Splice_Site	NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				CTATTTAAAAGGTAAATAGGA	0.403																																					.		Atlas-SNP	.											GPC5,NS,carcinoma,0,1	GPC5	140	.	0			c.1021-1G>T						.						91.0	96.0	94.0					13																	92380785		2203	4300	6503	SO:0001630	splice_region_variant	2262	exon4			TTAAAAGGTAAAT	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1021-1G>T	chr13.hg19:g.92380785G>T		48.0	0.0		71.0	3.0	NM_004466	B2R726|O60436|Q9BX27	Splice_Site	SNP	ENST00000377067.3	hg19	CCDS9468.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.922269	0.73213	.	.	ENSG00000179399	ENST00000377067	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3925	0.87436	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPC5	91178786	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.826000	0.69293	2.792000	0.96026	0.557000	0.71058	.	.	.		0.403	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	Intron
OR11G2	390439	hgsc.bcm.edu	37	14	20666182	20666182	+	Missense_Mutation	SNP	G	G	A	rs77471263		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:20666182G>A	ENST00000357366.3	+	1	688	c.688G>A	c.(688-690)Ggc>Agc	p.G230S		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TTGCAAAAAAGGCCCTGTGAT	0.458																																					p.G230S		Atlas-SNP	.											.	OR11G2	73	.	0			c.G688A						.						137.0	136.0	136.0					14																	20666182		2203	4300	6503	SO:0001583	missense	390439	exon1			AAAAAAGGCCCTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"""GPCR / Class A : Olfactory receptors"""	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.688G>A	chr14.hg19:g.20666182G>A	ENSP00000349930:p.Gly230Ser	229.0	0.0		322.0	26.0	NM_001005503	Q6IF09|Q96R33	Missense_Mutation	SNP	ENST00000357366.3	hg19	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	g	3.284	-0.146469	0.06627	.	.	ENSG00000196832	ENST00000357366	T	0.00029	8.91	4.93	-0.555	0.11807	GPCR, rhodopsin-like superfamily (1);	0.809795	0.10548	N	0.661787	T	0.00039	0.0001	N	0.00746	-1.225	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04115	-1.0976	10	0.48119	T	0.1	.	4.3832	0.11304	0.0809:0.1204:0.2455:0.5532	rs55781225;rs59982948	230	Q8NGC1	O11G2_HUMAN	S	230	ENSP00000349930:G230S	ENSP00000349930:G230S	G	+	1	0	OR11G2	19736022	0.000000	0.05858	0.002000	0.10522	0.062000	0.15995	-0.406000	0.07187	-0.288000	0.09051	-0.271000	0.10264	GGC	.	.		0.458	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1		
OR11G2	390439	hgsc.bcm.edu	37	14	20666184	20666184	+	Silent	SNP	C	C	G	rs74538160		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:20666184C>G	ENST00000357366.3	+	1	690	c.690C>G	c.(688-690)ggC>ggG	p.G230G		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GCAAAAAAGGCCCTGTGATAG	0.458																																					p.G230G		Atlas-SNP	.											.	OR11G2	73	.	0			c.C690G						.						140.0	139.0	139.0					14																	20666184		2203	4300	6503	SO:0001819	synonymous_variant	390439	exon1			AAAAGGCCCTGTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"""GPCR / Class A : Olfactory receptors"""	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.690C>G	chr14.hg19:g.20666184C>G		223.0	0.0		316.0	15.0	NM_001005503	Q6IF09|Q96R33	Silent	SNP	ENST00000357366.3	hg19	CCDS32032.1																																																																																			.	.		0.458	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21555549	21555549	+	Silent	SNP	G	G	A	rs373398882		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:21555549G>A	ENST00000298694.4	+	21	4441	c.4314G>A	c.(4312-4314)tcG>tcA	p.S1438S	ARHGEF40_ENST00000298693.3_Intron|RP11-998D10.7_ENST00000554733.2_lincRNA			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1438						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CCGGCCTTTCGCCGGGAGCCT	0.697																																					p.S1438S		Atlas-SNP	.											ARHGEF40_ENST00000298694,NS,carcinoma,0,1	ARHGEF40	84	.	0			c.G4314A						.	G		0,4400		0,0,2200	39.0	45.0	43.0		4314	-10.6	0.6	14		43	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ARHGEF40	NM_018071.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		1438/1520	21555549	1,12995	2200	4298	6498	SO:0001819	synonymous_variant	55701	exon21			CCTTTCGCCGGGA		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.4314G>A	chr14.hg19:g.21555549G>A		18.0	1.0		14.0	2.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.		0.697	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
ABHD4	63874	hgsc.bcm.edu	37	14	23072501	23072501	+	Nonsense_Mutation	SNP	C	C	T	rs148116289		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23072501C>T	ENST00000428304.2	+	3	389	c.319C>T	c.(319-321)Cga>Tga	p.R107*	ABHD4_ENST00000544562.1_3'UTR	NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	107					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(3)|prostate(1)	14	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0153)		TGGCTTCGGGCGAAGCTCAAG	0.607																																					p.R107X		Atlas-SNP	.											ABHD4,colon,carcinoma,0,1	ABHD4	30	.	0			c.C319T						.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	46.0	45.0	45.0		319	-0.8	1.0	14	dbSNP_134	45	0,8600		0,0,4300	no	stop-gained	ABHD4	NM_022060.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		107/343	23072501	1,13005	2203	4300	6503	SO:0001587	stop_gained	63874	exon3			TTCGGGCGAAGCT	AK022878	CCDS9572.1	14q11.1	2006-10-06			ENSG00000100439	ENSG00000100439		"""Abhydrolase domain containing"""	20154	protein-coding gene	gene with protein product							Standard	NM_022060		Approved	FLJ12816	uc001wgm.3	Q8TB40	OTTHUMG00000028686	ENST00000428304.2:c.319C>T	chr14.hg19:g.23072501C>T	ENSP00000414558:p.Arg107*	53.0	0.0		87.0	4.0	NM_022060	B4DDH7|Q9H9E0	Nonsense_Mutation	SNP	ENST00000428304.2	hg19	CCDS9572.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489471	0.64074	2.27E-4	0.0	ENSG00000100439	ENST00000428304;ENST00000216327;ENST00000542041	.	.	.	5.6	-0.807	0.10872	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-6.2819	15.5016	0.75703	0.5876:0.4124:0.0:0.0	.	.	.	.	X	107;41;83	.	ENSP00000216327:R41X	R	+	1	2	ABHD4	22142341	0.993000	0.37304	0.992000	0.48379	0.796000	0.44982	0.426000	0.21363	-0.029000	0.13827	0.655000	0.94253	CGA	.	C|1.000;T|0.000		0.607	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3		
ACIN1	22985	hgsc.bcm.edu	37	14	23548777	23548777	+	Silent	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23548777T>A	ENST00000262710.1	-	6	2268	c.1941A>T	c.(1939-1941)tcA>tcT	p.S647S	ACIN1_ENST00000457657.1_Silent_p.S607S|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Silent_p.S589S|ACIN1_ENST00000555053.1_Silent_p.S647S	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	647	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TGCTTGATGCTGAACGAGAAC	0.493																																					p.S647S		Atlas-SNP	.											.	ACIN1	147	.	0			c.A1941T						.						222.0	211.0	215.0					14																	23548777		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			TGATGCTGAACGA	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1941A>T	chr14.hg19:g.23548777T>A		148.0	0.0		240.0	15.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.		0.493	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
ACIN1	22985	hgsc.bcm.edu	37	14	23549875	23549875	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23549875T>A	ENST00000262710.1	-	6	1170	c.843A>T	c.(841-843)gaA>gaT	p.E281D	ACIN1_ENST00000457657.1_Missense_Mutation_p.E241D|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Missense_Mutation_p.E223D|ACIN1_ENST00000555053.1_Missense_Mutation_p.E281D	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	281	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		cttcatcatcttcttcctcct	0.448																																					p.E281D		Atlas-SNP	.											.	ACIN1	147	.	0			c.A843T						.						152.0	140.0	144.0					14																	23549875		2203	4300	6503	SO:0001583	missense	22985	exon6			ATCATCTTCTTCC	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.843A>T	chr14.hg19:g.23549875T>A	ENSP00000262710:p.Glu281Asp	141.0	0.0		210.0	10.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	1.446	-0.566196	0.03910	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.19532	2.14;2.14;2.14	5.57	-4.9	0.03094	.	.	.	.	.	T	0.05547	0.0146	N	0.03608	-0.345	0.09310	N	0.999991	B;B	0.14012	0.009;0.003	B;B	0.13407	0.009;0.004	T	0.39313	-0.9620	9	0.11485	T	0.65	-2.0759	1.0346	0.01545	0.1683:0.2523:0.3136:0.2658	.	281;281	G3V3M7;Q9UKV3	.;ACINU_HUMAN	D	281;241;281	ENSP00000262710:E281D;ENSP00000405677:E241D;ENSP00000451328:E281D	ENSP00000262710:E281D	E	-	3	2	ACIN1	22619715	0.061000	0.20836	0.065000	0.19835	0.152000	0.21847	-0.672000	0.05244	-0.454000	0.07066	0.528000	0.53228	GAA	.	.		0.448	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
ACIN1	22985	hgsc.bcm.edu	37	14	23549881	23549881	+	Silent	SNP	C	C	T	rs3841035|rs57580458	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23549881C>T	ENST00000262710.1	-	6	1164	c.837G>A	c.(835-837)gaG>gaA	p.E279E	ACIN1_ENST00000457657.1_Silent_p.E239E|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Silent_p.E221E|ACIN1_ENST00000555053.1_Silent_p.E279E	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	279	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		catcttcttcctcctcctcct	0.458																																					p.E279E		Atlas-SNP	.											.	ACIN1	147	.	0			c.G837A						.						131.0	127.0	128.0					14																	23549881		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			TTCTTCCTCCTCC	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.837G>A	chr14.hg19:g.23549881C>T		86.0	0.0		148.0	20.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.		0.458	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
ACIN1	22985	hgsc.bcm.edu	37	14	23549902	23549902	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:23549902T>C	ENST00000262710.1	-	6	1143	c.816A>G	c.(814-816)gaA>gaG	p.E272E	ACIN1_ENST00000457657.1_Silent_p.E232E|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Silent_p.E214E|ACIN1_ENST00000555053.1_Silent_p.E272E	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	272	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		cctcctcttcttcctcctctG	0.478																																					p.E272E		Atlas-SNP	.											.	ACIN1	147	.	0			c.A816G						.						123.0	121.0	122.0					14																	23549902		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			CTCTTCTTCCTCC	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.816A>G	chr14.hg19:g.23549902T>C		118.0	0.0		182.0	11.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.		0.478	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
PPP2R3C	55012	hgsc.bcm.edu	37	14	35577440	35577440	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:35577440T>A	ENST00000261475.5	-	5	760	c.407A>T	c.(406-408)cAa>cTa	p.Q136L	PPP2R3C_ENST00000555644.1_Missense_Mutation_p.Q136L	NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	136					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		TGTGAAAAATTGCCTAAGAAA	0.284																																					p.Q136L		Atlas-SNP	.											.	PPP2R3C	44	.	0			c.A407T						.						47.0	51.0	50.0					14																	35577440		2202	4295	6497	SO:0001583	missense	55012	exon5			AAAAATTGCCTAA	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	17485	protein-coding gene	gene with protein product		615902	"""chromosome 14 open reading frame 10"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"""	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.407A>T	chr14.hg19:g.35577440T>A	ENSP00000261475:p.Gln136Leu	53.0	0.0		102.0	17.0	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Missense_Mutation	SNP	ENST00000261475.5	hg19	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.987577	0.35036	.	.	ENSG00000092020	ENST00000261475;ENST00000554361;ENST00000555644;ENST00000557278	T;T	0.28069	1.63;1.63	5.53	5.53	0.82687	.	0.277847	0.41097	D	0.000953	T	0.11922	0.0290	N	0.02539	-0.55	0.37520	D	0.917518	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.19877	-1.0292	10	0.09338	T	0.73	-7.8834	11.6506	0.51286	0.0:0.0:0.1481:0.8519	.	136;136	Q86US5;Q969Q6	.;P2R3C_HUMAN	L	136;108;136;136	ENSP00000261475:Q136L;ENSP00000450716:Q108L	ENSP00000261475:Q136L	Q	-	2	0	PPP2R3C	34647191	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.810000	0.62598	2.104000	0.64026	0.528000	0.53228	CAA	.	.		0.284	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917	
MAP4K5	11183	hgsc.bcm.edu	37	14	50923302	50923302	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:50923302A>G	ENST00000013125.4	-	14	1265	c.947T>C	c.(946-948)aTc>aCc	p.I316T	RP11-406H23.2_ENST00000555257.1_lincRNA	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	316					activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATGACGAATGATTGCATGGGG	0.318																																					p.I316T		Atlas-SNP	.											.	MAP4K5	48	.	0			c.T947C						.						64.0	59.0	61.0					14																	50923302		1844	4086	5930	SO:0001583	missense	11183	exon14			CGAATGATTGCAT	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.947T>C	chr14.hg19:g.50923302A>G	ENSP00000013125:p.Ile316Thr	64.0	0.0		127.0	7.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.33	3.092439	0.55968	.	.	ENSG00000012983	ENST00000013125	T	0.12984	2.63	5.8	5.8	0.92144	Protein kinase-like domain (1);	0.427648	0.27773	N	0.017917	T	0.08802	0.0218	N	0.14661	0.345	0.30483	N	0.772132	B;B	0.12013	0.0;0.005	B;B	0.09377	0.0;0.004	T	0.13495	-1.0507	10	0.12430	T	0.62	.	15.1301	0.72517	1.0:0.0:0.0:0.0	.	316;316	B2R928;Q9Y4K4	.;M4K5_HUMAN	T	316	ENSP00000013125:I316T	ENSP00000013125:I316T	I	-	2	0	MAP4K5	49993052	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.751000	0.62169	2.213000	0.71641	0.528000	0.53228	ATC	.	.		0.318	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
WDHD1	11169	hgsc.bcm.edu	37	14	55467661	55467661	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:55467661C>T	ENST00000360586.3	-	9	808	c.743G>A	c.(742-744)gGt>gAt	p.G248D	WDHD1_ENST00000420358.2_Missense_Mutation_p.G125D|WDHD1_ENST00000421192.1_Missense_Mutation_p.G125D	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	248					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						ATTAATACTACCTGCAGCTAA	0.333																																					p.G248D		Atlas-SNP	.											.	WDHD1	82	.	0			c.G743A						.						159.0	163.0	162.0					14																	55467661		2203	4300	6503	SO:0001583	missense	11169	exon9			ATACTACCTGCAG	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"""WD repeat domain containing"""	23170	protein-coding gene	gene with protein product	"""CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"""	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.743G>A	chr14.hg19:g.55467661C>T	ENSP00000353793:p.Gly248Asp	207.0	0.0		306.0	128.0	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	hg19	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040405	0.93630	.	.	ENSG00000198554	ENST00000360586;ENST00000421192;ENST00000420358	T;T;T	0.70164	4.5;-0.46;-0.46	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);Translation initiation factor 2A, beta propellor-like domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.87014	0.6072	M	0.93898	3.47	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.89426	0.3713	10	0.59425	D	0.04	.	19.5251	0.95201	0.0:1.0:0.0:0.0	.	248	O75717	WDHD1_HUMAN	D	248;125;125	ENSP00000353793:G248D;ENSP00000391049:G125D;ENSP00000399349:G125D	ENSP00000353793:G248D	G	-	2	0	WDHD1	54537411	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.562000	0.67346	2.615000	0.88500	0.591000	0.81541	GGT	.	.		0.333	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086	
SNAPC1	6617	hgsc.bcm.edu	37	14	62233751	62233751	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:62233751A>G	ENST00000216294.4	+	2	390	c.286A>G	c.(286-288)Aag>Gag	p.K96E	RP11-618G20.1_ENST00000555937.1_RNA	NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	96	SNAPC3-binding.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		ACCAAAACAAAAGGTAATACT	0.274																																					p.K96E	NSCLC(27;223 907 37180 39193 46568)	Atlas-SNP	.											.	SNAPC1	32	.	0			c.A286G						.						84.0	82.0	82.0					14																	62233751		2203	4298	6501	SO:0001583	missense	6617	exon2			AAACAAAAGGTAA	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"""small nuclear RNA activating complex, polypeptide 1, 43kD"""			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.286A>G	chr14.hg19:g.62233751A>G	ENSP00000216294:p.Lys96Glu	97.0	0.0		86.0	4.0	NM_003082		Missense_Mutation	SNP	ENST00000216294.4	hg19	CCDS9755.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.292265	0.80914	.	.	ENSG00000023608	ENST00000216294	.	.	.	6.06	4.86	0.63082	.	0.142009	0.64402	D	0.000004	T	0.74711	0.3752	M	0.80422	2.495	0.42701	D	0.993611	D	0.58970	0.984	P	0.56612	0.802	T	0.78996	-0.1983	9	0.62326	D	0.03	-21.1355	12.9864	0.58594	0.7604:0.2396:0.0:0.0	.	96	Q16533	SNPC1_HUMAN	E	96	.	ENSP00000216294:K96E	K	+	1	0	SNAPC1	61303504	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.686000	0.54685	2.324000	0.78689	0.533000	0.62120	AAG	.	.		0.274	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082	
NEK9	91754	hgsc.bcm.edu	37	14	75590877	75590877	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:75590877T>C	ENST00000238616.5	-	2	427	c.269A>G	c.(268-270)gAg>gGg	p.E90G	RP11-950C14.7_ENST00000556236.1_RNA	NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	90	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		ACGTTCCTTCTCAGACAGCCG	0.468																																					p.E90G		Atlas-SNP	.											.	NEK9	64	.	0			c.A269G						.						175.0	131.0	146.0					14																	75590877		2203	4300	6503	SO:0001583	missense	91754	exon2			TCCTTCTCAGACA	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"""NIMA (never in mitosis gene a)- related kinase 9"""			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.269A>G	chr14.hg19:g.75590877T>C	ENSP00000238616:p.Glu90Gly	125.0	0.0		133.0	6.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	T	35	5.441862	0.96187	.	.	ENSG00000119638	ENST00000238616;ENST00000540227	T	0.67345	-0.26	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	L	0.39467	1.215	0.80722	D	1	P	0.52692	0.955	P	0.49085	0.6	T	0.69154	-0.5220	10	0.52906	T	0.07	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	90	Q8TD19	NEK9_HUMAN	G	90;72	ENSP00000238616:E90G	ENSP00000238616:E90G	E	-	2	0	NEK9	74660630	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.213000	0.72194	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.468	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116	
DICER1	23405	hgsc.bcm.edu	37	14	95556981	95556981	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:95556981C>T	ENST00000526495.1	-	29	5914	c.5623G>A	c.(5623-5625)Gac>Aac	p.D1875N	DICER1_ENST00000541352.1_Silent_p.T1820T|DICER1_ENST00000527414.1_Missense_Mutation_p.D1875N|DICER1_ENST00000527416.2_5'UTR|DICER1_ENST00000556045.1_Missense_Mutation_p.D773N|DICER1_ENST00000343455.3_Missense_Mutation_p.D1875N|DICER1_ENST00000393063.1_Missense_Mutation_p.D1875N			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1875	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		ACCTTCCCGTCGTAAGTTCTC	0.423			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.D1875N		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	DICER1	181	.	0			c.G5623A						.						165.0	168.0	167.0					14																	95556981		2203	4300	6503	SO:0001583	missense	23405	exon28	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TCCCGTCGTAAGT	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.5623G>A	chr14.hg19:g.95556981C>T	ENSP00000437256:p.Asp1875Asn	211.0	0.0		326.0	118.0	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	C	33	5.227452	0.95173	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	6.07	6.07	0.98685	Double-stranded RNA-binding (2);	0.095905	0.64402	D	0.000001	T	0.52725	0.1752	.	.	.	0.80722	D	1	B;P	0.48589	0.431;0.912	B;B	0.34138	0.104;0.176	T	0.54403	-0.8299	9	0.34782	T	0.22	-26.5162	20.6593	0.99626	0.0:1.0:0.0:0.0	.	773;1875	B3KRG4;Q9UPY3	.;DICER_HUMAN	N	1875;1875;1875;1875;773	ENSP00000343745:D1875N;ENSP00000437256:D1875N;ENSP00000376783:D1875N;ENSP00000435681:D1875N;ENSP00000451041:D773N	ENSP00000343745:D1875N	D	-	1	0	DICER1	94626734	1.000000	0.71417	0.571000	0.28486	0.931000	0.56810	7.324000	0.79115	2.885000	0.99019	0.655000	0.94253	GAC	.	.		0.423	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
ZNF839	55778	hgsc.bcm.edu	37	14	102798159	102798159	+	Silent	SNP	G	G	A	rs368513189		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:102798159G>A	ENST00000558850.1	+	3	1394	c.1044G>A	c.(1042-1044)tcG>tcA	p.S348S	ZNF839_ENST00000559185.1_Silent_p.S348S|ZNF839_ENST00000442396.2_Silent_p.S464S|ZNF839_ENST00000262236.5_Silent_p.S348S	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	348							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGAGGGCGTCGCCAAGCAAAG	0.567																																					p.S464S		Atlas-SNP	.											ZNF839,NS,carcinoma,0,1	ZNF839	41	.	0			c.G1392A						.	G		1,4027		0,1,2013	26.0	30.0	29.0		1392	-7.6	0.0	14		29	0,8354		0,0,4177	no	coding-synonymous	ZNF839	NM_018335.3		0,1,6190	AA,AG,GG		0.0,0.0248,0.0081		464/928	102798159	1,12381	2014	4177	6191	SO:0001819	synonymous_variant	55778	exon3			GGCGTCGCCAAGC	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1044G>A	chr14.hg19:g.102798159G>A		24.0	0.0		38.0	3.0	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	hg19	CCDS58336.1																																																																																			.	.		0.567	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
CEP170B	283638	hgsc.bcm.edu	37	14	105360106	105360106	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105360106C>T	ENST00000414716.3	+	16	4419	c.4191C>T	c.(4189-4191)ttC>ttT	p.F1397F	CEP170B_ENST00000556508.1_Silent_p.F1362F|CEP170B_ENST00000418279.1_Silent_p.F1327F|CEP170B_ENST00000453495.1_Silent_p.F1433F	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1432						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGGTGATCTTCGATAACCTGA	0.652																																					p.F1397F		Atlas-SNP	.											KIAA0284_ENST00000414716,NS,carcinoma,0,2	.	.	.	0			c.C4191T						.						40.0	43.0	42.0					14																	105360106		2021	4165	6186	SO:0001819	synonymous_variant	283638	exon16			GATCTTCGATAAC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.4191C>T	chr14.hg19:g.105360106C>T		24.0	0.0		45.0	3.0	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	hg19	CCDS45175.1																																																																																			.	.		0.652	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
GPR132	29933	hgsc.bcm.edu	37	14	105517686	105517686	+	Missense_Mutation	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105517686A>T	ENST00000329797.3	-	4	1699	c.788T>A	c.(787-789)cTc>cAc	p.L263H	GPR132_ENST00000539291.2_Missense_Mutation_p.L263H|GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Missense_Mutation_p.L254H	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	263					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GGCTTTGACGAGGAGAACCAG	0.577																																					p.L263H		Atlas-SNP	.											.	GPR132	40	.	0			c.T788A						.						102.0	103.0	103.0					14																	105517686		2203	4300	6503	SO:0001583	missense	29933	exon4			TTGACGAGGAGAA	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"""GPCR / Class A : Orphans"""	17482	protein-coding gene	gene with protein product	"""G2 accumulation"""	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.788T>A	chr14.hg19:g.105517686A>T	ENSP00000328818:p.Leu263His	59.0	0.0		193.0	41.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Missense_Mutation	SNP	ENST00000329797.3	hg19	CCDS9997.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638117	0.67130	.	.	ENSG00000183484	ENST00000329797;ENST00000392585;ENST00000539291	T;T;T	0.47869	0.83;0.83;0.83	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.70404	0.3220	M	0.84219	2.685	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75955	-0.3135	10	0.87932	D	0	.	13.857	0.63534	1.0:0.0:0.0:0.0	.	254;263	B4E144;Q9UNW8	.;GP132_HUMAN	H	263;254;263	ENSP00000328818:L263H;ENSP00000376364:L254H;ENSP00000438094:L263H	ENSP00000328818:L263H	L	-	2	0	GPR132	104588731	1.000000	0.71417	0.412000	0.26496	0.288000	0.27193	9.071000	0.93980	1.865000	0.54081	0.460000	0.39030	CTC	.	.		0.577	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345	
BTBD6	90135	hgsc.bcm.edu	37	14	105716119	105716119	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105716119G>A	ENST00000392554.3	+	4	865	c.568G>A	c.(568-570)Gtc>Atc	p.V190I	BRF1_ENST00000546474.1_Intron|BRF1_ENST00000440513.3_Intron|BTBD6_ENST00000536364.1_Missense_Mutation_p.V190I|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000463376.2_Missense_Mutation_p.V115I|BRF1_ENST00000551787.1_5'Flank|BTBD6_ENST00000327471.3_Missense_Mutation_p.V115I|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000379937.2_Intron			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	190						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		GAACGCCTGCGTCCTGCTGTC	0.592																																					p.V190I		Atlas-SNP	.											.	BTBD6	24	.	0			c.G568A						.						49.0	53.0	51.0					14																	105716119		2202	4300	6502	SO:0001583	missense	90135	exon5			GCCTGCGTCCTGC	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.568G>A	chr14.hg19:g.105716119G>A	ENSP00000376337:p.Val190Ile	50.0	0.0		99.0	31.0	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	hg19	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228519	0.58777	.	.	ENSG00000184887	ENST00000536364;ENST00000537513;ENST00000392554;ENST00000463376;ENST00000327471	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.69;-0.69	4.63	4.63	0.57726	BTB/Kelch-associated (1);	0.000000	0.85682	D	0.000000	T	0.70133	0.3189	L	0.52905	1.665	0.80722	D	1	B	0.31519	0.327	B	0.31245	0.126	T	0.71189	-0.4666	10	0.44086	T	0.13	-44.1425	14.9721	0.71243	0.0:0.0:1.0:0.0	.	190	Q96KE9	BTBD6_HUMAN	I	190;190;190;115;115	ENSP00000443091:V190I;ENSP00000446223:V190I;ENSP00000376337:V190I;ENSP00000418150:V115I;ENSP00000329361:V115I	ENSP00000329361:V115I	V	+	1	0	BTBD6	104787164	1.000000	0.71417	0.985000	0.45067	0.710000	0.40934	6.556000	0.73932	2.102000	0.63906	0.462000	0.41574	GTC	.	.		0.592	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
OCA2	4948	hgsc.bcm.edu	37	15	28230328	28230328	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:28230328G>A	ENST00000354638.3	-	13	1401	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	OCA2_ENST00000353809.5_Missense_Mutation_p.R392W|OCA2_ENST00000382996.2_Missense_Mutation_p.R416W	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	416					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.R416G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CGGGAGAGCCGGTATGCCTGG	0.567									Oculocutaneous Albinism																												p.R416W		Atlas-SNP	.											OCA2,NS,carcinoma,0,1	OCA2	173	.	1	Substitution - Missense(1)	lung(1)	c.C1246T						.						81.0	64.0	70.0					15																	28230328		2203	4300	6503	SO:0001583	missense	4948	exon13	Familial Cancer Database		AGAGCCGGTATGC		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1246C>T	chr15.hg19:g.28230328G>A	ENSP00000346659:p.Arg416Trp	50.0	0.0		40.0	3.0	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	hg19	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184732	0.94885	.	.	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.85556	-2.0;-2.0;-2.0	5.03	3.12	0.35913	Divalent ion symporter (1);	0.347413	0.30850	N	0.008744	D	0.89588	0.6758	M	0.69823	2.125	0.25752	N	0.985042	D;D	0.69078	0.997;0.994	P;P	0.59825	0.864;0.846	D	0.83610	0.0133	10	0.87932	D	0	0.0027	13.4265	0.61028	0.0:0.0:0.7138:0.2862	.	392;416	Q04671-2;Q04671	.;P_HUMAN	W	416;392;416	ENSP00000346659:R416W;ENSP00000261276:R392W;ENSP00000372457:R416W	ENSP00000261276:R392W	R	-	1	2	OCA2	25903923	0.995000	0.38212	0.218000	0.23776	0.738000	0.42128	2.287000	0.43505	0.592000	0.29728	0.561000	0.74099	CGG	.	.		0.567	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
TMEM87A	25963	hgsc.bcm.edu	37	15	42556385	42556385	+	Missense_Mutation	SNP	A	A	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:42556385A>C	ENST00000389834.4	-	4	572	c.308T>G	c.(307-309)tTg>tGg	p.L103W	TMEM87A_ENST00000568432.1_5'UTR|TMEM87A_ENST00000307216.6_Missense_Mutation_p.L103W|TMEM87A_ENST00000448392.1_Missense_Mutation_p.L42W	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	103						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		TTCCAAATACAACTCTACTTC	0.353																																					p.L103W		Atlas-SNP	.											.	TMEM87A	56	.	0			c.T308G						.						123.0	123.0	123.0					15																	42556385		2203	4299	6502	SO:0001583	missense	25963	exon4			AAATACAACTCTA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.308T>G	chr15.hg19:g.42556385A>C	ENSP00000374484:p.Leu103Trp	211.0	0.0		220.0	69.0	NM_001110503	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	A	5.471	0.271964	0.10349	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305;ENST00000307216	.	.	.	5.12	0.727	0.18254	.	1.021790	0.07834	N	0.961879	T	0.14787	0.0357	N	0.08118	0	0.09310	N	1	B;P;P	0.39862	0.139;0.612;0.692	B;B;B	0.38712	0.013;0.062;0.28	T	0.13845	-1.0494	9	0.52906	T	0.07	-0.0032	2.9635	0.05900	0.0888:0.1558:0.4345:0.3208	.	103;42;103	Q8NBN3;Q8NBN3-3;Q8NBN3-2	TM87A_HUMAN;.;.	W	103;42;79;103	.	ENSP00000305894:L103W	L	-	2	0	TMEM87A	40343677	0.004000	0.15560	0.465000	0.27155	0.041000	0.13682	0.013000	0.13310	0.011000	0.14865	-1.075000	0.02238	TTG	.	.		0.353	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497	
ZNF609	23060	hgsc.bcm.edu	37	15	64967011	64967011	+	Missense_Mutation	SNP	T	T	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:64967011T>A	ENST00000326648.3	+	4	2086	c.1958T>A	c.(1957-1959)cTa>cAa	p.L653Q		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	653						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCCAAGAGCCTAAAGTCAGCC	0.473																																					p.L653Q		Atlas-SNP	.											.	ZNF609	106	.	0			c.T1958A						.						59.0	63.0	61.0					15																	64967011		2203	4299	6502	SO:0001583	missense	23060	exon4			AGAGCCTAAAGTC	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"""Zinc fingers, C2H2-type"""	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.1958T>A	chr15.hg19:g.64967011T>A	ENSP00000316527:p.Leu653Gln	90.0	0.0		107.0	5.0	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	hg19	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.017690	0.54576	.	.	ENSG00000180357	ENST00000326648	T	0.51071	0.72	5.79	5.79	0.91817	.	0.279106	0.36519	N	0.002555	T	0.52869	0.1761	L	0.50333	1.59	0.54753	D	0.999988	P	0.45176	0.852	P	0.50896	0.653	T	0.43556	-0.9384	10	0.17832	T	0.49	-9.2984	16.1298	0.81418	0.0:0.0:0.0:1.0	.	653	O15014	ZN609_HUMAN	Q	653	ENSP00000316527:L653Q	ENSP00000316527:L653Q	L	+	2	0	ZNF609	62754064	1.000000	0.71417	0.989000	0.46669	0.978000	0.69477	6.289000	0.72696	2.208000	0.71279	0.482000	0.46254	CTA	.	.		0.473	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833	
TMC3	342125	hgsc.bcm.edu	37	15	81625157	81625157	+	Missense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr15:81625157G>T	ENST00000359440.5	-	22	3041	c.2906C>A	c.(2905-2907)gCt>gAt	p.A969D	RP11-761I4.3_ENST00000560973.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.A970D|RP11-761I4.3_ENST00000559781.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						AAAATGAGGAGCCCGACGGAG	0.562																																					p.A969D		Atlas-SNP	.											.	TMC3	112	.	0			c.C2906A						.						14.0	15.0	14.0					15																	81625157		1832	4072	5904	SO:0001583	missense	342125	exon22			TGAGGAGCCCGAC	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2906C>A	chr15.hg19:g.81625157G>T	ENSP00000352413:p.Ala969Asp	47.0	0.0		72.0	18.0	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	hg19	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.124492	0.37533	.	.	ENSG00000188869	ENST00000359440	T	0.64991	-0.13	5.42	0.139	0.14798	.	1.300320	0.06203	U	0.683653	T	0.53514	0.1801	L	0.54323	1.7	0.09310	N	1	B	0.31125	0.309	B	0.25140	0.058	T	0.47169	-0.9138	10	0.72032	D	0.01	0.0156	5.7645	0.18219	0.1932:0.0:0.5731:0.2337	.	969	Q7Z5M5	TMC3_HUMAN	D	969	ENSP00000352413:A969D	ENSP00000352413:A969D	A	-	2	0	TMC3	79412212	0.044000	0.20184	0.000000	0.03702	0.013000	0.08279	2.217000	0.42880	0.009000	0.14813	0.655000	0.94253	GCT	.	.		0.562	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
RAB40C	57799	hgsc.bcm.edu	37	16	675504	675504	+	Missense_Mutation	SNP	G	G	A	rs141847125		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:675504G>A	ENST00000248139.3	+	4	540	c.337G>A	c.(337-339)Gat>Aat	p.D113N	RAB40C_ENST00000538492.1_Missense_Mutation_p.D113N|RAB40C_ENST00000539661.1_Missense_Mutation_p.D113N|RAB40C_ENST00000535977.1_Missense_Mutation_p.D113N	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	113					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				CAAGGAGATCGATGAGGTAGG	0.642																																					p.D113N	Melanoma(123;1631 1690 28262 44104 44957)	Atlas-SNP	.											RAB40C,NS,carcinoma,0,1	RAB40C	32	.	0			c.G337A						.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4402		0,0,2201	76.0	62.0	67.0		337,337,337,337,337	5.1	0.9	16	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	RAB40C	NM_001172663.1,NM_001172664.1,NM_001172665.1,NM_001172666.1,NM_021168.4	23,23,23,23,23	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	113/282,113/282,113/282,113/263,113/282	675504	1,13001	2201	4300	6501	SO:0001583	missense	57799	exon4			GAGATCGATGAGG	Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"""RAB, member RAS oncogene"""	18285	protein-coding gene	gene with protein product			"""RAS-like, family 8, member C"""	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.337G>A	chr16.hg19:g.675504G>A	ENSP00000248139:p.Asp113Asn	40.0	0.0		40.0	2.0	NM_021168	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Missense_Mutation	SNP	ENST00000248139.3	hg19	CCDS10413.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626602	0.66901	0.0	1.16E-4	ENSG00000197562	ENST00000535977;ENST00000539661;ENST00000538492;ENST00000248139	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	5.06	5.06	0.68205	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	N	0.17631	0.505	0.80722	D	1	P;P	0.35411	0.5;0.5	B;B	0.37198	0.243;0.243	T	0.75622	-0.3254	10	0.59425	D	0.04	.	17.7613	0.88465	0.0:0.0:1.0:0.0	.	113;113	Q96S21;Q5PXE8	RB40C_HUMAN;.	N	113	ENSP00000438492:D113N;ENSP00000445050:D113N;ENSP00000438382:D113N;ENSP00000248139:D113N	ENSP00000248139:D113N	D	+	1	0	RAB40C	615505	1.000000	0.71417	0.936000	0.37596	0.477000	0.33069	9.691000	0.98679	2.507000	0.84556	0.655000	0.94253	GAT	.	G|1.000;A|0.000		0.642	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168	
XYLT1	64131	hgsc.bcm.edu	37	16	17211760	17211760	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:17211760A>G	ENST00000261381.6	-	11	2384	c.2300T>C	c.(2299-2301)gTg>gCg	p.V767A		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	767					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTGCATACCCACCGGCTCATC	0.562																																					p.V767A		Atlas-SNP	.											.	XYLT1	147	.	0			c.T2300C						.						132.0	109.0	117.0					16																	17211760		2197	4300	6497	SO:0001583	missense	64131	exon11			ATACCCACCGGCT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2300T>C	chr16.hg19:g.17211760A>G	ENSP00000261381:p.Val767Ala	154.0	0.0		144.0	7.0	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385672	0.82792	.	.	ENSG00000103489	ENST00000261381	T	0.48522	0.81	5.08	5.08	0.68730	.	0.055804	0.64402	D	0.000001	T	0.62073	0.2398	M	0.62016	1.91	0.58432	D	0.999999	D	0.63046	0.992	P	0.60541	0.876	T	0.64188	-0.6466	10	0.51188	T	0.08	-20.0042	14.3324	0.66566	1.0:0.0:0.0:0.0	.	767	Q86Y38	XYLT1_HUMAN	A	767	ENSP00000261381:V767A	ENSP00000261381:V767A	V	-	2	0	XYLT1	17119261	1.000000	0.71417	0.680000	0.29994	0.911000	0.54048	7.514000	0.81750	2.026000	0.59711	0.379000	0.24179	GTG	.	.		0.562	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
ARHGAP17	55114	hgsc.bcm.edu	37	16	24955110	24955110	+	Missense_Mutation	SNP	C	C	T	rs149340407		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:24955110C>T	ENST00000289968.6	-	15	1384	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N	ARHGAP17_ENST00000303665.5_Missense_Mutation_p.D439N|ARHGAP17_ENST00000441763.2_3'UTR	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	439	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		AAGAACCAGTCGGCATGCTGA	0.413																																					p.D439N		Atlas-SNP	.											ARHGAP17_ENST00000289968,NS,carcinoma,0,2	ARHGAP17	138	.	0			c.G1315A						.						121.0	99.0	107.0					16																	24955110		2197	4300	6497	SO:0001583	missense	55114	exon15			ACCAGTCGGCATG	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"""Rho GTPase activating proteins"""	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.1315G>A	chr16.hg19:g.24955110C>T	ENSP00000289968:p.Asp439Asn	89.0	1.0		74.0	5.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	hg19	CCDS32409.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549485	0.65311	.	.	ENSG00000140750	ENST00000289968;ENST00000303665;ENST00000455311	T;T	0.12879	2.64;2.64	5.91	4.95	0.65309	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.160830	0.29126	N	0.013078	T	0.17959	0.0431	M	0.76727	2.345	0.80722	D	1	B;B	0.28324	0.056;0.207	B;B	0.17433	0.018;0.009	T	0.01805	-1.1270	10	0.66056	D	0.02	.	12.1212	0.53893	0.0:0.9149:0.0:0.0851	.	439;439	Q68EM7-2;Q68EM7	.;RHG17_HUMAN	N	439	ENSP00000289968:D439N;ENSP00000303130:D439N	ENSP00000289968:D439N	D	-	1	0	ARHGAP17	24862611	1.000000	0.71417	0.890000	0.34922	0.871000	0.50021	4.533000	0.60615	1.473000	0.48159	0.655000	0.94253	GAC	.	C|1.000;A|0.000		0.413	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
SULT1A2	6799	hgsc.bcm.edu	37	16	28606943	28606943	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:28606943C>T	ENST00000395630.1	-	3	552	c.202G>A	c.(202-204)Gaa>Aaa	p.E68K	SULT1A2_ENST00000533150.1_Missense_Mutation_p.E68K|SULT1A2_ENST00000335715.4_Missense_Mutation_p.E68K	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	68					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)			NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						TGACACTTTTCCAGGTCACCG	0.587																																					p.E68K		Atlas-SNP	.											.	SULT1A2	27	.	0			c.G202A						.						94.0	86.0	89.0					16																	28606943		2197	4300	6497	SO:0001583	missense	6799	exon3			ACTTTTCCAGGTC	U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	2.8.2.1	"""Sulfotransferases, cytosolic"""	11454	protein-coding gene	gene with protein product		601292		STP2		8661000, 8912648	Standard	NM_001054		Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000395630.1:c.202G>A	chr16.hg19:g.28606943C>T	ENSP00000378992:p.Glu68Lys	99.0	0.0		121.0	47.0	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	hg19	CCDS10636.1	.	.	.	.	.	.	.	.	.	.	c	9.160	1.018388	0.19355	.	.	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630;ENST00000526384	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	4.7	1.52	0.23074	Sulfotransferase domain (1);	0.411184	0.24403	N	0.038833	T	0.72779	0.3503	L	0.47078	1.49	0.19945	N	0.999944	B	0.06786	0.001	B	0.08055	0.003	T	0.61505	-0.7049	10	0.48119	T	0.1	.	4.6656	0.12664	0.0:0.539:0.1788:0.2822	.	68	P50226	ST1A2_HUMAN	K	68	ENSP00000435271:E68K;ENSP00000338742:E68K;ENSP00000378992:E68K;ENSP00000435358:E68K	ENSP00000338742:E68K	E	-	1	0	SULT1A2	28514444	0.006000	0.16342	0.036000	0.18154	0.031000	0.12232	0.366000	0.20365	0.383000	0.24910	0.556000	0.70494	GAA	.	.		0.587	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054	
SPNS1	83985	hgsc.bcm.edu	37	16	28986619	28986619	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:28986619C>T	ENST00000311008.11	+	1	524	c.147C>T	c.(145-147)cgC>cgT	p.R49R	SPNS1_ENST00000565975.1_Silent_p.R94R|SPNS1_ENST00000334536.8_Silent_p.R49R|SPNS1_ENST00000352260.7_Silent_p.R49R|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000323081.8_5'UTR|RP11-264B17.3_ENST00000569969.1_RNA	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	49					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)		p.R49R(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						GGCTGCAGCGCATCACCGGCC	0.677																																					p.R49R		Atlas-SNP	.											SPNS1,NS,carcinoma,0,1	SPNS1	47	.	1	Substitution - coding silent(1)	lung(1)	c.C147T						.						21.0	25.0	24.0					16																	28986619		2196	4299	6495	SO:0001819	synonymous_variant	83985	exon1			GCAGCGCATCACC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.147C>T	chr16.hg19:g.28986619C>T		42.0	0.0		46.0	2.0	NM_001142451	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	hg19	CCDS10646.1																																																																																			.	.		0.677	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
SRCAP	10847	hgsc.bcm.edu	37	16	30750366	30750366	+	Missense_Mutation	SNP	C	C	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:30750366C>G	ENST00000262518.4	+	34	9390	c.9005C>G	c.(9004-9006)cCa>cGa	p.P3002R	SRCAP_ENST00000395059.2_Missense_Mutation_p.P2940R|SRCAP_ENST00000344771.4_Missense_Mutation_p.P2844R|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	3002	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCAACGTCCCCACCCAAACGG	0.597																																					p.P3002R		Atlas-SNP	.											.	SRCAP	298	.	0			c.C9005G						.						149.0	117.0	127.0					16																	30750366		2197	4300	6497	SO:0001583	missense	10847	exon34			CGTCCCCACCCAA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.9005C>G	chr16.hg19:g.30750366C>G	ENSP00000262518:p.Pro3002Arg	54.0	0.0		84.0	6.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	8.005	0.756188	0.15846	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.93488	-3.2;-3.23;-3.22	5.13	5.13	0.70059	.	0.000000	0.49916	D	0.000133	D	0.91546	0.7330	N	0.08118	0	0.28469	N	0.915492	D;D	0.69078	0.997;0.995	D;P	0.65010	0.931;0.854	D	0.87078	0.2164	10	0.87932	D	0	-8.6141	13.9377	0.64034	0.0:1.0:0.0:0.0	.	2940;3002	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	R	3002;2940;2844	ENSP00000262518:P3002R;ENSP00000378499:P2940R;ENSP00000343042:P2844R	ENSP00000262518:P3002R	P	+	2	0	SRCAP	30657867	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.813000	0.69201	2.663000	0.90544	0.563000	0.77884	CCA	.	.		0.597	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
RLTPR	146206	hgsc.bcm.edu	37	16	67686234	67686234	+	Missense_Mutation	SNP	A	A	G	rs144268948|rs374451388	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:67686234A>G	ENST00000334583.6	+	27	3137	c.2809A>G	c.(2809-2811)Aag>Gag	p.K937E	RLTPR_ENST00000545661.1_Missense_Mutation_p.K901E	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	937	Pro-rich.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		ggaagaggagaaggagaaggT	0.557																																					p.K937E		Atlas-SNP	.											.	RLTPR	124	.	0			c.A2809G						.						52.0	55.0	54.0					16																	67686234		1955	4157	6112	SO:0001583	missense	146206	exon27			GAGGAGAAGGAGA	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.2809A>G	chr16.hg19:g.67686234A>G	ENSP00000334958:p.Lys937Glu	15.0	0.0		10.0	4.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	A	0.044	-1.274756	0.01410	.	.	ENSG00000159753	ENST00000334583;ENST00000398282;ENST00000545661	T;T	0.12569	2.67;2.67	3.05	-3.05	0.05396	.	1.639460	0.03537	N	0.223270	T	0.03053	0.0090	N	0.00210	-1.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39623	-0.9605	10	0.17832	T	0.49	-8.7017	8.1769	0.31287	0.6821:0.0:0.3179:0.0	.	901;937	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	E	937;34;901	ENSP00000334958:K937E;ENSP00000441481:K901E	ENSP00000334958:K937E	K	+	1	0	RLTPR	66243735	0.001000	0.12720	0.006000	0.13384	0.033000	0.12548	-0.018000	0.12568	-0.705000	0.05035	-1.280000	0.01385	AAG	.	.		0.557	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
EDC4	23644	hgsc.bcm.edu	37	16	67912905	67912905	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:67912905G>A	ENST00000358933.5	+	12	1572	c.1333G>A	c.(1333-1335)Gcc>Acc	p.A445T	EDC4_ENST00000574770.1_3'UTR|AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	445					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		GGAGGGCCACGCCTGCTTCAG	0.597																																					p.A445T		Atlas-SNP	.											EDC4,colon,carcinoma,0,1	EDC4	101	.	0			c.G1333A						.						69.0	58.0	62.0					16																	67912905		2198	4300	6498	SO:0001583	missense	23644	exon12			GGCCACGCCTGCT	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.1333G>A	chr16.hg19:g.67912905G>A	ENSP00000351811:p.Ala445Thr	31.0	0.0		60.0	3.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601849	0.87055	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	.	.	.	5.53	5.53	0.82687	.	0.050730	0.85682	D	0.000000	T	0.55800	0.1943	L	0.31294	0.92	0.80722	D	1	D;D;D	0.67145	0.996;0.964;0.985	P;B;P	0.50617	0.646;0.359;0.466	T	0.50250	-0.8850	9	0.30854	T	0.27	-18.2934	17.412	0.87488	0.0:0.0:1.0:0.0	.	377;64;445	B7Z7V8;Q6P2E9-2;Q6P2E9	.;.;EDC4_HUMAN	T	445;377	.	ENSP00000351811:A445T	A	+	1	0	EDC4	66470406	1.000000	0.71417	0.979000	0.43373	0.848000	0.48234	9.657000	0.98554	2.882000	0.98803	0.655000	0.94253	GCC	.	.		0.597	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	
CTRL	1506	hgsc.bcm.edu	37	16	67964673	67964673	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:67964673G>A	ENST00000574481.1	-	4	835	c.274C>T	c.(274-276)Cga>Tga	p.R92*	CTRL_ENST00000576408.1_5'UTR	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	92	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		TTTGATGATCGGTCATACTCG	0.637																																					p.R92X		Atlas-SNP	.											.	CTRL	11	.	0			c.C274T						.						64.0	66.0	65.0					16																	67964673		2198	4300	6498	SO:0001587	stop_gained	1506	exon4			ATGATCGGTCATA		CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.274C>T	chr16.hg19:g.67964673G>A	ENSP00000458537:p.Arg92*	86.0	0.0		80.0	4.0	NM_001907		Nonsense_Mutation	SNP	ENST00000574481.1	hg19	CCDS10852.1	.	.	.	.	.	.	.	.	.	.	G	37	6.444316	0.97572	.	.	ENSG00000141086	ENST00000319955	.	.	.	5.42	3.38	0.38709	.	0.328530	0.28476	N	0.015212	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	0.175	8.5848	0.33651	0.0721:0.0:0.6548:0.2731	.	.	.	.	X	92	.	ENSP00000322629:R92X	R	-	1	2	CTRL	66522174	0.992000	0.36948	0.009000	0.14445	0.152000	0.21847	2.609000	0.46317	1.350000	0.45770	0.655000	0.94253	CGA	.	.		0.637	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3		
COG4	25839	hgsc.bcm.edu	37	16	70543864	70543864	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:70543864T>C	ENST00000323786.5	-	6	820	c.799A>G	c.(799-801)Aga>Gga	p.R267G	COG4_ENST00000393612.4_Missense_Mutation_p.R263G	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	263					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				ACTGCAGCTCTCCGATCACTC	0.478																																					p.R267G		Atlas-SNP	.											COG4,colon,carcinoma,0,1	COG4	64	.	0			c.A799G						.						134.0	116.0	122.0					16																	70543864		2198	4300	6498	SO:0001583	missense	25839	exon6			CAGCTCTCCGATC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.799A>G	chr16.hg19:g.70543864T>C	ENSP00000315775:p.Arg267Gly	83.0	0.0		66.0	3.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126204	0.77549	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612	T;T	0.48201	0.84;0.82	5.61	3.25	0.37280	Conserved oligomeric Golgi complex, subunit 4 (2);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	0.994;1.0	D;D	0.79784	0.914;0.993	T	0.70163	-0.4947	10	0.87932	D	0	-12.1058	13.3485	0.60589	0.0:0.0:0.4654:0.5346	.	262;263	Q6PIW8;Q9H9E3	.;COG4_HUMAN	G	267;263;263	ENSP00000315775:R267G;ENSP00000377236:R263G	ENSP00000315775:R267G	R	-	1	2	COG4	69101365	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	2.155000	0.42301	0.361000	0.24292	0.421000	0.28195	AGA	.	.		0.478	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
MON1B	22879	hgsc.bcm.edu	37	16	77227419	77227419	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr16:77227419C>T	ENST00000248248.3	+	3	570	c.220C>T	c.(220-222)Cgg>Tgg	p.R74W	MON1B_ENST00000545553.1_Intron|MON1B_ENST00000439557.2_Intron|MON1B_ENST00000320859.6_Missense_Mutation_p.R74W	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	74										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						AAGCACCTCTCGGCTCTGGAG	0.637																																					p.R74W		Atlas-SNP	.											MON1B,colon,carcinoma,0,1	MON1B	55	.	0			c.C220T						.						55.0	57.0	56.0					16																	77227419		2198	4300	6498	SO:0001583	missense	22879	exon3			ACCTCTCGGCTCT	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"""MON1 homolog B (yeast)"""			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.220C>T	chr16.hg19:g.77227419C>T	ENSP00000248248:p.Arg74Trp	54.0	0.0		44.0	3.0	NM_014940	B4DDZ0|O94949	Missense_Mutation	SNP	ENST00000248248.3	hg19	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.688529	0.29962	.	.	ENSG00000103111	ENST00000248248;ENST00000320859	.	.	.	3.61	1.59	0.23543	.	1.974950	0.02637	N	0.104904	T	0.11452	0.0279	N	0.08118	0	0.20563	N	0.999886	P	0.51537	0.946	B	0.30495	0.116	T	0.25187	-1.0139	9	0.72032	D	0.01	.	6.3215	0.21221	0.1184:0.4881:0.3935:0.0	.	74	Q7L1V2	MON1B_HUMAN	W	74	.	ENSP00000248248:R74W	R	+	1	2	MON1B	75784920	0.035000	0.19736	0.231000	0.23993	0.194000	0.23727	0.899000	0.28417	0.476000	0.27440	0.563000	0.77884	CGG	.	.		0.637	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940	
SENP3	26168	hgsc.bcm.edu	37	17	7470288	7470288	+	Splice_Site	SNP	A	A	G	rs76586164		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:7470288A>G	ENST00000429205.2	+	8	1356	c.1307A>G	c.(1306-1308)aAg>aGg	p.K436R	SENP3_ENST00000321337.7_Splice_Site|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	436	Protease.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TCCGTACCAAAGGGTTATGAT	0.398																																					p.K436R		Atlas-SNP	.											.	SENP3	18	.	0			c.A1307G						.						193.0	199.0	197.0					17																	7470288		989	2111	3100	SO:0001630	splice_region_variant	26168	exon8			TACCAAAGGGTTA	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1306-1A>G	chr17.hg19:g.7470288A>G		178.0	0.0		155.0	14.0	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Missense_Mutation	SNP	ENST00000429205.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.977344|3.977344	0.74360|0.74360	.|.	.|.	ENSG00000161956|ENSG00000161956	ENST00000321337|ENST00000429205	.|T	.|0.28895	.|1.59	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54902	.|0.1887	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	.|D	.|0.69078	.|0.997	.|D	.|0.77004	.|0.989	.|T	.|0.55755	.|-0.8091	.|8	.|0.45353	.|T	.|0.12	.|-15.252	13.941|13.941	0.64054|0.64054	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|436	.|Q9H4L4	.|SENP3_HUMAN	.|R	-1|436	.|ENSP00000403712:K436R	.|ENSP00000403712:K436R	.|K	+|+	.|2	.|0	SENP3|SENP3	7411012|7411012	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.000000|0.000000	0.12993|0.12993	2.179000|2.179000	0.69175|0.69175	0.421000|0.421000	0.28195|0.28195	.|AAG	.	A|0.500;G|0.500		0.398	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Missense_Mutation
TP53	7157	hgsc.bcm.edu	37	17	7578478	7578478	+	Missense_Mutation	SNP	G	G	T	rs137852790|rs137852791		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:7578478G>T	ENST00000269305.4	-	5	641	c.452C>A	c.(451-453)cCc>cAc	p.P151H	TP53_ENST00000455263.2_Missense_Mutation_p.P151H|TP53_ENST00000420246.2_Missense_Mutation_p.P151H|TP53_ENST00000413465.2_Missense_Mutation_p.P151H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.P151H|TP53_ENST00000445888.2_Missense_Mutation_p.P151H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	151	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934874). {ECO:0000269|PubMed:7682763}.|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P151H(31)|p.P151R(9)|p.0?(8)|p.P151L(7)|p.T150fs*16(6)|p.?(5)|p.P58H(2)|p.P19H(2)|p.P151_V173del23(1)|p.P152_P153del(1)|p.P152fs*28(1)|p.T57fs*16(1)|p.P151del(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.P153fs*28(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.P58R(1)|p.Q144_G154del11(1)|p.P19R(1)|p.Q144fs*16(1)|p.P152fs*14(1)|p.P151fs*30(1)|p.T18fs*16(1)|p.T150_P151delTP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCGGGCGGGGGTGTGGAATC	0.607		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.P151H	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,adenocarcinoma,-1,2	TP53	33396	.	90	Substitution - Missense(53)|Deletion - Frameshift(14)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Insertion - Frameshift(2)	lung(17)|large_intestine(13)|ovary(10)|skin(8)|oesophagus(8)|breast(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|central_nervous_system(4)|bone(4)|upper_aerodigestive_tract(3)|soft_tissue(2)|urinary_tract(2)|liver(2)|vulva(1)	c.C452A						.						54.0	55.0	55.0					17																	7578478		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCGGGGGTGTGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.452C>A	chr17.hg19:g.7578478G>T	ENSP00000269305:p.Pro151His	61.0	0.0		68.0	17.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040562	0.55003	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99887	-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53;-7.53	5.59	4.63	0.57726	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110207	0.64402	D	0.000007	D	0.99891	0.9948	M	0.91406	3.205	0.53688	D	0.999972	D;P;D;P;P;P;D	0.89917	0.99;0.807;1.0;0.793;0.948;0.84;1.0	P;P;D;P;P;P;D	0.97110	0.84;0.754;0.995;0.625;0.841;0.868;1.0	D	0.96236	0.9172	10	0.87932	D	0	-14.1156	12.4691	0.55777	0.0812:0.0:0.9188:0.0	.	112;151;151;58;151;151;151	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	151;151;151;151;151;151;140;58;19;58;19;151	ENSP00000410739:P151H;ENSP00000352610:P151H;ENSP00000269305:P151H;ENSP00000398846:P151H;ENSP00000391127:P151H;ENSP00000391478:P151H;ENSP00000425104:P19H;ENSP00000423862:P58H;ENSP00000424104:P151H	ENSP00000269305:P151H	P	-	2	0	TP53	7519203	1.000000	0.71417	0.974000	0.42286	0.058000	0.15608	6.711000	0.74675	1.515000	0.48885	0.655000	0.94253	CCC	.	.		0.607	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
DNAH2	146754	hgsc.bcm.edu	37	17	7674169	7674169	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:7674169A>G	ENST00000572933.1	+	27	5740	c.4280A>G	c.(4279-4281)gAc>gGc	p.D1427G	DNAH2_ENST00000389173.2_Missense_Mutation_p.D1427G			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1427	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AAGGATGTGGACCACTGGGAA	0.502																																					p.D1427G		Atlas-SNP	.											.	DNAH2	498	.	0			c.A4280G						.						176.0	152.0	160.0					17																	7674169		2203	4300	6503	SO:0001583	missense	146754	exon26			ATGTGGACCACTG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.4280A>G	chr17.hg19:g.7674169A>G	ENSP00000458355:p.Asp1427Gly	113.0	0.0		122.0	6.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193466	0.78902	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.61859	0.07	4.84	4.84	0.62591	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.74435	0.3716	M	0.81802	2.56	0.80722	D	1	D	0.63880	0.993	D	0.68621	0.959	T	0.74694	-0.3579	10	0.33940	T	0.23	.	13.8202	0.63315	1.0:0.0:0.0:0.0	.	1427	Q9P225	DYH2_HUMAN	G	1427	ENSP00000373825:D1427G	ENSP00000353818:D1427G	D	+	2	0	DNAH2	7614894	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	6.099000	0.71466	2.151000	0.67156	0.455000	0.32223	GAC	.	.		0.502	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
MYH10	4628	hgsc.bcm.edu	37	17	8480586	8480586	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:8480586A>G	ENST00000269243.4	-	5	739	c.601T>C	c.(601-603)Tca>Cca	p.S201P	MYH10_ENST00000379980.4_Missense_Mutation_p.S201P|MYH10_ENST00000396239.1_Missense_Mutation_p.S201P|MYH10_ENST00000360416.3_Missense_Mutation_p.S201P	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	201	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CCTTTATGTGAAGAAGCAACA	0.343																																					p.S201P		Atlas-SNP	.											.	MYH10	148	.	0			c.T601C						.						114.0	116.0	116.0					17																	8480586		2203	4300	6503	SO:0001583	missense	4628	exon5			TATGTGAAGAAGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.601T>C	chr17.hg19:g.8480586A>G	ENSP00000269243:p.Ser201Pro	89.0	0.0		87.0	4.0	NM_005964	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.842738	0.91197	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.01	5.01	0.66863	Myosin head, motor domain (2);	0.060192	0.64402	D	0.000002	D	0.93164	0.7823	M	0.75085	2.285	0.80722	D	1	P;D;B	0.53312	0.595;0.959;0.452	P;P;P	0.61397	0.868;0.888;0.778	D	0.93742	0.7051	10	0.62326	D	0.03	.	14.8427	0.70237	1.0:0.0:0.0:0.0	.	201;201;201	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	P	201	ENSP00000269243:S201P;ENSP00000353590:S201P;ENSP00000379539:S201P;ENSP00000369315:S201P	ENSP00000269243:S201P	S	-	1	0	MYH10	8421311	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.776000	0.91776	2.223000	0.72356	0.533000	0.62120	TCA	.	.		0.343	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
KIAA0100	9703	hgsc.bcm.edu	37	17	26961982	26961982	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:26961982C>A	ENST00000528896.2	-	16	2697	c.2623G>T	c.(2623-2625)Gag>Tag	p.E875*	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Nonsense_Mutation_p.E732*|RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Nonsense_Mutation_p.E732*	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	875						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GAGAAGTGCTCAACCTTTAAG	0.473																																					p.E875X		Atlas-SNP	.											KIAA0100,right_upper_lobe,carcinoma,0,1	KIAA0100	175	.	0			c.G2623T						.						162.0	180.0	174.0					17																	26961982		2203	4300	6503	SO:0001587	stop_gained	9703	exon16			AGTGCTCAACCTT	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2623G>T	chr17.hg19:g.26961982C>A	ENSP00000436773:p.Glu875*	71.0	1.0		89.0	4.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Nonsense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	c	40	8.404047	0.98796	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	.	.	.	5.89	4.92	0.64577	.	0.474372	0.25427	N	0.030748	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0105	0.47659	0.0:0.1154:0.6419:0.2427	.	.	.	.	X	875;845;875;732	.	ENSP00000005905:E875X	E	-	1	0	KIAA0100	23986109	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.798000	0.38814	1.509000	0.48786	-0.234000	0.12200	GAG	.	.		0.473	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
NSRP1	84081	hgsc.bcm.edu	37	17	28499575	28499575	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:28499575A>G	ENST00000247026.5	+	3	193	c.130A>G	c.(130-132)Agc>Ggc	p.S44G	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	44					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						TGTGAGTGAAAGCCTTCAGAG	0.393																																					p.S44G		Atlas-SNP	.											.	NSRP1	49	.	0			c.A130G						.						60.0	58.0	59.0					17																	28499575		2203	4300	6503	SO:0001583	missense	84081	exon3			AGTGAAAGCCTTC	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"""coiled-coil domain containing 55"""	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.130A>G	chr17.hg19:g.28499575A>G	ENSP00000247026:p.Ser44Gly	65.0	0.0		96.0	4.0	NM_032141	Q6FI71	Missense_Mutation	SNP	ENST00000247026.5	hg19	CCDS11255.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.039002	0.93630	.	.	ENSG00000126653	ENST00000247026	T	0.51325	0.71	5.73	5.73	0.89815	.	0.038368	0.85682	D	0.000000	T	0.65312	0.2679	M	0.77616	2.38	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.65010	-0.6272	10	0.33141	T	0.24	-10.367	15.1352	0.72558	1.0:0.0:0.0:0.0	.	44	Q9H0G5	NSRP1_HUMAN	G	44	ENSP00000247026:S44G	ENSP00000247026:S44G	S	+	1	0	NSRP1	25523701	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.683000	0.68189	2.308000	0.77769	0.533000	0.62120	AGC	.	.		0.393	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141	
MYO19	80179	hgsc.bcm.edu	37	17	34856750	34856750	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:34856750C>T	ENST00000431794.3	-	23	2819	c.2297G>A	c.(2296-2298)cGc>cAc	p.R766H	MYO19_ENST00000268852.9_Missense_Mutation_p.R566H	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	766	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CTGGATGCAGCGGGCACACTG	0.672																																					p.R766H		Atlas-SNP	.											MYO19_ENST00000431794,NS,carcinoma,0,2	MYO19	130	.	0			c.G2297A						.						18.0	21.0	20.0					17																	34856750		2138	4243	6381	SO:0001583	missense	80179	exon24			ATGCAGCGGGCAC	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.2297G>A	chr17.hg19:g.34856750C>T	ENSP00000409936:p.Arg766His	67.0	1.0		44.0	2.0	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	hg19	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.684872	0.29872	.	.	ENSG00000141140	ENST00000431794;ENST00000268852	T;T	0.71579	-0.58;-0.58	5.12	3.09	0.35607	.	0.000000	0.38897	N	0.001535	T	0.52597	0.1744	L	0.38838	1.175	0.80722	D	1	B;B	0.27700	0.186;0.03	B;B	0.12837	0.008;0.004	T	0.51980	-0.8636	10	0.46703	T	0.11	.	4.3091	0.10962	0.1823:0.6288:0.0:0.1889	.	766;566	Q96H55;Q96H55-4	MYO19_HUMAN;.	H	766;566	ENSP00000409936:R766H;ENSP00000268852:R566H	ENSP00000268852:R566H	R	-	2	0	MYO19	31930863	0.999000	0.42202	1.000000	0.80357	0.949000	0.60115	0.752000	0.26362	1.267000	0.44247	0.462000	0.41574	CGC	.	.		0.672	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
CACNB1	782	hgsc.bcm.edu	37	17	37341067	37341067	+	Silent	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:37341067G>T	ENST00000394303.3	-	8	906	c.699C>A	c.(697-699)atC>atA	p.I233I	CACNB1_ENST00000582877.1_5'Flank|CACNB1_ENST00000394310.3_Silent_p.I233I|CACNB1_ENST00000344140.5_Silent_p.I278I	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	233					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GTCCCACCAGGATGATGGGCC	0.592																																					p.I278I	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.C834A						.						57.0	50.0	52.0					17																	37341067		2203	4300	6503	SO:0001819	synonymous_variant	782	exon8			CACCAGGATGATG		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"""Calcium channel subunits"""	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.699C>A	chr17.hg19:g.37341067G>T		89.0	0.0		131.0	23.0	NM_199247	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Silent	SNP	ENST00000394303.3	hg19	CCDS42311.1																																																																																			.	.		0.592	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3		
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39459053	39459053	+	Silent	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:39459053G>A	ENST00000391353.1	-	1	50	c.51C>T	c.(49-51)ccC>ccT	p.P17P		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	17	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											TGGTGATGGTGGGCACAGCTG	0.522																																					p.P17P		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.C51T						.																																			SO:0001819	synonymous_variant	100533177	exon1			GATGGTGGGCACA		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.51C>T	chr17.hg19:g.39459053G>A		57.0	0.0		58.0	13.0	NM_001257309		Silent	SNP	ENST00000391353.1	hg19																																																																																				.	.		0.522	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
KANSL1	284058	hgsc.bcm.edu	37	17	44249469	44249469	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:44249469T>C	ENST00000262419.6	-	2	511	c.41A>G	c.(40-42)gAa>gGa	p.E14G	KANSL1_ENST00000574590.1_Missense_Mutation_p.E14G|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000575318.1_Missense_Mutation_p.E14G|KANSL1_ENST00000572904.1_Missense_Mutation_p.E14G|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000432791.1_Missense_Mutation_p.E14G	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	14					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											ATGGTGTGCTTCAGCTGCTGC	0.597																																					p.E14G		Atlas-SNP	.											KIAA1267,NS,neuroblastoma,0,1	.	.	.	0			c.A41G						.						59.0	70.0	66.0					17																	44249469		2203	4300	6503	SO:0001583	missense	284058	exon2			TGTGCTTCAGCTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.41A>G	chr17.hg19:g.44249469T>C	ENSP00000262419:p.Glu14Gly	32.0	1.0		65.0	3.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.219184	0.58560	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.19938	2.11;2.11	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72075	0.976;0.976	T	0.09707	-1.0662	10	0.72032	D	0.01	-12.3283	15.3292	0.74193	0.0:0.0:0.0:1.0	.	14;14	C9JHY2;Q7Z3B3	.;K1267_HUMAN	G	14	ENSP00000262419:E14G;ENSP00000387393:E14G	ENSP00000262419:E14G	E	-	2	0	KIAA1267	41605246	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.484000	0.81180	2.291000	0.77112	0.533000	0.62120	GAA	.	.		0.597	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
CDC27	996	hgsc.bcm.edu	37	17	45232068	45232068	+	Silent	SNP	A	A	G	rs74710570		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:45232068A>G	ENST00000066544.3	-	8	1020	c.927T>C	c.(925-927)gaT>gaC	p.D309D	CDC27_ENST00000531206.1_Silent_p.D309D|CDC27_ENST00000446365.2_Silent_p.D248D|CDC27_ENST00000527547.1_Silent_p.D309D|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	309					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|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 K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TGGATGGCACATCAATTACAG	0.373																																					p.D309D		Atlas-SNP	.											.	CDC27	337	.	0			c.T927C						.						49.0	49.0	49.0					17																	45232068		2203	4300	6503	SO:0001819	synonymous_variant	996	exon8			TGGCACATCAATT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.927T>C	chr17.hg19:g.45232068A>G		50.0	0.0		101.0	5.0	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.373	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
LRRC46	90506	hgsc.bcm.edu	37	17	45914305	45914305	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:45914305C>T	ENST00000269025.4	+	8	1148	c.785C>T	c.(784-786)cCt>cTt	p.P262L		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	262										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GAGACAGTCCCTGAGGCCGTC	0.647																																					p.P262L		Atlas-SNP	.											.	LRRC46	25	.	0			c.C785T						.						80.0	85.0	83.0					17																	45914305		2203	4300	6503	SO:0001583	missense	90506	exon8			CAGTCCCTGAGGC		CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.785C>T	chr17.hg19:g.45914305C>T	ENSP00000269025:p.Pro262Leu	86.0	0.0		114.0	6.0	NM_033413	A8K9Q0	Missense_Mutation	SNP	ENST00000269025.4	hg19	CCDS11518.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299764	0.40694	.	.	ENSG00000141294	ENST00000269025	T	0.74526	-0.85	4.98	2.97	0.34412	.	0.462400	0.18525	N	0.138655	T	0.68201	0.2975	M	0.68317	2.08	0.09310	N	1	B;B	0.30068	0.267;0.267	B;B	0.28139	0.086;0.086	T	0.63107	-0.6711	10	0.87932	D	0	-2.1674	6.3328	0.21279	0.1825:0.7229:0.0:0.0946	.	262;262	A8K9Q0;Q96FV0	.;LRC46_HUMAN	L	262	ENSP00000269025:P262L	ENSP00000269025:P262L	P	+	2	0	LRRC46	43269304	0.001000	0.12720	0.001000	0.08648	0.151000	0.21798	0.347000	0.20014	0.617000	0.30160	0.551000	0.68910	CCT	.	.		0.647	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413	
EME1	146956	hgsc.bcm.edu	37	17	48452982	48452982	+	Missense_Mutation	SNP	C	C	A	rs75511911		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:48452982C>A	ENST00000338165.4	+	2	495	c.413C>A	c.(412-414)cCc>cAc	p.P138H	EME1_ENST00000393271.2_Missense_Mutation_p.P138H|MRPL27_ENST00000442592.3_5'Flank|MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.P138H|MRPL27_ENST00000503633.1_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	138					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TGGAAAAAGCCCTTTCCAAAG	0.483								Direct reversal of damage;Homologous recombination																													p.P138H		Atlas-SNP	.											.	EME1	39	.	0			c.C413A						.						77.0	81.0	80.0					17																	48452982		2203	4300	6503	SO:0001583	missense	146956	exon2			AAAAGCCCTTTCC	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.413C>A	chr17.hg19:g.48452982C>A	ENSP00000339897:p.Pro138His	129.0	0.0		172.0	8.0	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	hg19	CCDS11565.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754870	0.49362	.	.	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.13778	2.56;2.56;2.56	4.57	4.57	0.56435	.	0.717920	0.12531	N	0.460753	T	0.20861	0.0502	L	0.32530	0.975	0.58432	D	0.999999	D;D	0.71674	0.998;0.997	P;P	0.61592	0.891;0.781	T	0.01232	-1.1411	10	0.51188	T	0.08	-33.761	7.0041	0.24826	0.0:0.845:0.0:0.155	.	138;138	Q96AY2-2;Q96AY2	.;EME1_HUMAN	H	138	ENSP00000339897:P138H;ENSP00000376952:P138H;ENSP00000421700:P138H	ENSP00000339897:P138H	P	+	2	0	EME1	45807981	0.000000	0.05858	0.621000	0.29145	0.790000	0.44656	0.319000	0.19522	2.357000	0.79964	0.650000	0.86243	CCC	.	.		0.483	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48603556	48603556	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:48603556C>T	ENST00000323776.5	+	14	2388	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	MYCBPAP_ENST00000436259.2_Silent_p.S705S	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ATGTGGACAGCACCAAGAGCC	0.602																																					p.S742S		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2226T						.						90.0	94.0	92.0					17																	48603556		2203	4300	6503	SO:0001819	synonymous_variant	84073	exon14			GGACAGCACCAAG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.2226C>T	chr17.hg19:g.48603556C>T		55.0	0.0		65.0	22.0	NM_032133		Silent	SNP	ENST00000323776.5	hg19	CCDS32680.2																																																																																			.	.		0.602	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
SCN4A	6329	hgsc.bcm.edu	37	17	62045610	62045610	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:62045610T>C	ENST00000435607.1	-	6	885	c.809A>G	c.(808-810)cAg>cGg	p.Q270R	SCN4A_ENST00000578147.1_Missense_Mutation_p.Q270R	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	270			Q -> K (in PMC). {ECO:0000269|PubMed:16786525, ECO:0000269|PubMed:18166706}.		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGAAGAGCTGCAGTCCTAC	0.567																																					p.Q270R		Atlas-SNP	.											.	SCN4A	205	.	0			c.A809G						.						120.0	125.0	123.0					17																	62045610		2173	4286	6459	SO:0001583	missense	6329	exon6			AAGAGCTGCAGTC	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.809A>G	chr17.hg19:g.62045610T>C	ENSP00000396320:p.Gln270Arg	143.0	0.0		186.0	8.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.887691	0.91814	.	.	ENSG00000007314	ENST00000435607	D	0.98978	-5.29	5.21	5.21	0.72293	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99527	0.9831	H	0.96805	3.885	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.98032	1.0377	10	0.87932	D	0	.	14.4261	0.67218	0.0:0.0:0.0:1.0	.	270	P35499	SCN4A_HUMAN	R	270	ENSP00000396320:Q270R	ENSP00000396320:Q270R	Q	-	2	0	SCN4A	59399342	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	2.194000	0.70268	0.533000	0.62120	CAG	.	.		0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ARSG	22901	hgsc.bcm.edu	37	17	66352820	66352820	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:66352820A>G	ENST00000448504.2	+	6	1375	c.579A>G	c.(577-579)agA>agG	p.R193R	ARSG_ENST00000452479.2_Silent_p.R29R|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	193					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACCTTCAAAGAGACTGTTACA	0.458																																					p.R193R		Atlas-SNP	.											.	ARSG	55	.	0			c.A579G						.						94.0	76.0	82.0					17																	66352820		2203	4300	6503	SO:0001819	synonymous_variant	22901	exon6			TCAAAGAGACTGT	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.579A>G	chr17.hg19:g.66352820A>G		81.0	0.0		111.0	5.0	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	hg19	CCDS11676.1																																																																																			.	.		0.458	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
FAM20A	54757	hgsc.bcm.edu	37	17	66538299	66538299	+	Silent	SNP	G	G	A	rs367996001		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:66538299G>A	ENST00000592554.1	-	7	1658	c.936C>T	c.(934-936)aaC>aaT	p.N312N	FAM20A_ENST00000226094.5_5'UTR|AC079210.1_ENST00000600820.1_5'Flank|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	312					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					AGAAGCACACGTTGCTCGCTG	0.577																																					p.N312N		Atlas-SNP	.											FAM20A,NS,carcinoma,0,1	FAM20A	35	.	0			c.C936T						.	G		1,4405	2.1+/-5.4	0,1,2202	89.0	72.0	77.0		936	5.1	1.0	17		77	0,8600		0,0,4300	no	coding-synonymous	FAM20A	NM_017565.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		312/542	66538299	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	54757	exon7			GCACACGTTGCTC	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.936C>T	chr17.hg19:g.66538299G>A		37.0	0.0		48.0	2.0	NM_017565	B2RN47|B2RN49|Q9UF95	Silent	SNP	ENST00000592554.1	hg19	CCDS11679.1																																																																																			.	.		0.577	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
ABCA10	10349	hgsc.bcm.edu	37	17	67190119	67190119	+	Missense_Mutation	SNP	T	T	A	rs140723420|rs111599831|rs79987301	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:67190119T>A	ENST00000269081.4	-	14	2266	c.1357A>T	c.(1357-1359)Att>Ttt	p.I453F	ABCA10_ENST00000416101.2_Intron	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	453	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GTATTATAAATAGTGGCTGAT	0.289																																					p.I453F		Atlas-SNP	.											.,1	ABCA10	209	.	0			c.A1357T						.						37.0	58.0	52.0					17																	67190119		1986	4296	6282	SO:0001583	missense	10349	exon14			TATAAATAGTGGC	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"""ATP binding cassette transporters / subfamily A"""	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.1357A>T	chr17.hg19:g.67190119T>A	ENSP00000269081:p.Ile453Phe	0.0	0.0		18.0	9.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484425	0.84854	.	.	ENSG00000154263	ENST00000269081	D	0.94417	-3.42	3.71	3.71	0.42584	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.32655	U	0.005806	D	0.92619	0.7655	L	0.52011	1.625	0.80722	D	1	P;P	0.46859	0.885;0.884	P;P	0.48141	0.464;0.568	D	0.91756	0.5416	10	0.66056	D	0.02	.	7.5133	0.27585	0.0:0.099:0.0:0.901	.	453;453	E5RFN6;Q8WWZ4	.;ABCAA_HUMAN	F	453	ENSP00000269081:I453F	ENSP00000269081:I453F	I	-	1	0	ABCA10	64701714	0.987000	0.35691	0.043000	0.18650	0.903000	0.53119	2.098000	0.41757	1.531000	0.49152	0.455000	0.32223	ATT	.	.		0.289	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	
KIF19	124602	hgsc.bcm.edu	37	17	72348385	72348385	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:72348385T>C	ENST00000389916.4	+	14	2024	c.1886T>C	c.(1885-1887)cTg>cCg	p.L629P	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	629					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CCGCAGCGCCTGGAAGAGCTC	0.697																																					p.L629P		Atlas-SNP	.											.	KIF19	102	.	0			c.T1886C						.						28.0	34.0	32.0					17																	72348385		1940	4131	6071	SO:0001583	missense	124602	exon14			AGCGCCTGGAAGA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.1886T>C	chr17.hg19:g.72348385T>C	ENSP00000374566:p.Leu629Pro	76.0	0.0		51.0	4.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.990669	0.74589	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.78364	-1.17;-1.13	5.23	5.23	0.72850	.	.	.	.	.	D	0.86381	0.5919	M	0.70595	2.14	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.74023	0.911;0.982	D	0.87031	0.2135	9	0.51188	T	0.08	.	14.1488	0.65367	0.0:0.0:0.0:1.0	.	629;587	Q2TAC6;F8VW50	KIF19_HUMAN;.	P	587;629	ENSP00000449134:L587P;ENSP00000374566:L629P	ENSP00000374566:L629P	L	+	2	0	KIF19	69859980	1.000000	0.71417	0.621000	0.29145	0.509000	0.34042	4.289000	0.59013	1.988000	0.58038	0.374000	0.22700	CTG	.	.		0.697	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
FBF1	85302	hgsc.bcm.edu	37	17	73915902	73915902	+	Missense_Mutation	SNP	C	C	T	rs374900201		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:73915902C>T	ENST00000586717.1	-	19	2216	c.1943G>A	c.(1942-1944)cGg>cAg	p.R648Q	FBF1_ENST00000319129.5_Missense_Mutation_p.R647Q|FBF1_ENST00000389570.4_Missense_Mutation_p.R648Q			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	648					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						GTTCTCTCTCCGGAGCCGCTC	0.632																																					p.R647Q		Atlas-SNP	.											.	FBF1	48	.	0			c.G1940A						.	C	GLN/ARG	0,4058		0,0,2029	89.0	90.0	90.0		1940	1.6	1.0	17		90	1,8359		0,1,4179	no	missense	FBF1	NM_001080542.1	43	0,1,6208	TT,TC,CC		0.012,0.0,0.0081	benign	647/1134	73915902	1,12417	2029	4180	6209	SO:0001583	missense	85302	exon19			TCTCTCCGGAGCC	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1943G>A	chr17.hg19:g.73915902C>T	ENSP00000465132:p.Arg648Gln	74.0	0.0		86.0	4.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.74	2.624379	0.46840	0.0	1.2E-4	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.18810	2.2;2.19	5.15	1.61	0.23674	.	.	.	.	.	T	0.11024	0.0269	N	0.25789	0.76	0.41875	D	0.990293	P;P;B	0.45283	0.855;0.541;0.341	B;B;B	0.34489	0.184;0.064;0.048	T	0.20405	-1.0276	9	0.21014	T	0.42	-19.3766	10.6484	0.45634	0.0:0.6896:0.0:0.3104	.	662;648;647	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	Q	648;648;647;661	ENSP00000374221:R648Q;ENSP00000324292:R647Q	ENSP00000324292:R647Q	R	-	2	0	FBF1	71427497	0.113000	0.22115	0.994000	0.49952	0.750000	0.42670	0.833000	0.27504	0.589000	0.29677	-0.126000	0.14955	CGG	.	.		0.632	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
TEN1	100134934	hgsc.bcm.edu	37	17	73996268	73996268	+	Silent	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:73996268G>T	ENST00000397640.1	+	4	595	c.297G>T	c.(295-297)ggG>ggT	p.G99G	TEN1_ENST00000416485.1_Silent_p.G98G|CDK3_ENST00000425876.2_5'Flank|CDK3_ENST00000448471.1_5'Flank|TEN1_ENST00000588202.1_3'UTR|TEN1-CDK3_ENST00000567351.1_RNA	NM_001113324.2	NP_001106795.2	Q86WV5	TEN1L_HUMAN	TEN1 CST complex subunit	99						nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			breast(1)	1						GTGTGGAGGGGATGAACCTGC	0.612																																					p.G99G		Atlas-SNP	.											.	TEN1	4	.	0			c.G297T						.						72.0	69.0	70.0					17																	73996268		692	1591	2283	SO:0001819	synonymous_variant	100134934	exon4			GGAGGGGATGAAC		CCDS45780.1, CCDS45780.2	17q25.1	2013-05-23	2013-05-23	2011-06-14	ENSG00000257949	ENSG00000257949			37242	protein-coding gene	gene with protein product		613130	"""chromosome 17 open reading frame 106"", ""TEN1 telomerase capping complex subunit homolog (S. cerevisiae)"""	C17orf106		19854130	Standard	NM_001113324		Approved	FLJ39785		Q86WV5	OTTHUMG00000132686	ENST00000397640.1:c.297G>T	chr17.hg19:g.73996268G>T		46.0	0.0		67.0	18.0	NM_001113324	I3L0C7	Silent	SNP	ENST00000397640.1	hg19	CCDS45780.2																																																																																			.	.		0.612	TEN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255983.1	NM_001113324	
ENPP7	339221	hgsc.bcm.edu	37	17	77704969	77704969	+	Missense_Mutation	SNP	C	C	T	rs193920826		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:77704969C>T	ENST00000328313.5	+	1	289	c.68C>T	c.(67-69)cCg>cTg	p.P23L		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GCCGGAGCACCGGTACAAAGT	0.652																																					p.P23L		Atlas-SNP	.											ENPP7,NS,adenoma,0,1	ENPP7	63	.	0			c.C68T						.						28.0	27.0	27.0					17																	77704969		2202	4299	6501	SO:0001583	missense	339221	exon1			GAGCACCGGTACA	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.68C>T	chr17.hg19:g.77704969C>T	ENSP00000332656:p.Pro23Leu	45.0	0.0		42.0	3.0	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	hg19	CCDS11763.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.742901	0.49151	.	.	ENSG00000182156	ENST00000328313	T	0.74737	-0.87	4.59	4.59	0.56863	Alkaline-phosphatase-like, core domain (1);	1.015840	0.07879	N	0.969273	T	0.55386	0.1917	N	0.08118	0	0.58432	D	0.999996	B	0.29955	0.263	B	0.17979	0.02	T	0.50725	-0.8794	10	0.54805	T	0.06	-28.7668	10.2818	0.43543	0.0:0.9057:0.0:0.0943	.	23	Q6UWV6	ENPP7_HUMAN	L	23	ENSP00000332656:P23L	ENSP00000332656:P23L	P	+	2	0	ENPP7	75319564	1.000000	0.71417	0.020000	0.16555	0.003000	0.03518	6.679000	0.74513	2.372000	0.80975	0.561000	0.74099	CCG	.	.		0.652	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80972391	80972391	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr17:80972391T>C	ENST00000320865.3	-	5	360	c.347A>G	c.(346-348)gAc>gGc	p.D116G	B3GNTL1_ENST00000576599.1_5'UTR|B3GNTL1_ENST00000571954.1_5'UTR	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	116							transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			CATCATGACGTCATCCTGCAG	0.512																																					p.D116G		Atlas-SNP	.											.	B3GNTL1	40	.	0			c.A347G						.						128.0	99.0	109.0					17																	80972391		2203	4300	6503	SO:0001583	missense	146712	exon5			ATGACGTCATCCT	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"""Glycosyltransferase family 2 domain containing"""	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.347A>G	chr17.hg19:g.80972391T>C	ENSP00000319979:p.Asp116Gly	73.0	0.0		118.0	5.0	NM_001009905	Q6GV30|Q8WUT3	Missense_Mutation	SNP	ENST00000320865.3	hg19	CCDS32778.1	.	.	.	.	.	.	.	.	.	.	t	13.66	2.304449	0.40795	.	.	ENSG00000175711	ENST00000320865	T	0.65549	-0.16	4.15	4.15	0.48705	Glycosyl transferase, family 2 (1);	0.000000	0.85682	U	0.000000	D	0.83986	0.5373	H	0.96691	3.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87366	0.2347	9	.	.	.	-27.4857	9.8082	0.40805	0.0:0.0:0.0:1.0	.	116	Q67FW5	B3GNL_HUMAN	G	116	ENSP00000319979:D116G	.	D	-	2	0	B3GNTL1	78565680	1.000000	0.71417	0.995000	0.50966	0.039000	0.13416	3.229000	0.51278	1.899000	0.54978	0.362000	0.22060	GAC	.	.		0.512	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
PTPRM	5797	hgsc.bcm.edu	37	18	8384641	8384641	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:8384641A>G	ENST00000332175.8	+	28	4999	c.3962A>G	c.(3961-3963)gAg>gGg	p.E1321G	PTPRM_ENST00000580170.1_Missense_Mutation_p.E1334G|PTPRM_ENST00000400053.4_Missense_Mutation_p.E1259G|PTPRM_ENST00000444013.1_Missense_Mutation_p.E1108G|PTPRM_ENST00000400060.4_Missense_Mutation_p.E1335G	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1321	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GACCTGGAAGAGGACATCATC	0.463																																					p.E1334G		Atlas-SNP	.											.	PTPRM	185	.	0			c.A4001G						.						146.0	127.0	133.0					18																	8384641		2203	4300	6503	SO:0001583	missense	5797	exon30			TGGAAGAGGACAT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3962A>G	chr18.hg19:g.8384641A>G	ENSP00000331418:p.Glu1321Gly	94.0	0.0		128.0	6.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.164727	0.57476	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	5.41	5.41	0.78517	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.87943	0.6305	L	0.33293	1	0.58432	D	0.999999	P;B;D	0.69078	0.947;0.006;0.997	P;B;D	0.79108	0.88;0.004;0.992	D	0.87183	0.2229	10	0.35671	T	0.21	.	15.4745	0.75468	1.0:0.0:0.0:0.0	.	1108;1334;1321	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	G	1321;1335;1259;1108	ENSP00000331418:E1321G;ENSP00000382933:E1335G;ENSP00000382927:E1259G;ENSP00000387608:E1108G	ENSP00000331418:E1321G	E	+	2	0	PTPRM	8374641	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.281000	0.72632	2.049000	0.60858	0.372000	0.22366	GAG	.	.		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
MTCL1	23255	hgsc.bcm.edu	37	18	8813094	8813094	+	Missense_Mutation	SNP	G	G	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:8813094G>C	ENST00000306329.11	+	10	3679	c.3679G>C	c.(3679-3681)Gtc>Ctc	p.V1227L	SOGA2_ENST00000359865.3_Missense_Mutation_p.V908L|SOGA2_ENST00000518815.1_Missense_Mutation_p.V261L|SOGA2_ENST00000306285.7_Missense_Mutation_p.V261L|SOGA2_ENST00000400050.3_Missense_Mutation_p.V867L|SOGA2_ENST00000517570.1_Missense_Mutation_p.V867L																							TCACAGCCTGGTCATGGACCT	0.587																																					p.V908L		Atlas-SNP	.											.	.	.	.	0			c.G2722C						.						53.0	50.0	51.0					18																	8813094		2203	4300	6503	SO:0001583	missense	23255	exon12			AGCCTGGTCATGG																												ENST00000306329.11:c.3679G>C	chr18.hg19:g.8813094G>C	ENSP00000305027:p.Val1227Leu	135.0	0.0		156.0	14.0	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.56|18.56	3.650848|3.650848	0.67472|0.67472	.|.	.|.	ENSG00000168502|ENSG00000168502	ENST00000519823|ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	.|T;T;T;T	.|0.36340	.|2.36;2.35;2.36;1.26	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.000000	.|0.43579	.|D	.|0.000549	T|T	0.38374|0.38374	0.1038|0.1038	M|M	0.77103|0.77103	2.36|2.36	0.31616|0.31616	N|N	0.6509|0.6509	.|B;B	.|0.31077	.|0.307;0.259	.|B;B	.|0.22753	.|0.031;0.041	T|T	0.53613|0.53613	-0.8414|-0.8414	5|10	.|0.54805	.|T	.|0.06	-25.4183|-25.4183	12.7885|12.7885	0.57520|0.57520	0.0787:0.0:0.9213:0.0|0.0787:0.0:0.9213:0.0	.|.	.|1218;908	.|Q9Y4B5;Q9Y4B5-3	.|CC165_HUMAN;.	A|L	41|929;867;908;867;261	.|ENSP00000429556:V867L;ENSP00000352927:V908L;ENSP00000382924:V867L;ENSP00000303670:V261L	.|ENSP00000303670:V261L	G|V	+|+	2|1	0|0	CCDC165|CCDC165	8803094|8803094	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.757000|4.757000	0.62213|0.62213	2.586000|2.586000	0.87340|0.87340	0.462000|0.462000	0.41574|0.41574	GGT|GTC	.	.		0.587	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
FHOD3	80206	hgsc.bcm.edu	37	18	34298575	34298575	+	Missense_Mutation	SNP	G	G	A	rs369061380		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:34298575G>A	ENST00000359247.4	+	15	2738	c.2738G>A	c.(2737-2739)cGc>cAc	p.R913H	FHOD3_ENST00000592128.1_De_novo_Start_OutOfFrame|FHOD3_ENST00000590592.1_Missense_Mutation_p.R1105H|FHOD3_ENST00000257209.4_Missense_Mutation_p.R930H|FHOD3_ENST00000591635.1_Missense_Mutation_p.R126H|FHOD3_ENST00000445677.1_Missense_Mutation_p.R892H	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	913	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				AACAACCGACGCTGCAGAGAA	0.473																																					p.R930H		Atlas-SNP	.											FHOD3,colon,carcinoma,0,1	FHOD3	210	.	0			c.G2789A						.	G	HIS/ARG	0,4406		0,0,2203	130.0	133.0	132.0		2789	4.5	1.0	18		132	1,8599	1.2+/-3.3	0,1,4299	no	missense	FHOD3	NM_025135.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	930/1440	34298575	1,13005	2203	4300	6503	SO:0001583	missense	80206	exon16			ACCGACGCTGCAG	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.2738G>A	chr18.hg19:g.34298575G>A	ENSP00000352186:p.Arg913His	68.0	0.0		67.0	3.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	G	9.057	0.993585	0.19043	0.0	1.16E-4	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.32988	1.44;1.43;1.44	4.46	4.46	0.54185	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.188903	0.48286	D	0.000198	T	0.44393	0.1291	L	0.56769	1.78	0.46241	D	0.99894	D;D;B	0.60575	0.985;0.988;0.063	P;P;B	0.54499	0.71;0.754;0.013	T	0.44467	-0.9326	10	0.52906	T	0.07	.	15.6858	0.77409	0.0:0.0:1.0:0.0	.	892;913;930	Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;FHOD3_HUMAN;.	H	930;913;892	ENSP00000257209:R930H;ENSP00000352186:R913H;ENSP00000411430:R892H	ENSP00000257209:R930H	R	+	2	0	FHOD3	32552573	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	2.427000	0.44740	2.034000	0.60081	0.555000	0.69702	CGC	.	.		0.473	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
SMAD2	4087	hgsc.bcm.edu	37	18	45375012	45375012	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr18:45375012T>C	ENST00000402690.2	-	8	1225	c.831A>G	c.(829-831)atA>atG	p.I277M	SMAD2_ENST00000586040.1_Missense_Mutation_p.I247M|SMAD2_ENST00000262160.6_Missense_Mutation_p.I277M|SMAD2_ENST00000356825.4_Missense_Mutation_p.I247M|SMAD2_ENST00000591214.1_Missense_Mutation_p.I247M	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	277	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						CATAATATGCTATCGAACACC	0.363																																					p.I277M		Atlas-SNP	.											.	SMAD2	85	.	0			c.A831G						.						86.0	80.0	82.0					18																	45375012		2203	4300	6503	SO:0001583	missense	4087	exon8			ATATGCTATCGAA	U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"""SMADs"""	6768	protein-coding gene	gene with protein product		601366	"""MAD, mothers against decapentaplegic homolog 2 (Drosophila)"", ""SMAD, mothers against DPP homolog 2 (Drosophila)"""	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.831A>G	chr18.hg19:g.45375012T>C	ENSP00000384449:p.Ile277Met	88.0	0.0		73.0	4.0	NM_005901		Missense_Mutation	SNP	ENST00000402690.2	hg19	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891762	0.72524	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.98075	-4.7;-4.7;-4.7	5.81	4.64	0.57946	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98943	0.9641	M	0.93507	3.425	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.998;0.975;0.994	D	0.99139	1.0855	10	0.87932	D	0	.	12.8817	0.58020	0.0:0.0:0.1407:0.8593	.	247;247;277	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	M	277;247;277	ENSP00000262160:I277M;ENSP00000349282:I247M;ENSP00000384449:I277M	ENSP00000262160:I277M	I	-	3	3	SMAD2	43629010	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.068000	0.64364	1.007000	0.39238	0.482000	0.46254	ATA	.	.		0.363	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901	
PLPPR3	79948	hgsc.bcm.edu	37	19	814544	814544	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:814544A>G	ENST00000520876.3	-	7	799	c.721T>C	c.(721-723)Ttt>Ctt	p.F241L	LPPR3_ENST00000359894.2_Missense_Mutation_p.F269L|MIR3187_ENST00000583431.1_RNA	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		241						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GCGATGGCAAAGGCGAAGACC	0.647																																					p.F269L		Atlas-SNP	.											.	.	.	.	0			c.T805C						.						60.0	61.0	61.0					19																	814544		2195	4300	6495	SO:0001583	missense	0	exon6			TGGCAAAGGCGAA																												ENST00000520876.3:c.721T>C	chr19.hg19:g.814544A>G	ENSP00000430297:p.Phe241Leu	32.0	0.0		32.0	4.0	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.1|24.1	4.491003|4.491003	0.84962|0.84962	.|.	.|.	ENSG00000129951|ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876|ENST00000517665;ENST00000521445	T;T|.	0.72942|.	-0.7;-0.7|.	4.66|4.66	4.66|4.66	0.58398|0.58398	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.41604|0.41604	0.1166|0.1166	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999991|0.999991	P;P;D|.	0.71674|.	0.92;0.884;0.998|.	P;P;D|.	0.80764|.	0.662;0.772;0.994|.	T|T	0.29882|0.29882	-0.9997|-0.9997	10|5	0.21540|.	T|.	0.41|.	-16.1034|-16.1034	13.2541|13.2541	0.60068|0.60068	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	242;241;269|.	Q6T4P5-2;Q6T4P5;Q6T4P5-3|.	.;LPPR3_HUMAN;.|.	L|P	242;269;241|29;190	ENSP00000352962:F269L;ENSP00000430297:F241L|.	ENSP00000300947:F242L|.	F|L	-|-	1|2	0|0	AC006273.1|AC006273.1	765544|765544	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.732000|0.732000	0.41865|0.41865	8.658000|8.658000	0.91110|0.91110	1.734000|1.734000	0.51633|0.51633	0.454000|0.454000	0.30748|0.30748	TTT|CTT	.	.		0.647	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
STXBP2	6813	hgsc.bcm.edu	37	19	7707395	7707395	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:7707395G>A	ENST00000221283.5	+	10	906	c.875G>A	c.(874-876)cGc>cAc	p.R292H	STXBP2_ENST00000414284.2_Missense_Mutation_p.R289H|STXBP2_ENST00000441779.2_Missense_Mutation_p.R303H	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	292			R -> H (in FHL5; leads to a complete loss of the ability to interact with STX11). {ECO:0000269|PubMed:19804848}.		leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						GTGGAGCTTCGCCACATGCAT	0.662																																					p.R303H		Atlas-SNP	.											STXBP2,colon,carcinoma,0,1	STXBP2	63	.	0			c.G908A						.						125.0	122.0	123.0					19																	7707395		2203	4300	6503	SO:0001583	missense	6813	exon10			AGCTTCGCCACAT	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.875G>A	chr19.hg19:g.7707395G>A	ENSP00000221283:p.Arg292His	70.0	0.0		91.0	4.0	NM_001272034	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	hg19	CCDS12181.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609163	0.66558	.	.	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902	T;T;T	0.81078	-1.45;-1.45;-1.45	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.91690	0.7373	M	0.92833	3.35	0.53688	D	0.999976	D;D;D;D	0.89917	1.0;0.997;1.0;1.0	D;D;D;D	0.91635	0.999;0.946;0.998;0.999	D	0.93738	0.7047	10	0.87932	D	0	-5.1595	15.1021	0.72288	0.0:0.0:1.0:0.0	.	303;258;289;292	E7EQD5;B4DY46;Q15833-2;Q15833	.;.;.;STXB2_HUMAN	H	292;289;303;292	ENSP00000221283:R292H;ENSP00000409471:R289H;ENSP00000413606:R303H	ENSP00000221283:R292H	R	+	2	0	STXBP2	7613395	1.000000	0.71417	0.641000	0.29422	0.022000	0.10575	9.860000	0.99555	2.147000	0.66899	0.591000	0.81541	CGC	.	.		0.662	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949	
ZNF317	57693	hgsc.bcm.edu	37	19	9271064	9271064	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:9271064A>G	ENST00000247956.6	+	7	1048	c.743A>G	c.(742-744)aAg>aGg	p.K248R	ZNF317_ENST00000360385.3_Missense_Mutation_p.K216R	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						ACCGGGGAGAAGCCTTACGAG	0.547																																					p.K248R		Atlas-SNP	.											.	ZNF317	61	.	0			c.A743G						.						105.0	98.0	101.0					19																	9271064		2203	4300	6503	SO:0001583	missense	57693	exon7			GGGAGAAGCCTTA	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"""Zinc fingers, C2H2-type"", ""-"""	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.743A>G	chr19.hg19:g.9271064A>G	ENSP00000247956:p.Lys248Arg	56.0	0.0		93.0	4.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	hg19	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.327789	0.60743	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.24908	1.83;1.83	3.61	3.61	0.41365	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44483	D	0.000445	T	0.33294	0.0858	N	0.21142	0.635	0.41650	D	0.98912	D;D	0.76494	0.999;0.999	D;D	0.81914	0.991;0.995	T	0.12142	-1.0559	10	0.56958	D	0.05	-26.8205	10.7948	0.46453	1.0:0.0:0.0:0.0	.	216;248	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	R	248;216	ENSP00000247956:K248R;ENSP00000353554:K216R	ENSP00000247956:K248R	K	+	2	0	ZNF317	9132064	0.828000	0.29307	0.380000	0.26093	0.330000	0.28571	1.604000	0.36804	1.882000	0.54519	0.482000	0.46254	AAG	.	.		0.547	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933	
CALR	811	hgsc.bcm.edu	37	19	13054664	13054664	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:13054664T>C	ENST00000316448.5	+	9	1264	c.1191T>C	c.(1189-1191)gaT>gaC	p.D397D	CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000541222.1_5'Flank|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000592268.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	397	Asp/Glu/Lys-rich.|C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|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)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	atgaggaggatgaggaggaca	0.572																																					p.D397D		Atlas-SNP	.											.	CALR	31	.	0			c.T1191C						.						275.0	214.0	235.0					19																	13054664		2203	4296	6499	SO:0001819	synonymous_variant	811	exon9			GGAGGATGAGGAG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"""Sicca syndrome antigen A (autoantigen Ro; calreticulin)"", ""autoantigen Ro"""	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1191T>C	chr19.hg19:g.13054664T>C		127.0	0.0		136.0	9.0	NM_004343	Q6IAT4|Q9UDG2	Silent	SNP	ENST00000316448.5	hg19	CCDS12288.1																																																																																			.	.		0.572	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343	
PIK3R2	5296	hgsc.bcm.edu	37	19	18266738	18266738	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:18266738C>T	ENST00000593731.1	+	2	609	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W	PIK3R2_ENST00000222254.8_Missense_Mutation_p.R17W			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	17	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	CCCGTTCCGCCGGGAGCGGCC	0.731																																					p.R17W		Atlas-SNP	.											.	PIK3R2	48	.	0			c.C49T						.						6.0	5.0	6.0					19																	18266738		1931	3824	5755	SO:0001583	missense	5296	exon2			TTCCGCCGGGAGC		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"""SH2 domain containing"""	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.49C>T	chr19.hg19:g.18266738C>T	ENSP00000471914:p.Arg17Trp	17.0	0.0		16.0	7.0	NM_005027	Q5EAT5|Q9UPH9	Missense_Mutation	SNP	ENST00000593731.1	hg19	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489309	0.84962	.	.	ENSG00000105647	ENST00000222254	T	0.08008	3.14	4.34	3.18	0.36537	Src homology-3 domain (3);	0.064269	0.64402	D	0.000009	T	0.11665	0.0284	L	0.38175	1.15	0.30854	N	0.734226	D	0.69078	0.997	P	0.53490	0.727	T	0.01413	-1.1361	10	0.87932	D	0	-27.3178	8.7743	0.34751	0.3481:0.6519:0.0:0.0	.	17	O00459	P85B_HUMAN	W	17	ENSP00000222254:R17W	ENSP00000222254:R17W	R	+	1	2	PIK3R2	18127738	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.487000	0.66863	2.140000	0.66376	0.462000	0.41574	CGG	.	.		0.731	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027	
ZNF714	148206	hgsc.bcm.edu	37	19	21299777	21299777	+	Missense_Mutation	SNP	G	G	A	rs111443257		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:21299777G>A	ENST00000596143.1	+	5	632	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	103					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(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAGGTTATGAACTAAACCA	0.328																																					p.E103K		Atlas-SNP	.											.	ZNF714	121	.	0			c.G307A						.						39.0	38.0	38.0					19																	21299777		2190	4291	6481	SO:0001583	missense	148206	exon5			GGTTATGAACTAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.307G>A	chr19.hg19:g.21299777G>A	ENSP00000472368:p.Glu103Lys	205.0	0.0		304.0	18.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	0.388	-0.924824	0.02377	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.394	0.394	0.16299	.	.	.	.	.	T	0.22322	0.0538	L	0.27975	0.815	0.09310	N	1	B;P	0.37781	0.004;0.608	B;B	0.35413	0.004;0.202	T	0.14062	-1.0486	7	0.56958	D	0.05	.	.	.	.	.	104;103	Q96N38-2;A6NEM4	.;.	K	103	.	ENSP00000291770:E103K	E	+	1	0	ZNF714	21091617	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.857000	0.04286	0.452000	0.26830	0.456000	0.33151	GAA	.	.		0.328	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
ZNF429	353088	hgsc.bcm.edu	37	19	21720474	21720474	+	Missense_Mutation	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:21720474A>T	ENST00000358491.4	+	4	1827	c.1619A>T	c.(1618-1620)gAa>gTa	p.E540V	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	540					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TACAAATGTGAAGAATGTGGC	0.363																																					p.E540V		Atlas-SNP	.											.	ZNF429	338	.	0			c.A1619T						.						41.0	46.0	44.0					19																	21720474		2134	4269	6403	SO:0001583	missense	353088	exon4			AATGTGAAGAATG	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1619A>T	chr19.hg19:g.21720474A>T	ENSP00000351280:p.Glu540Val	32.0	0.0		42.0	10.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	1.769	-0.484820	0.04352	.	.	ENSG00000197013	ENST00000358491	T	0.07800	3.16	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17619	0.0423	M	0.63169	1.94	0.09310	N	1	D	0.67145	0.996	D	0.63957	0.92	T	0.11251	-1.0595	9	0.48119	T	0.1	.	3.6737	0.08284	0.7461:0.0:0.2539:0.0	.	540	Q86V71	ZN429_HUMAN	V	540	ENSP00000351280:E540V	ENSP00000351280:E540V	E	+	2	0	ZNF429	21512314	0.000000	0.05858	0.285000	0.24819	0.285000	0.27093	-0.758000	0.04766	0.251000	0.21505	0.248000	0.18094	GAA	.	.		0.363	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
ZNF726	730087	hgsc.bcm.edu	37	19	24115505	24115505	+	Missense_Mutation	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:24115505C>T	ENST00000594466.1	+	4	692	c.587C>T	c.(586-588)aCt>aTt	p.T196I	ZNF726_ENST00000322487.7_Missense_Mutation_p.T196I|CTB-92J24.3_ENST00000596326.1_RNA|ZNF726_ENST00000575986.1_Intron|ZNF726_ENST00000334589.5_Intron	NM_001244038.1	NP_001230967.1	A6NNF4	ZN726_HUMAN	zinc finger protein 726	196					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGCATATATACTACAGAGAAG	0.313																																					p.T196I		Atlas-SNP	.											.	.	.	.	0			c.C587T						.																																			SO:0001583	missense	730087	exon4			TATATACTACAGA	DQ036016, BC046415	CCDS59372.1	19p12	2013-01-08			ENSG00000213967	ENSG00000213967		"""Zinc fingers, C2H2-type"", ""-"""	32462	protein-coding gene	gene with protein product							Standard	NM_001244038		Approved		uc021urw.1	A6NNF4	OTTHUMG00000167681	ENST00000594466.1:c.587C>T	chr19.hg19:g.24115505C>T	ENSP00000471516:p.Thr196Ile	46.0	0.0		46.0	12.0	NM_001244038	M0R0X8|Q86Y87	Missense_Mutation	SNP	ENST00000594466.1	hg19	CCDS59372.1	.	.	.	.	.	.	.	.	.	.	c	0.068	-1.208114	0.01568	.	.	ENSG00000213967	ENST00000322487	T	0.18810	2.19	0.823	0.823	0.18812	.	.	.	.	.	T	0.17662	0.0424	.	.	.	0.21822	N	0.999527	.	.	.	.	.	.	T	0.26258	-1.0108	6	0.49607	T	0.09	.	3.2493	0.06808	0.0:0.6535:0.0:0.3465	.	.	.	.	I	196	ENSP00000317125:T196I	ENSP00000317125:T196I	T	+	2	0	ZNF726	23907345	0.998000	0.40836	0.090000	0.20809	0.089000	0.18198	1.627000	0.37050	0.193000	0.20303	0.196000	0.17591	ACT	.	.		0.313	ZNF726-005	PUTATIVE	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466443.1	XM_001715134	
ZNF536	9745	hgsc.bcm.edu	37	19	30934614	30934614	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:30934614G>A	ENST00000355537.3	+	2	292	c.145G>A	c.(145-147)Gag>Aag	p.E49K		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	49					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.E49K(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					TGCCTTCCCCGAGCTCCATCC	0.667																																					p.E49K		Atlas-SNP	.											ZNF536,rectum,carcinoma,0,2	ZNF536	424	.	1	Substitution - Missense(1)	large_intestine(1)	c.G145A						.						67.0	68.0	68.0					19																	30934614		2203	4300	6503	SO:0001583	missense	9745	exon2			TTCCCCGAGCTCC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.145G>A	chr19.hg19:g.30934614G>A	ENSP00000347730:p.Glu49Lys	58.0	0.0		47.0	2.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629857	0.46944	.	.	ENSG00000198597	ENST00000355537	T	0.09445	2.98	5.37	4.32	0.51571	.	0.160306	0.56097	D	0.000036	T	0.15652	0.0377	L	0.32530	0.975	0.50313	D	0.999861	P;D	0.69078	0.952;0.997	B;P	0.53954	0.278;0.738	T	0.08146	-1.0736	10	0.18710	T	0.47	-33.2908	16.3674	0.83338	0.0:0.1321:0.8679:0.0	.	49;49	A7E228;O15090	.;ZN536_HUMAN	K	49	ENSP00000347730:E49K	ENSP00000347730:E49K	E	+	1	0	ZNF536	35626454	1.000000	0.71417	0.966000	0.40874	0.941000	0.58515	7.788000	0.85771	1.382000	0.46385	0.462000	0.41574	GAG	.	.		0.667	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
ZNF507	22847	hgsc.bcm.edu	37	19	32873386	32873386	+	Missense_Mutation	SNP	G	G	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:32873386G>C	ENST00000311921.4	+	5	2566	c.2374G>C	c.(2374-2376)Ggg>Cgg	p.G792R	ZNF507_ENST00000544431.1_Missense_Mutation_p.G796R|ZNF507_ENST00000355898.5_Missense_Mutation_p.G792R	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	792					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					CTCTCTGTGTGGGTATGTGTG	0.398																																					p.G792R		Atlas-SNP	.											.	ZNF507	92	.	0			c.G2374C						.						294.0	292.0	292.0					19																	32873386		2203	4300	6503	SO:0001583	missense	22847	exon6			CTGTGTGGGTATG	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"""Zinc fingers, C2H2-type"""	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2374G>C	chr19.hg19:g.32873386G>C	ENSP00000312277:p.Gly792Arg	178.0	0.0		196.0	37.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	hg19	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.839148	0.91117	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.36340	4.32;4.32;1.26	5.36	5.36	0.76844	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.043473	0.85682	D	0.000000	T	0.64170	0.2574	M	0.79343	2.45	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.67565	-0.5638	10	0.87932	D	0	.	19.4637	0.94929	0.0:0.0:1.0:0.0	.	792	Q8TCN5	ZN507_HUMAN	R	792;792;796	ENSP00000348162:G792R;ENSP00000312277:G792R;ENSP00000441549:G796R	ENSP00000312277:G792R	G	+	1	0	ZNF507	37565226	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.374000	0.97172	2.675000	0.91044	0.655000	0.94253	GGG	.	.		0.398	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910	
ZNF793	390927	hgsc.bcm.edu	37	19	38023312	38023312	+	Missense_Mutation	SNP	C	C	T	rs201422659		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:38023312C>T	ENST00000587143.1	+	4	305	c.70C>T	c.(70-72)Cgg>Tgg	p.R24W	ZNF793_ENST00000587986.1_Missense_Mutation_p.R24W|ZNF793_ENST00000589319.1_Missense_Mutation_p.R24W|ZNF793_ENST00000588578.1_Missense_Mutation_p.R24W|ZNF793_ENST00000542455.1_Missense_Mutation_p.R24W|ZNF793_ENST00000445217.1_Missense_Mutation_p.R24W			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAGTGGCACCGGCTGAGTCC	0.473													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19875	0.0		0.0	False		,,,				2504	0.0				p.R24W	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											ZNF793_ENST00000445217,colon,carcinoma,0,1	ZNF793	50	.	0			c.C70T						.						62.0	66.0	65.0					19																	38023312		2184	4299	6483	SO:0001583	missense	390927	exon6			TGGCACCGGCTGA	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"""Zinc fingers, C2H2-type"", ""-"""	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.70C>T	chr19.hg19:g.38023312C>T	ENSP00000468605:p.Arg24Trp	83.0	1.0		93.0	5.0	NM_001013659	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	hg19	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.422892	0.25639	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.01787	4.64;4.64	3.53	-1.31	0.09230	Krueppel-associated box (4);	.	.	.	.	T	0.01124	0.0037	N	0.20304	0.555	0.09310	N	1	B;B	0.13145	0.007;0.004	B;B	0.09377	0.004;0.001	T	0.48514	-0.9029	9	0.37606	T	0.19	.	0.6134	0.00765	0.4069:0.2371:0.1313:0.2247	.	24;24	Q6ZN11;E9PGN4	ZN793_HUMAN;.	W	24;24;24;23	ENSP00000444355:R24W;ENSP00000396402:R24W	ENSP00000318811:R23W	R	+	1	2	ZNF793	42715152	0.000000	0.05858	0.837000	0.33122	0.675000	0.39556	-0.261000	0.08694	-0.360000	0.08138	-0.217000	0.12591	CGG	.	.		0.473	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659	
ZC3H4	23211	hgsc.bcm.edu	37	19	47575245	47575245	+	Missense_Mutation	SNP	C	C	G	rs381976		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:47575245C>G	ENST00000253048.5	-	13	1973	c.1936G>C	c.(1936-1938)Gca>Cca	p.A646P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	646	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		tgcatgtctgcgtgcatgtca	0.662																																					p.A646P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1936C						.						31.0	35.0	34.0					19																	47575245		2118	4259	6377	SO:0001583	missense	23211	exon13			TGTCTGCGTGCAT	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1936G>C	chr19.hg19:g.47575245C>G	ENSP00000253048:p.Ala646Pro	52.0	0.0		67.0	15.0	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	1.939	-0.444005	0.04604	.	.	ENSG00000130749	ENST00000253048	T	0.17528	2.27	5.21	5.21	0.72293	.	0.405917	0.24076	N	0.041773	T	0.08044	0.0201	N	0.08118	0	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.32877	-0.9890	10	0.02654	T	1	.	13.2185	0.59873	0.0:0.1603:0.8397:0.0	rs381976;rs381976	646	Q9UPT8	ZC3H4_HUMAN	P	646	ENSP00000253048:A646P	ENSP00000253048:A646P	A	-	1	0	ZC3H4	52267085	1.000000	0.71417	0.916000	0.36221	0.011000	0.07611	4.019000	0.57181	1.200000	0.43188	-0.132000	0.14878	GCA	.	C|1.000;|0.000		0.662	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
ZC3H4	23211	hgsc.bcm.edu	37	19	47575267	47575267	+	Silent	SNP	C	C	G	rs200656728		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:47575267C>G	ENST00000253048.5	-	13	1951	c.1914G>C	c.(1912-1914)ccG>ccC	p.P638P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	638	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ggtgcatgtccgggtgcatgt	0.667																																					p.P638P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1914C						.						34.0	38.0	36.0					19																	47575267		2110	4239	6349	SO:0001819	synonymous_variant	23211	exon13			CATGTCCGGGTGC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1914G>C	chr19.hg19:g.47575267C>G		56.0	0.0		65.0	6.0	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	hg19	CCDS42582.1																																																																																			.	C|1.000;A|0.000		0.667	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
EHD2	30846	hgsc.bcm.edu	37	19	48244338	48244338	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:48244338T>C	ENST00000263277.3	+	6	1532	c.1281T>C	c.(1279-1281)ccT>ccC	p.P427P	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.P291P	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	427					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		AGCGGGGACCTGACGAGGCCA	0.657																																					p.P427P		Atlas-SNP	.											EHD2,NS,carcinoma,0,1	EHD2	59	.	0			c.T1281C						.						60.0	55.0	57.0					19																	48244338		2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			GGGACCTGACGAG	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1281T>C	chr19.hg19:g.48244338T>C		28.0	0.0		16.0	2.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	hg19	CCDS12704.1																																																																																			.	.		0.657	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
SPACA4	171169	hgsc.bcm.edu	37	19	49110448	49110448	+	Silent	SNP	C	C	T	rs371143349		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:49110448C>T	ENST00000321762.1	+	1	449	c.213C>T	c.(211-213)tgC>tgT	p.C71C	FAM83E_ENST00000263266.3_Intron	NM_133498.2	NP_598005.1	Q8TDM5	SACA4_HUMAN	sperm acrosome associated 4	71	UPAR/Ly6 1.				cell adhesion (GO:0007155)	anchored component of membrane (GO:0031225)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)		p.C71C(1)|p.C71*(1)		central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		CCACCAGCTGCGGCCTTGAGG	0.652													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17724	0.0		0.0	False		,,,				2504	0.0				p.C71C		Atlas-SNP	.											SPACA4,NS,carcinoma,0,2	SPACA4	9	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	lung(1)|central_nervous_system(1)	c.C213T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	35.0	32.0	33.0		,213	-3.8	0.7	19		33	1,8599		0,1,4299	no	intron,coding-synonymous	FAM83E,SPACA4	NM_017708.3,NM_133498.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	,71/125	49110448	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	171169	exon1			CAGCTGCGGCCTT		CCDS12725.1	19q13.33	2013-10-24			ENSG00000177202	ENSG00000177202			16441	protein-coding gene	gene with protein product		609932					Standard	NM_133498		Approved	SAMP14	uc002pjo.3	Q8TDM5	OTTHUMG00000183316	ENST00000321762.1:c.213C>T	chr19.hg19:g.49110448C>T		49.0	1.0		40.0	2.0	NM_133498		Silent	SNP	ENST00000321762.1	hg19	CCDS12725.1																																																																																			.	.		0.652	SPACA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466149.1	NM_133498	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965915	49965915	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:49965915G>A	ENST00000293350.4	+	8	1164	c.1001G>A	c.(1000-1002)cGa>cAa	p.R334Q	CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.R283Q|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.R171Q|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.R169Q	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	334						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGGAGTGGCCGAGGGCTGGAT	0.672																																					p.R334Q		Atlas-SNP	.											ALDH16A1,bladder,carcinoma,0,2	ALDH16A1	54	.	0			c.G1001A						.						36.0	39.0	38.0					19																	49965915		2203	4297	6500	SO:0001583	missense	126133	exon8			GTGGCCGAGGGCT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1001G>A	chr19.hg19:g.49965915G>A	ENSP00000293350:p.Arg334Gln	67.0	0.0		39.0	2.0	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.426447	0.62733	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.93	-4.21	0.03812	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	1.500260	0.03928	N	0.284783	T	0.23451	0.0567	L	0.45581	1.43	0.22412	N	0.999126	P;P;P	0.46142	0.709;0.873;0.873	B;B;B	0.38194	0.131;0.267;0.267	T	0.43097	-0.9412	10	0.49607	T	0.09	-13.5058	6.2294	0.20726	0.2432:0.3699:0.3869:0.0	.	171;283;334	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	Q	334;283;171;169	ENSP00000293350:R334Q;ENSP00000410142:R283Q;ENSP00000445088:R171Q;ENSP00000398675:R169Q	ENSP00000293350:R334Q	R	+	2	0	ALDH16A1	54657727	0.001000	0.12720	0.275000	0.24674	0.988000	0.76386	-0.352000	0.07701	-0.315000	0.08703	0.485000	0.47835	CGA	.	.		0.672	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
SIGLECL1	284369	hgsc.bcm.edu	37	19	51770669	51770669	+	Silent	SNP	G	G	T	rs369648100		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:51770669G>T	ENST00000316401.7	+	5	834	c.453G>T	c.(451-453)gcG>gcT	p.A151A	SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Silent_p.A57A|CTD-3187F8.2_ENST00000597569.1_RNA	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	515	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										AAGCTGCAGCGATCAGAGCAA	0.468																																					p.A151A		Atlas-SNP	.											C19orf75,rectum,carcinoma,0,1	.	.	.	0			c.G453T						.						117.0	118.0	117.0					19																	51770669		2203	4300	6503	SO:0001819	synonymous_variant	284369	exon5			TGCAGCGATCAGA	AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 75"", ""sialic acid binding Ig-like lectin 23, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 7"""	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.453G>T	chr19.hg19:g.51770669G>T		44.0	0.0		64.0	3.0	NM_173635	Q8IYH7	Silent	SNP	ENST00000316401.7	hg19	CCDS12827.1																																																																																			.	.		0.468	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635	
ZNF816	125893	hgsc.bcm.edu	37	19	53453990	53453990	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:53453990A>G	ENST00000357666.4	-	5	1338	c.1038T>C	c.(1036-1038)tgT>tgC	p.C346C	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Silent_p.C346C|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						AAGTCTTGCCACACTCATTAC	0.423																																					p.C346C		Atlas-SNP	.											.	ZNF816	73	.	0			c.T1038C						.						153.0	157.0	156.0					19																	53453990		2203	4300	6503	SO:0001819	synonymous_variant	125893	exon4			CTTGCCACACTCA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"""Zinc fingers, C2H2-type"", ""-"""	26995	protein-coding gene	gene with protein product			"""zinc finger protein 816A"""	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.1038T>C	chr19.hg19:g.53453990A>G		82.0	0.0		109.0	5.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Silent	SNP	ENST00000357666.4	hg19	CCDS33096.1																																																																																			.	.		0.423	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665	
PEG3	5178	hgsc.bcm.edu	37	19	57334962	57334962	+	Splice_Site	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:57334962G>A	ENST00000326441.9	-	5	843	c.480C>T	c.(478-480)ttC>ttT	p.F160F	ZIM2_ENST00000599935.1_Silent_p.F34F|ZIM2_ENST00000221722.5_Silent_p.F34F|ZIM2_ENST00000593931.1_Silent_p.F34F|ZIM2_ENST00000593711.1_Silent_p.F34F|PEG3_ENST00000423103.2_Splice_Site_p.F160F|ZIM2_ENST00000391708.3_Silent_p.F34F|PEG3_ENST00000593695.1_Splice_Site_p.F34F|PEG3_ENST00000594706.1_5'Flank|ZIM2_ENST00000601070.1_Silent_p.F34F|PEG3_ENST00000598410.1_Silent_p.F34F	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	160					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ACTCACCACTGAAAGAATGGA	0.577																																					p.F160F		Atlas-SNP	.											.	PEG3	414	.	0			c.C480T						.						243.0	172.0	196.0					19																	57334962		2203	4300	6503	SO:0001630	splice_region_variant	5178	exon4			ACCACTGAAAGAA	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.481+1C>T	chr19.hg19:g.57334962G>A		47.0	0.0		70.0	15.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	hg19	CCDS12948.1																																																																																			.	.		0.577	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		Silent
ZNF814	730051	hgsc.bcm.edu	37	19	58385536	58385536	+	Missense_Mutation	SNP	A	A	G	rs200607098|rs377684394	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr19:58385536A>G	ENST00000435989.2	-	3	1456	c.1222T>C	c.(1222-1224)Tat>Cat	p.Y408H	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	408					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CCACATTCATAATGTTTTTTG	0.393																																					p.Y408H		Atlas-SNP	.											.	ZNF814	93	.	0			c.T1222C						.						110.0	89.0	96.0					19																	58385536		692	1591	2283	SO:0001583	missense	730051	exon3			ATTCATAATGTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1222T>C	chr19.hg19:g.58385536A>G	ENSP00000410545:p.Tyr408His	118.0	0.0		201.0	12.0	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.27	1.588723	0.28357	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.60040	0.22	2.33	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40171	0.1106	L	0.33753	1.03	0.09310	N	1	B	0.30741	0.293	B	0.28305	0.088	T	0.32052	-0.9921	9	0.54805	T	0.06	.	3.051	0.06169	0.6575:0.0:0.1336:0.2089	.	408	B7Z6K7	ZN814_HUMAN	H	408;270	ENSP00000410545:Y408H	ENSP00000365378:Y270H	Y	-	1	0	ZNF814	63077348	0.002000	0.14202	0.001000	0.08648	0.011000	0.07611	1.779000	0.38624	0.155000	0.19261	-0.804000	0.03201	TAT	.	.		0.393	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
DOK5	55816	hgsc.bcm.edu	37	20	53226977	53226977	+	Missense_Mutation	SNP	A	A	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:53226977A>C	ENST00000262593.5	+	6	1000	c.650A>C	c.(649-651)gAg>gCg	p.E217A	DOK5_ENST00000395939.1_Missense_Mutation_p.E109A	NM_018431.3	NP_060901.2	Q9P104	DOK5_HUMAN	docking protein 5	217	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|skin(1)	19			Colorectal(105;0.202)			CGAGACGGGGAGGCCATCTAT	0.483																																					p.E217A		Atlas-SNP	.											.	DOK5	54	.	0			c.A650C						.						86.0	77.0	80.0					20																	53226977		2203	4300	6503	SO:0001583	missense	55816	exon6			ACGGGGAGGCCAT	AF132732	CCDS13446.1, CCDS13447.1	20q13.2	2013-01-10	2002-11-28	2002-11-29	ENSG00000101134	ENSG00000101134		"""Pleckstrin homology (PH) domain containing"""	16173	protein-coding gene	gene with protein product		608334	"""chromosome 20 open reading frame 180"""	C20orf180		11470823	Standard	XM_005260451		Approved	dJ805C22.1	uc002xwy.3	Q9P104	OTTHUMG00000032778	ENST00000262593.5:c.650A>C	chr20.hg19:g.53226977A>C	ENSP00000262593:p.Glu217Ala	143.0	0.0		171.0	20.0	NM_018431	Q5T7Y0|Q5TE53|Q8TEW7|Q96H13|Q9BZ24|Q9NQF4|Q9Y411	Missense_Mutation	SNP	ENST00000262593.5	hg19	CCDS13446.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.430303	0.83776	.	.	ENSG00000101134	ENST00000262593;ENST00000395939	T;T	0.76448	-1.02;-1.02	5.54	5.54	0.83059	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.000000	0.85682	D	0.000000	D	0.87192	0.6116	M	0.78223	2.4	0.58432	D	0.999999	P;P	0.52577	0.868;0.954	P;D	0.67725	0.563;0.953	D	0.87147	0.2206	10	0.42905	T	0.14	-14.1726	14.8793	0.70519	1.0:0.0:0.0:0.0	.	109;217	Q9P104-2;Q9P104	.;DOK5_HUMAN	A	217;109	ENSP00000262593:E217A;ENSP00000379270:E109A	ENSP00000262593:E217A	E	+	2	0	DOK5	52660384	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	9.181000	0.94874	2.115000	0.64714	0.533000	0.62120	GAG	.	.		0.483	DOK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079777.2		
ZNF831	128611	hgsc.bcm.edu	37	20	57767832	57767832	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:57767832C>T	ENST00000371030.2	+	1	1758	c.1758C>T	c.(1756-1758)gaC>gaT	p.D586D		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	586							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					AGGACACAGACGCAAAGAGAA	0.672																																					p.D586D		Atlas-SNP	.											ZNF831,NS,carcinoma,0,2	ZNF831	287	.	0			c.C1758T						.						19.0	23.0	22.0					20																	57767832		2033	4167	6200	SO:0001819	synonymous_variant	128611	exon1			CACAGACGCAAAG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1758C>T	chr20.hg19:g.57767832C>T		36.0	0.0		34.0	2.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.672	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
PCMTD2	55251	hgsc.bcm.edu	37	20	62904798	62904798	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:62904798T>C	ENST00000308824.6	+	6	1058	c.931T>C	c.(931-933)Tgt>Cgt	p.C311R	PCMTD2_ENST00000299468.7_Intron|PCMTD2_ENST00000369758.4_Missense_Mutation_p.C284R|PCMTD2_ENST00000266078.7_3'UTR|PCMTD2_ENST00000609372.1_Missense_Mutation_p.C161R	NM_018257.2	NP_060727.2	Q9NV79	PCMD2_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	311						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(9)|upper_aerodigestive_tract(1)	17	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					TGACAACAGCTGTGAAGACTT	0.517																																					p.C311R		Atlas-SNP	.											.	PCMTD2	35	.	0			c.T931C						.						84.0	103.0	96.0					20																	62904798		2203	4300	6503	SO:0001583	missense	55251	exon6			AACAGCTGTGAAG	AK001745	CCDS13559.1, CCDS46631.1	20q13.33	2012-10-02	2005-10-06	2005-10-06	ENSG00000203880	ENSG00000203880			15882	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 36"""	C20orf36			Standard	NM_018257		Approved	FLJ10883	uc002yil.4	Q9NV79	OTTHUMG00000033029	ENST00000308824.6:c.931T>C	chr20.hg19:g.62904798T>C	ENSP00000307854:p.Cys311Arg	43.0	0.0		59.0	4.0	NM_018257	E1P5H3|Q8IW60|Q9H4K2	Missense_Mutation	SNP	ENST00000308824.6	hg19	CCDS13559.1	.	.	.	.	.	.	.	.	.	.	.	11.22	1.574402	0.28092	.	.	ENSG00000203880	ENST00000369758;ENST00000308824;ENST00000266078	T;T;T	0.41400	1.02;1.61;1.0	5.41	3.12	0.35913	.	0.368603	0.31358	N	0.007786	T	0.28167	0.0695	N	0.22421	0.69	0.58432	D	0.999992	B;B	0.29716	0.09;0.255	B;B	0.33042	0.033;0.157	T	0.04454	-1.0950	10	0.33940	T	0.23	-8.3258	8.6567	0.34068	0.1193:0.0:0.2496:0.6311	.	284;311	Q9NV79-2;Q9NV79	.;PCMD2_HUMAN	R	284;311;87	ENSP00000358773:C284R;ENSP00000307854:C311R;ENSP00000266078:C87R	ENSP00000266078:C87R	C	+	1	0	PCMTD2	62375242	0.985000	0.35326	0.253000	0.24343	0.963000	0.63663	0.585000	0.23879	0.344000	0.23847	-0.257000	0.10917	TGT	.	.		0.517	PCMTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080301.1	NM_018257	
ADAMTS1	9510	hgsc.bcm.edu	37	21	28212774	28212774	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:28212774A>G	ENST00000284984.3	-	5	1940	c.1486T>C	c.(1486-1488)Tcc>Ccc	p.S496P		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	496	Disintegrin.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		CAGTGTTTGGAGTCCTCCCCA	0.577																																					p.S496P		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.T1486C						.						73.0	63.0	66.0					21																	28212774		2203	4300	6503	SO:0001583	missense	9510	exon5			GTTTGGAGTCCTC	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1486T>C	chr21.hg19:g.28212774A>G	ENSP00000284984:p.Ser496Pro	64.0	0.0		70.0	4.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694959	0.88830	.	.	ENSG00000154734	ENST00000284984	T	0.63255	-0.03	5.14	5.14	0.70334	ADAM, cysteine-rich (1);	.	.	.	.	D	0.82999	0.5159	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.86269	0.1660	9	0.49607	T	0.09	.	15.4124	0.74937	1.0:0.0:0.0:0.0	.	496	Q9UHI8	ATS1_HUMAN	P	496	ENSP00000284984:S496P	ENSP00000284984:S496P	S	-	1	0	ADAMTS1	27134645	1.000000	0.71417	0.933000	0.37362	0.894000	0.52154	8.761000	0.91691	2.284000	0.76573	0.528000	0.53228	TCC	.	.		0.577	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
LTN1	26046	hgsc.bcm.edu	37	21	30339226	30339226	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:30339226C>T	ENST00000361371.5	-	10	1666	c.1587G>A	c.(1585-1587)ttG>ttA	p.L529L	LTN1_ENST00000389194.2_Silent_p.L575L|LTN1_ENST00000389195.2_Silent_p.L575L			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	529					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TACTTGACTTCAATGAGCTCT	0.378																																					p.L575L		Atlas-SNP	.											LTN1,colon,carcinoma,0,1	LTN1	141	.	0			c.G1725A						.						67.0	63.0	64.0					21																	30339226		2203	4300	6503	SO:0001819	synonymous_variant	26046	exon10			TGACTTCAATGAG	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1587G>A	chr21.hg19:g.30339226C>T		104.0	0.0		110.0	5.0	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	hg19																																																																																				.	.		0.378	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
SYNJ1	8867	hgsc.bcm.edu	37	21	34003927	34003927	+	Nonsense_Mutation	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:34003927A>T	ENST00000322229.7	-	31	4099	c.4100T>A	c.(4099-4101)tTg>tAg	p.L1367*	SYNJ1_ENST00000357345.3_3'UTR|SYNJ1_ENST00000433931.2_Nonsense_Mutation_p.L1406*|SYNJ1_ENST00000382491.3_Nonsense_Mutation_p.L1320*|SYNJ1_ENST00000382499.2_3'UTR			O43426	SYNJ1_HUMAN	synaptojanin 1	1367	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TACAGAACTCAAAACATTACT	0.458																																					p.L1406X		Atlas-SNP	.											.	SYNJ1	253	.	0			c.T4217A						.						70.0	75.0	74.0					21																	34003927		2203	4300	6503	SO:0001587	stop_gained	8867	exon32			GAACTCAAAACAT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.4100T>A	chr21.hg19:g.34003927A>T	ENSP00000322234:p.Leu1367*	124.0	0.0		135.0	8.0	NM_003895	O43425|O94984|Q4KMR1	Nonsense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	A	41	8.763780	0.98945	.	.	ENSG00000159082	ENST00000382491;ENST00000433931;ENST00000322229	.	.	.	5.04	-0.125	0.13519	.	0.597733	0.14761	N	0.299971	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9321	0.19144	0.4574:0.1409:0.4017:0.0	.	.	.	.	X	1320;1406;1367	.	ENSP00000322234:L1367X	L	-	2	0	SYNJ1	32925798	0.726000	0.28059	0.412000	0.26496	0.995000	0.86356	0.813000	0.27225	0.025000	0.15241	0.523000	0.50628	TTG	.	.		0.458	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
KCNJ15	3772	hgsc.bcm.edu	37	21	39671581	39671581	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:39671581G>A	ENST00000328656.4	+	4	701	c.398G>A	c.(397-399)cGt>cAt	p.R133H	KCNJ15_ENST00000398934.1_Missense_Mutation_p.R133H|KCNJ15_ENST00000398930.1_Missense_Mutation_p.R133H|KCNJ15_ENST00000398932.1_Missense_Mutation_p.R133H|KCNJ15_ENST00000398938.2_Missense_Mutation_p.R133H	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	133					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	TATGGAGTCCGTTCCATCACA	0.502																																					p.C133Y		Atlas-SNP	.											KCNJ15,NS,carcinoma,0,1	KCNJ15	43	.	0			c.G398A						.						107.0	105.0	106.0					21																	39671581		2203	4300	6503	SO:0001583	missense	3772	exon4			GAGTCCGTTCCAT	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.398G>A	chr21.hg19:g.39671581G>A	ENSP00000331698:p.Arg133His	92.0	0.0		100.0	4.0	NM_002243	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918617	0.92249	.	.	ENSG00000157551	ENST00000328656;ENST00000398928;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	D;D;D;D;D;D;D;D;D	0.97016	-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21	5.83	5.83	0.93111	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98789	0.9592	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99236	1.0883	9	.	.	.	.	20.1338	0.98010	0.0:0.0:1.0:0.0	.	133	Q99712	IRK15_HUMAN	H	133	ENSP00000331698:R133H;ENSP00000381902:R133H;ENSP00000381911:R133H;ENSP00000381905:R133H;ENSP00000414487:R133H;ENSP00000381904:R133H;ENSP00000381907:R133H;ENSP00000381901:R133H;ENSP00000400849:R133H	.	R	+	2	0	KCNJ15	38593451	1.000000	0.71417	0.996000	0.52242	0.903000	0.53119	9.869000	0.99810	2.770000	0.95276	0.655000	0.94253	CGT	.	.		0.502	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
DSCAM	1826	hgsc.bcm.edu	37	21	42064802	42064802	+	Missense_Mutation	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:42064802G>T	ENST00000400454.1	-	3	919	c.442C>A	c.(442-444)Ccc>Acc	p.P148T		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	148	Ig-like C2-type 2.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				ACCGAGGAGGGGATAATGCAC	0.532																																					p.P148T	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.,1	DSCAM	347	.	0			c.C442A						.						143.0	140.0	141.0					21																	42064802		2027	4181	6208	SO:0001583	missense	1826	exon3			AGGAGGGGATAAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.442C>A	chr21.hg19:g.42064802G>T	ENSP00000383303:p.Pro148Thr	52.0	0.0		52.0	3.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.235957	0.79800	.	.	ENSG00000171587	ENST00000400454	T	0.13196	2.61	5.93	4.87	0.63330	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.064020	0.64402	D	0.000005	T	0.39809	0.1092	M	0.91561	3.22	0.51233	D	0.999917	P	0.52842	0.956	P	0.55545	0.778	T	0.44757	-0.9307	10	0.49607	T	0.09	.	16.0065	0.80367	0.0745:0.0:0.9255:0.0	.	148	O60469	DSCAM_HUMAN	T	148	ENSP00000383303:P148T	ENSP00000383303:P148T	P	-	1	0	DSCAM	40986672	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.856000	0.86956	2.814000	0.96858	0.655000	0.94253	CCC	.	.		0.532	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45523364	45523364	+	Silent	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:45523364G>A	ENST00000291574.4	+	23	3907	c.3732G>A	c.(3730-3732)ctG>ctA	p.L1244L		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1244					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						CACAAGTCCTGGTCATCCCCA	0.607																																					p.L1244L		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.G3732A						.						39.0	36.0	37.0					21																	45523364		2203	4300	6503	SO:0001819	synonymous_variant	7109	exon23			AGTCCTGGTCATC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.3732G>A	chr21.hg19:g.45523364G>A		106.0	0.0		58.0	4.0	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	hg19	CCDS13704.1																																																																																			.	.		0.607	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
FAM207A	85395	hgsc.bcm.edu	37	21	46380029	46380029	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:46380029A>G	ENST00000291634.6	+	3	346	c.298A>G	c.(298-300)Acc>Gcc	p.T100A	FAM207A_ENST00000397826.3_Missense_Mutation_p.T85A|FAM207A_ENST00000479127.1_3'UTR	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	100																	AGAGGCCAAGACCGTTTTGCC	0.577																																					p.T100A		Atlas-SNP	.											.	.	.	.	0			c.A298G						.						122.0	96.0	105.0					21																	46380029		2203	4300	6503	SO:0001583	missense	85395	exon3			GCCAAGACCGTTT		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.298A>G	chr21.hg19:g.46380029A>G	ENSP00000291634:p.Thr100Ala	69.0	0.0		62.0	4.0	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	hg19	CCDS13718.1	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.461415	0.01062	.	.	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.39406	1.08;1.08;1.08	3.24	-4.79	0.03200	.	0.600804	0.17242	N	0.181492	T	0.18635	0.0447	N	0.13098	0.295	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.09377	0.002;0.004	T	0.31280	-0.9949	10	0.09843	T	0.71	-0.1904	11.2394	0.48960	0.2498:0.0:0.7502:0.0	.	85;100	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	A	100;85;85	ENSP00000291634:T100A;ENSP00000380926:T85A;ENSP00000404964:T85A	ENSP00000291634:T100A	T	+	1	0	C21orf70	45204457	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.654000	0.05354	-1.117000	0.02965	-0.417000	0.06048	ACC	.	.		0.577	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
MCM3AP	8888	hgsc.bcm.edu	37	21	47676785	47676785	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr21:47676785C>A	ENST00000397708.1	-	18	4104	c.3850G>T	c.(3850-3852)Gag>Tag	p.E1284*	AP001469.9_ENST00000430259.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP_ENST00000291688.1_Nonsense_Mutation_p.E1284*			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1284					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.E1284K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ATGGGGCACTCTGCGCTGGGC	0.667																																					p.E1284X		Atlas-SNP	.											MCM3AP,NS,carcinoma,0,1	MCM3AP	146	.	1	Substitution - Missense(1)	ovary(1)	c.G3850T						.						15.0	19.0	17.0					21																	47676785		2199	4295	6494	SO:0001587	stop_gained	8888	exon17			GGCACTCTGCGCT	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3850G>T	chr21.hg19:g.47676785C>A	ENSP00000380820:p.Glu1284*	79.0	0.0		31.0	2.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Nonsense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	41	9.035785	0.99044	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	.	.	.	5.59	4.69	0.59074	.	0.152400	0.56097	D	0.000025	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-25.131	16.3994	0.83633	0.0:0.8682:0.1318:0.0	.	.	.	.	X	1284	.	ENSP00000291688:E1284X	E	-	1	0	MCM3AP	46501213	1.000000	0.71417	0.997000	0.53966	0.498000	0.33706	5.315000	0.65810	1.333000	0.45449	0.655000	0.94253	GAG	.	.		0.667	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
SNAP29	9342	hgsc.bcm.edu	37	22	21235343	21235343	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:21235343A>G	ENST00000215730.7	+	3	569	c.441A>G	c.(439-441)aaA>aaG	p.K147K		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	147					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			AAAGATTGAAAGAAGCTATAA	0.378																																					p.K147K		Atlas-SNP	.											.	SNAP29	22	.	0			c.A441G						.						69.0	63.0	65.0					22																	21235343		2203	4300	6503	SO:0001819	synonymous_variant	9342	exon3			ATTGAAAGAAGCT	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.441A>G	chr22.hg19:g.21235343A>G		101.0	0.0		84.0	4.0	NM_004782		Silent	SNP	ENST00000215730.7	hg19	CCDS13784.1																																																																																			.	.		0.378	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
MMP11	4320	hgsc.bcm.edu	37	22	24124435	24124435	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:24124435C>T	ENST00000215743.3	+	7	1150	c.1098C>T	c.(1096-1098)gaC>gaT	p.D366D		NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	366					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D366D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	gggtgtacgacggtgaaaagc	0.652																																					p.D366D		Atlas-SNP	.											MMP11,NS,carcinoma,0,1	MMP11	53	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1098T						.						63.0	65.0	64.0					22																	24124435		2203	4300	6503	SO:0001819	synonymous_variant	4320	exon7			GTACGACGGTGAA		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"""matrix metalloproteinase 11 (stromelysin 3)"""	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1098C>T	chr22.hg19:g.24124435C>T		39.0	0.0		39.0	2.0	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Silent	SNP	ENST00000215743.3	hg19	CCDS13816.1																																																																																			.	.		0.652	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940	
SMARCB1	6598	hgsc.bcm.edu	37	22	24175869	24175869	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:24175869G>A	ENST00000263121.7	+	8	1293	c.1097G>A	c.(1096-1098)cGc>cAc	p.R366H	SMARCB1_ENST00000407082.3_Missense_Mutation_p.R320H|SMARCB1_ENST00000407422.3_Missense_Mutation_p.R357H|SMARCB1_ENST00000344921.6_Missense_Mutation_p.R375H|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	366					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.R366P(1)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				AAGAAGATCCGCGACCAGGAC	0.632			"""D, N, F, S"""		malignant rhabdoid	malignant rhabdoid																															p.R366H		Atlas-SNP	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"""		M	SMARCB1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	SMARCB1	586	.	4	Unknown(2)|Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(4)	c.G1097A						.						126.0	108.0	114.0					22																	24175869		2203	4300	6503	SO:0001583	missense	6598	exon8			AGATCCGCGACCA	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"""sucrose nonfermenting, yeast, homolog-like 1"", ""integrase interactor 1"", ""malignant rhabdoid tumor suppressor"", ""protein phosphatase 1, regulatory subunit 144"""	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1097G>A	chr22.hg19:g.24175869G>A	ENSP00000263121:p.Arg366His	38.0	0.0		33.0	2.0	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	hg19	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041973	0.93685	.	.	ENSG00000099956	ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	4.76	4.76	0.60689	.	0.100539	0.64402	D	0.000006	D	0.89577	0.6755	M	0.88979	2.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.987;0.991	D	0.90634	0.4569	10	0.48119	T	0.1	-16.5216	17.2148	0.86940	0.0:0.0:1.0:0.0	.	375;357;366	G5E975;Q17S11;Q12824	.;.;SNF5_HUMAN	H	375;366;357;320	ENSP00000340883:R375H;ENSP00000263121:R366H;ENSP00000383984:R357H;ENSP00000385226:R320H	ENSP00000263121:R366H	R	+	2	0	SMARCB1	22505869	1.000000	0.71417	0.909000	0.35828	0.991000	0.79684	9.552000	0.98115	2.387000	0.81309	0.543000	0.68304	CGC	.	.		0.632	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073	
GGT1	2678	hgsc.bcm.edu	37	22	25023537	25023537	+	Missense_Mutation	SNP	G	G	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:25023537G>A	ENST00000400382.1	+	12	1914	c.1159G>A	c.(1159-1161)Gtc>Atc	p.V387I	GGT1_ENST00000400380.1_Missense_Mutation_p.V387I|GGT1_ENST00000404223.1_Missense_Mutation_p.V43I|GGT1_ENST00000403838.1_Missense_Mutation_p.V43I|GGT1_ENST00000404532.1_Missense_Mutation_p.V43I|GGT1_ENST00000401885.1_Missense_Mutation_p.V43I|GGT1_ENST00000406383.2_Missense_Mutation_p.V387I|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Missense_Mutation_p.V387I|GGT1_ENST00000404920.1_Missense_Mutation_p.V43I|GGT1_ENST00000248923.4_Missense_Mutation_p.V387I			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	387					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	CCTGTCTGTCGTCGCAGAGGA	0.662																																					p.V387I		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	.	0			c.G1159A						.						13.0	14.0	14.0					22																	25023537		2192	4250	6442	SO:0001583	missense	2678	exon12			TCTGTCGTCGCAG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1159G>A	chr22.hg19:g.25023537G>A	ENSP00000383232:p.Val387Ile	52.0	0.0		43.0	2.0	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	hg19	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	2.274	-0.366356	0.05069	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19;3.19	3.36	1.17	0.20885	.	0.198041	0.42172	N	0.000751	T	0.06280	0.0162	L	0.35249	1.045	0.34240	D	0.677567	B	0.15930	0.015	B	0.11329	0.006	T	0.22661	-1.0210	10	0.31617	T	0.26	-45.1165	8.9047	0.35517	0.1879:0.0:0.8121:0.0	.	387	P19440	GGT1_HUMAN	I	387;387;387;387;387;387;43;43;43;43;43	ENSP00000248923:V387I;ENSP00000393537:V387I;ENSP00000383232:V387I;ENSP00000383233:V387I;ENSP00000383231:V387I;ENSP00000385975:V387I;ENSP00000384381:V43I;ENSP00000385445:V43I;ENSP00000384820:V43I;ENSP00000385016:V43I;ENSP00000385001:V43I	ENSP00000248923:V387I	V	+	1	0	GGT1	23353537	1.000000	0.71417	0.127000	0.21898	0.210000	0.24377	2.905000	0.48727	0.255000	0.21593	-1.954000	0.00483	GTC	.	.		0.662	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
MYO18B	84700	hgsc.bcm.edu	37	22	26164267	26164267	+	Silent	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:26164267C>A	ENST00000407587.2	+	4	553	c.384C>A	c.(382-384)gcC>gcA	p.A128A	MYO18B_ENST00000536101.1_Silent_p.A128A|MYO18B_ENST00000335473.7_Silent_p.A128A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	128						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GTGAGAAGGCCCAGGAGCTGG	0.597																																					p.A128A		Atlas-SNP	.											.	MYO18B	322	.	0			c.C384A						.						39.0	45.0	43.0					22																	26164267		1995	4156	6151	SO:0001819	synonymous_variant	84700	exon4			GAAGGCCCAGGAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.384C>A	chr22.hg19:g.26164267C>A		89.0	0.0		89.0	5.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
CRYBA4	1413	hgsc.bcm.edu	37	22	27026346	27026346	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:27026346T>C	ENST00000354760.3	+	6	521	c.486T>C	c.(484-486)taT>taC	p.Y162Y	CRYBA4_ENST00000466315.1_3'UTR	NM_001886.2	NP_001877.1	P53673	CRBA4_HUMAN	crystallin, beta A4	162	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(6)|liver(1)|lung(6)|skin(3)|urinary_tract(2)	18						GATTTCAGTATGTGCTGGAAT	0.537																																					p.Y162Y		Atlas-SNP	.											.	CRYBA4	33	.	0			c.T486C						.						126.0	100.0	109.0					22																	27026346		2203	4300	6503	SO:0001819	synonymous_variant	1413	exon6			TCAGTATGTGCTG		CCDS13841.1	22q12.1	2008-06-10			ENSG00000196431	ENSG00000196431			2396	protein-coding gene	gene with protein product		123631				8999933, 960806	Standard	NM_001886		Approved		uc003acz.4	P53673	OTTHUMG00000150983	ENST00000354760.3:c.486T>C	chr22.hg19:g.27026346T>C		98.0	0.0		89.0	4.0	NM_001886	Q4VB22|Q6ICE4	Silent	SNP	ENST00000354760.3	hg19	CCDS13841.1																																																																																			.	.		0.537	CRYBA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320793.1	NM_001886	
HMGXB4	10042	hgsc.bcm.edu	37	22	35660647	35660647	+	Missense_Mutation	SNP	C	C	T	rs560951498		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:35660647C>T	ENST00000216106.5	+	5	394	c.266C>T	c.(265-267)tCg>tTg	p.S89L	HMGXB4_ENST00000444518.2_5'UTR	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	89					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTAGATATTTCGTCTTTGGAA	0.403													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21536	0.0		0.0	False		,,,				2504	0.0				p.S89L		Atlas-SNP	.											HMGXB4,NS,carcinoma,0,1	HMGXB4	52	.	0			c.C266T						.						100.0	109.0	106.0					22																	35660647		2201	4299	6500	SO:0001583	missense	10042	exon5			ATATTTCGTCTTT	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"""High mobility group / Non-canonical"""	5003	protein-coding gene	gene with protein product		604702	"""high-mobility group protein 2-like 1"""	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.266C>T	chr22.hg19:g.35660647C>T	ENSP00000216106:p.Ser89Leu	50.0	0.0		42.0	2.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.454587	0.26161	.	.	ENSG00000100281	ENST00000216106	T	0.19532	2.14	5.71	5.71	0.89125	.	0.513334	0.21865	N	0.067976	T	0.20292	0.0488	L	0.27053	0.805	0.80722	D	1	B	0.15141	0.012	B	0.12156	0.007	T	0.03344	-1.1046	10	0.72032	D	0.01	-1.1235	19.8545	0.96752	0.0:1.0:0.0:0.0	.	89	Q9UGU5	HMGX4_HUMAN	L	89	ENSP00000216106:S89L	ENSP00000216106:S89L	S	+	2	0	HMGXB4	33990647	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	5.311000	0.65786	2.695000	0.91970	0.563000	0.77884	TCG	.	.		0.403	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487	
CELSR1	9620	hgsc.bcm.edu	37	22	46794440	46794440	+	Missense_Mutation	SNP	C	C	A			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr22:46794440C>A	ENST00000262738.3	-	11	5506	c.5507G>T	c.(5506-5508)gGa>gTa	p.G1836V		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1836	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCCTCGGAATCCACGGCGCAC	0.672																																					p.G1836V		Atlas-SNP	.											.	CELSR1	242	.	0			c.G5507T						.						52.0	45.0	47.0					22																	46794440		2203	4300	6503	SO:0001583	missense	9620	exon11			CGGAATCCACGGC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5507G>T	chr22.hg19:g.46794440C>A	ENSP00000262738:p.Gly1836Val	97.0	0.0		71.0	22.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.062264	0.55432	.	.	ENSG00000075275	ENST00000262738	T	0.72505	-0.66	4.93	4.93	0.64822	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.64402	U	0.000002	D	0.85847	0.5792	M	0.85945	2.785	0.80722	D	1	D;P	0.89917	1.0;0.771	D;P	0.97110	1.0;0.475	D	0.87832	0.2645	10	0.56958	D	0.05	.	17.7518	0.88436	0.0:1.0:0.0:0.0	.	157;1836	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	V	1836	ENSP00000262738:G1836V	ENSP00000262738:G1836V	G	-	2	0	CELSR1	45173104	1.000000	0.71417	0.077000	0.20336	0.185000	0.23345	6.762000	0.74950	2.284000	0.76573	0.591000	0.81541	GGA	.	.		0.672	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
PLCXD1	55344	hgsc.bcm.edu	37	X	215776	215776	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:215776T>C	ENST00000381657.2	+	7	1260	c.746T>C	c.(745-747)gTg>gCg	p.V249A	PLCXD1_ENST00000399012.1_Missense_Mutation_p.V249A|PLCXD1_ENST00000381663.3_Missense_Mutation_p.V249A	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	249					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGGTTGTTCGTGGCCGGCATC	0.617																																					p.V249A		Atlas-SNP	.											.	PLCXD1	18	.	0			c.T746C						.						111.0	96.0	101.0					X																	215776		2203	4296	6499	SO:0001583	missense	55344	exon7			TGTTCGTGGCCGG	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"""Pseudoautosomal regions / PAR1"""	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.746T>C	chrX.hg19:g.215776T>C	ENSP00000371073:p.Val249Ala	123.0	0.0		76.0	4.0	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	hg19	CCDS14103.1	.	.	.	.	.	.	.	.	.	.	.	7.501	0.652707	0.14580	.	.	ENSG00000182378	ENST00000399012;ENST00000381657;ENST00000381663	T;T;T	0.29655	1.56;1.56;1.56	1.94	1.94	0.25998	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.000000	0.85682	D	0.000000	T	0.18676	0.0448	.	.	.	0.09310	N	1	B	0.26577	0.153	B	0.27796	0.083	T	0.16928	-1.0386	9	0.27082	T	0.32	-37.672	8.3073	0.32049	0.0:0.0:0.0:1.0	.	249	Q9NUJ7	PLCX1_HUMAN	A	249	ENSP00000381976:V249A;ENSP00000371073:V249A;ENSP00000371079:V249A	ENSP00000371073:V249A	V	+	2	0	PLCXD1	155776	1.000000	0.71417	0.644000	0.29465	0.029000	0.11900	4.999000	0.63934	0.835000	0.34877	0.337000	0.21675	GTG	.	.		0.617	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390	
MXRA5	25878	hgsc.bcm.edu	37	X	3241431	3241431	+	Missense_Mutation	SNP	A	A	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:3241431A>T	ENST00000217939.6	-	5	2449	c.2295T>A	c.(2293-2295)ttT>ttA	p.F765L		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	765						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GTCTAGATTCAAACACTCTGC	0.448																																					p.F765L		Atlas-SNP	.											.	MXRA5	815	.	0			c.T2295A						.						123.0	107.0	113.0					X																	3241431		2203	4300	6503	SO:0001583	missense	25878	exon5			AGATTCAAACACT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2295T>A	chrX.hg19:g.3241431A>T	ENSP00000217939:p.Phe765Leu	280.0	0.0		210.0	81.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	a	10.84	1.462709	0.26248	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64618	-0.11	3.63	-3.24	0.05094	.	0.000000	0.41605	U	0.000852	T	0.46268	0.1384	L	0.32530	0.975	0.25647	N	0.986139	B	0.15719	0.014	B	0.12156	0.007	T	0.28808	-1.0032	10	0.52906	T	0.07	.	12.7505	0.57306	0.8856:0.0:0.1144:0.0	.	765	Q9NR99	MXRA5_HUMAN	L	765	ENSP00000217939:F765L	ENSP00000217939:F765L	F	-	3	2	MXRA5	3251431	1.000000	0.71417	0.021000	0.16686	0.029000	0.11900	0.786000	0.26844	-0.933000	0.03737	-0.395000	0.06472	TTT	.	.		0.448	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329896	24329896	+	IGR	SNP	C	C	G	rs386824350		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:24329896C>G								AC096509.1 (25102 upstream) : AC004552.1 (37029 downstream)																							gcaggagcagcagcaggagca	0.612																																					p.A513P		Atlas-SNP	.											.	.	.	.	0			c.G1537C						.						10.0	9.0	10.0					X																	24329896		689	1584	2273	SO:0001628	intergenic_variant	170067	exon1			GAGCAGCAGCAGG																													chrX.hg19:g.24329896C>G		177.0	0.0		177.0	25.0	NM_001136233		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.612								
KCND1	3750	hgsc.bcm.edu	37	X	48823420	48823420	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:48823420T>C	ENST00000218176.3	-	2	2512	c.1215A>G	c.(1213-1215)ccA>ccG	p.P405P	KCND1_ENST00000376477.1_Silent_p.P28P	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	405					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	ACACAATGACTGGCACAGGCA	0.577																																					p.P405P		Atlas-SNP	.											.	KCND1	63	.	0			c.A1215G						.						136.0	91.0	106.0					X																	48823420		2203	4300	6503	SO:0001819	synonymous_variant	3750	exon2			AATGACTGGCACA	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1215A>G	chrX.hg19:g.48823420T>C		82.0	0.0		88.0	6.0	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	hg19	CCDS14314.1																																																																																			.	.		0.577	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979	
TAF1	6872	hgsc.bcm.edu	37	X	70607151	70607151	+	Missense_Mutation	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:70607151A>G	ENST00000373790.4	+	15	2315	c.2264A>G	c.(2263-2265)cAt>cGt	p.H755R	TAF1_ENST00000276072.3_Missense_Mutation_p.H776R|TAF1_ENST00000449580.1_Missense_Mutation_p.H755R|TAF1_ENST00000423759.1_Missense_Mutation_p.H776R	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	755	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ATTTATCTTCATAAGATGCCA	0.373																																					p.H776R		Atlas-SNP	.											.	TAF1	439	.	0			c.A2327G						.						137.0	127.0	131.0					X																	70607151		2203	4300	6503	SO:0001583	missense	6872	exon15			ATCTTCATAAGAT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2264A>G	chrX.hg19:g.70607151A>G	ENSP00000362895:p.His755Arg	256.0	0.0		235.0	86.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	20.9	4.068723	0.76301	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	5.03	5.03	0.67393	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.090151	0.85682	D	0.000000	T	0.52709	0.1751	M	0.89478	3.035	0.80722	D	1	D;P	0.76494	0.999;0.709	D;P	0.85130	0.997;0.781	T	0.62905	-0.6755	10	0.87932	D	0	.	14.1119	0.65126	1.0:0.0:0.0:0.0	.	755;776	P21675;P21675-2	TAF1_HUMAN;.	R	755;755;776;776	ENSP00000362895:H755R;ENSP00000389000:H755R;ENSP00000406549:H776R;ENSP00000276072:H776R	ENSP00000276072:H776R	H	+	2	0	TAF1	70523876	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.954000	0.93051	1.779000	0.52309	0.373000	0.22412	CAT	.	.		0.373	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
GLA	2717	hgsc.bcm.edu	37	X	100658874	100658874	+	Silent	SNP	G	G	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:100658874G>T	ENST00000218516.3	-	2	315	c.294C>A	c.(292-294)ccC>ccA	p.P98P	GLA_ENST00000479445.1_5'UTR|RPL36A-HNRNPH2_ENST00000409170.3_Intron	NM_000169.2	NP_000160.1	P06280	AGAL_HUMAN	galactosidase, alpha	98					glycoside catabolic process (GO:0016139)|glycosphingolipid catabolic process (GO:0046479)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|oligosaccharide metabolic process (GO:0009311)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|catalytic activity (GO:0003824)|galactoside binding (GO:0016936)|hydrolase activity (GO:0016787)|protein homodimerization activity (GO:0042803)|raffinose alpha-galactosidase activity (GO:0052692)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						AATCTCTTTGGGGAGCCATCC	0.478																																					p.P98P	Colon(193;776 2816 31189 44474)	Atlas-SNP	.											.	GLA	43	.	0			c.C294A						.						190.0	171.0	177.0					X																	100658874		2203	4300	6503	SO:0001819	synonymous_variant	2717	exon2			TCTTTGGGGAGCC	X16889	CCDS14484.1	Xq21.3-q22	2014-09-17			ENSG00000102393	ENSG00000102393	3.2.1.22		4296	protein-coding gene	gene with protein product		300644					Standard	NM_000169		Approved	GALA	uc004ehl.1	P06280	OTTHUMG00000022026	ENST00000218516.3:c.294C>A	chrX.hg19:g.100658874G>T		135.0	0.0		99.0	36.0	NM_000169	Q6LER7	Silent	SNP	ENST00000218516.3	hg19	CCDS14484.1																																																																																			.	.		0.478	GLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057540.1		
COL4A6	1288	hgsc.bcm.edu	37	X	107418370	107418370	+	Missense_Mutation	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:107418370T>C	ENST00000372216.4	-	30	3009	c.2909A>G	c.(2908-2910)gAc>gGc	p.D970G	COL4A6_ENST00000545689.1_Missense_Mutation_p.D969G|COL4A6_ENST00000394872.2_Missense_Mutation_p.D970G|COL4A6_ENST00000334504.7_Missense_Mutation_p.D969G|COL4A6_ENST00000538570.1_Missense_Mutation_p.D969G	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	970	Triple-helical region.				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)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						AGAGCCTTTGTCTCCTTTGAG	0.537									Alport syndrome with Diffuse Leiomyomatosis																												p.D970G	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.A2909G						.						182.0	163.0	170.0					X																	107418370		2203	4300	6503	SO:0001583	missense	1288	exon30	Familial Cancer Database		CCTTTGTCTCCTT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.2909A>G	chrX.hg19:g.107418370T>C	ENSP00000361290:p.Asp970Gly	122.0	0.0		106.0	5.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.679782	0.47886	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36;-3.36	5.08	5.08	0.68730	.	0.154911	0.30437	N	0.009625	D	0.94059	0.8096	L	0.41632	1.29	0.29469	N	0.857154	D;D;D;P	0.71674	0.992;0.992;0.998;0.93	P;P;D;P	0.74674	0.893;0.893;0.984;0.839	D	0.90259	0.4299	10	0.66056	D	0.02	.	10.3079	0.43691	0.0:0.0:0.1629:0.8371	.	969;969;970;969	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	G	970;969;970;969;969;969	ENSP00000361290:D970G;ENSP00000334733:D969G;ENSP00000378340:D970G;ENSP00000443707:D969G;ENSP00000445236:D969G	ENSP00000334733:D969G	D	-	2	0	COL4A6	107305026	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.069000	0.50026	1.952000	0.56665	0.481000	0.45027	GAC	.	.		0.537	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
RBMXL3	139804	hgsc.bcm.edu	37	X	114424946	114424946	+	Silent	SNP	C	C	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:114424946C>T	ENST00000424776.3	+	1	984	c.942C>T	c.(940-942)gcC>gcT	p.A314A	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	314							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						GCGGCGCTGCCCCTGTGTGGG	0.627																																					p.A314A		Atlas-SNP	.											.	RBMXL3	83	.	0			c.C942T						.						32.0	34.0	33.0					X																	114424946		692	1591	2283	SO:0001819	synonymous_variant	139804	exon1			CGCTGCCCCTGTG	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.942C>T	chrX.hg19:g.114424946C>T		144.0	0.0		130.0	11.0	NM_001145346	B4DXC0	Silent	SNP	ENST00000424776.3	hg19	CCDS55478.1																																																																																			.	.		0.627	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
FATE1	89885	hgsc.bcm.edu	37	X	150884642	150884642	+	Silent	SNP	A	A	G			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:150884642A>G	ENST00000370350.3	+	1	136	c.51A>G	c.(49-51)gcA>gcG	p.A17A		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	17						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					TGTCCCTGGCAGAAGAACTGA	0.537																																					p.A17A		Atlas-SNP	.											.	FATE1	30	.	0			c.A51G						.						87.0	66.0	74.0					X																	150884642		2040	3766	5806	SO:0001819	synonymous_variant	89885	exon1			CCTGGCAGAAGAA	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"""cancer/testis antigen 43"""	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.51A>G	chrX.hg19:g.150884642A>G		175.0	0.0		146.0	40.0	NM_033085		Silent	SNP	ENST00000370350.3	hg19	CCDS14700.1																																																																																			.	.		0.537	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085	
GABRQ	55879	hgsc.bcm.edu	37	X	151815446	151815446	+	Missense_Mutation	SNP	A	A	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:151815446A>C	ENST00000370306.2	+	4	364	c.344A>C	c.(343-345)aAa>aCa	p.K115T		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	115					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAGACTTGGAAAGATTCACGC	0.463																																					p.K115T		Atlas-SNP	.											.	GABRQ	131	.	0			c.A344C						.						247.0	191.0	210.0					X																	151815446		2203	4300	6503	SO:0001583	missense	55879	exon4			CTTGGAAAGATTC	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.344A>C	chrX.hg19:g.151815446A>C	ENSP00000359329:p.Lys115Thr	179.0	0.0		149.0	61.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921464	0.52653	.	.	ENSG00000147402	ENST00000370306	T	0.76448	-1.02	5.51	4.38	0.52667	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.46758	D	0.000265	T	0.72811	0.3507	L	0.27975	0.815	0.32420	N	0.549513	P	0.51791	0.948	P	0.57425	0.82	T	0.76170	-0.3057	10	0.51188	T	0.08	.	3.7045	0.08395	0.7044:0.0:0.2956:0.0	.	115	Q9UN88	GBRT_HUMAN	T	115	ENSP00000359329:K115T	ENSP00000359329:K115T	K	+	2	0	GABRQ	151566102	1.000000	0.71417	0.999000	0.59377	0.478000	0.33099	4.577000	0.60922	1.844000	0.53588	0.441000	0.28932	AAA	.	.		0.463	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
GJB1	2705	hgsc.bcm.edu	37	X	70445066	70445069	+	3'UTR	DEL	TGTT	TGTT	-			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:70445066_70445069delTGTT	ENST00000374022.3	+	0	1604_1607					NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa						cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					GTGGCTTGTGTGTTTGTCAAGTTC	0.456																																					.		Atlas-Indel,Pindel	.											.	GJB1	21	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	2705	.			.	X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"""Ion channels / Gap junction proteins (connexins)"""	4283	protein-coding gene	gene with protein product	"""Charcot-Marie-Tooth neuropathy, X-linked"", ""connexin 32"""	304040	"""gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)"", ""gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)"", ""gap junction protein, beta 1, 32kDa (connexin 32)"""	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.*660TGTT>-	chrX.hg19:g.70445066_70445069delTGTT		123.0	0.0		118.0	42.0	.	B2R8R2|D3DVV2|Q5U0S4	RNA	DEL	ENST00000374022.3	hg19	CCDS14408.1																																																																																			.	.		0.456	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166	
L1CAM	3897	hgsc.bcm.edu	37	X	153129904	153129904	+	Silent	SNP	T	T	C			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:153129904T>C	ENST00000370060.1	-	25	3384	c.3195A>G	c.(3193-3195)ccA>ccG	p.P1065P	L1CAM_ENST00000538883.1_Silent_p.P1067P|L1CAM_ENST00000370057.3_Silent_p.P1065P|L1CAM_ENST00000361981.3_Silent_p.P1060P|L1CAM_ENST00000361699.4_Silent_p.P1065P|L1CAM_ENST00000543994.1_Silent_p.P1067P|L1CAM_ENST00000370055.1_Silent_p.P1060P	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1065	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGACATACTGTGGCGAAAGGG	0.602																																					p.P1065P		Atlas-SNP	.											.	L1CAM	189	.	0			c.A3195G						.						125.0	109.0	115.0					X																	153129904		2203	4300	6503	SO:0001819	synonymous_variant	3897	exon24			ATACTGTGGCGAA	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	6470	protein-coding gene	gene with protein product		308840	"""antigen identified by monoclonal antibody R1"""	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.3195A>G	chrX.hg19:g.153129904T>C		80.0	0.0		97.0	4.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Silent	SNP	ENST00000370060.1	hg19	CCDS14733.1																																																																																			.	.		0.602	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	
GRAMD1B	57476	hgsc.bcm.edu	37	11	123489856	123489856	+	Frame_Shift_Del	DEL	C	C	-	rs148264959	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr11:123489856delC	ENST00000529750.1	+	19	2378	c.2051delC	c.(2050-2052)tccfs	p.S684fs	GRAMD1B_ENST00000450171.2_Frame_Shift_Del_p.S371fs|GRAMD1B_ENST00000456860.2_Frame_Shift_Del_p.S691fs|GRAMD1B_ENST00000322282.7_Frame_Shift_Del_p.S684fs	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	684						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CTCTTAGAGTCCCAACAAAAG	0.522																																					p.S684fs		Atlas-Indel,Pindel	.											.	GRAMD1B	122	.	0			c.2050delT						.						55.0	52.0	53.0					11																	123489856		1923	4119	6042	SO:0001589	frameshift_variant	57476	exon19			.	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.2051delC	chr11.hg19:g.123489856delC	ENSP00000436500:p.Ser684fs	49.0	0.0		50.0	14.0	NM_020716	Q6UW85|Q9ULL9	Frame_Shift_Del	DEL	ENST00000529750.1	hg19	CCDS53720.1																																																																																			.	.		0.522	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660	
HSPG2	3339	hgsc.bcm.edu	37	1	22159859	22159872	+	Frame_Shift_Del	DEL	AAGTAGGGCACCAC	AAGTAGGGCACCAC	-			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	AAGTAGGGCACCAC	AAGTAGGGCACCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr1:22159859_22159872delAAGTAGGGCACCAC	ENST00000374695.3	-	80	11063_11076	c.10984_10997delGTGGTGCCCTACTT	c.(10984-10998)gtggtgccctacttcfs	p.VVPYF3662fs	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3662	Ig-like C2-type 22.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGTCTGCGTGAAGTAGGGCACCACCCGCTCTGCC	0.603																																					p.3662_3666del		Atlas-Indel,Pindel	.											.	HSPG2	311	.	0			c.10985_10998del						.																																			SO:0001589	frameshift_variant	3339	exon80			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10984_10997delGTGGTGCCCTACTT	chr1.hg19:g.22159859_22159872delAAGTAGGGCACCAC	ENSP00000363827:p.Val3662fs	83.0	0.0		106.0	10.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.603	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
CUL1	8454	hgsc.bcm.edu	37	7	148456419	148456422	+	Frame_Shift_Del	DEL	CTGT	CTGT	-			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr7:148456419_148456422delCTGT	ENST00000325222.4	+	5	786_789	c.507_510delCTGT	c.(505-510)gactgtfs	p.DC169fs	CUL1_ENST00000602748.1_Frame_Shift_Del_p.DC169fs|CUL1_ENST00000409469.1_Frame_Shift_Del_p.DC169fs	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	169					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			CTTGGAGAGACTGTCTGTTCAGGC	0.397																																					p.169_170del		Atlas-Indel,Pindel	.											.	CUL1	80	.	0			c.506_509del						.																																			SO:0001589	frameshift_variant	8454	exon5			.	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.507_510delCTGT	chr7.hg19:g.148456423_148456426delCTGT	ENSP00000326804:p.Asp169fs	123.0	0.0		180.0	29.0	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Frame_Shift_Del	DEL	ENST00000325222.4	hg19	CCDS34772.1																																																																																			.	.		0.397	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592	
BIRC6	57448	hgsc.bcm.edu	37	2	32613893	32613893	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr2:32613893delA	ENST00000421745.2	+	4	855	c.721delA	c.(721-723)aaafs	p.K241fs		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	241					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGAACTCAAGAAAATAAATCA	0.448																																					p.K240fs	Pancreas(94;175 1509 16028 18060 45422)	Atlas-Indel,Pindel	.											.	BIRC6	838	.	0			c.720delG						.						154.0	131.0	138.0					2																	32613893		2203	4300	6503	SO:0001589	frameshift_variant	57448	exon4			.	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.721delA	chr2.hg19:g.32613893delA	ENSP00000393596:p.Lys241fs	168.0	0.0		171.0	30.0	NM_016252	Q9ULD1	Frame_Shift_Del	DEL	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.448	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
ODF2	4957	hgsc.bcm.edu	37	9	131256869	131256872	+	Frame_Shift_Del	DEL	TGAG	TGAG	-			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	TGAG	TGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr9:131256869_131256872delTGAG	ENST00000434106.3	+	17	2196_2199	c.1833_1836delTGAG	c.(1831-1836)gctgagfs	p.AE611fs	ODF2_ENST00000546203.1_Frame_Shift_Del_p.AE592fs|ODF2_ENST00000372791.3_Frame_Shift_Del_p.AE592fs|ODF2_ENST00000444119.2_Frame_Shift_Del_p.AE587fs|ODF2_ENST00000604420.1_Frame_Shift_Del_p.AE611fs|ODF2_ENST00000393533.2_Frame_Shift_Del_p.AE611fs|ODF2_ENST00000351030.3_Frame_Shift_Del_p.AE606fs|ODF2_ENST00000448249.3_Frame_Shift_Del_p.AE530fs|ODF2_ENST00000393527.3_Frame_Shift_Del_p.AE587fs|ODF2_ENST00000372814.3_Frame_Shift_Del_p.AE655fs|ODF2_ENST00000372807.5_Frame_Shift_Del_p.AE606fs	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	611					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.E588G(1)|p.E656G(1)|p.E612G(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CGAAGCTGGCTGAGTGCCAAGACC	0.578																																					p.675_676del		Atlas-Indel,Pindel	.											ODF2_ENST00000372814,NS,carcinoma,0,3	ODF2	227	.	3	Substitution - Missense(3)	kidney(3)	c.2024_2027del						.																																			SO:0001589	frameshift_variant	4957	exon17			.	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1833_1836delTGAG	chr9.hg19:g.131256869_131256872delTGAG	ENSP00000403453:p.Ala611fs	63.0	0.0		102.0	22.0	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Frame_Shift_Del	DEL	ENST00000434106.3	hg19	CCDS56588.1																																																																																			.	.		0.578	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
GPR132	29933	hgsc.bcm.edu	37	14	105517685	105517686	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:105517685_105517686insT	ENST00000329797.3	-	4	1699_1700	c.788_789insA	c.(787-789)ctcfs	p.L263fs	GPR132_ENST00000539291.2_Frame_Shift_Ins_p.L263fs|GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Frame_Shift_Ins_p.L254fs	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	263					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		CGGCTTTGACGAGGAGAACCAG	0.574																																					p.L263fs		Atlas-INDEL	.											.	GPR132	40	.	0			c.789_790insA						.																																			SO:0001589	frameshift_variant	29933	exon4			.	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"""GPCR / Class A : Orphans"""	17482	protein-coding gene	gene with protein product	"""G2 accumulation"""	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.788_789insA	chr14.hg19:g.105517685_105517686insT	ENSP00000328818:p.Leu263fs	59.0	0.0		193.0	39.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Frame_Shift_Ins	INS	ENST00000329797.3	hg19	CCDS9997.1																																																																																			.	.		0.574	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329882	24329884	+	IGR	DEL	TAA	TAA	-	rs386824350		TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	TAA	TAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chrX:24329882_24329884delTAA								AC096509.1 (25088 upstream) : AC004552.1 (37041 downstream)																							cagcagcagctaaagcaggagca	0.631																																					p.517_518del		Atlas-INDEL	.											.	.	.	.	0			c.1550_1552del						.			32,3237		3,13,13,1401,422						-0.8	0.0			8	18,5770		4,3,7,2100,1567	no	coding	FAM48B2	NM_001136233.1		7,16,20,3501,1989	A1A1,A1R,A1,RR,R		0.311,0.9789,0.5521				50,9007				SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24329882_24329884delTAA		170.0	0.0		162.0	10.0	NM_001136233		In_Frame_Del	DEL		hg19																																																																																				.	.	0	0.631								
ZNF512B	57473	hgsc.bcm.edu	37	20	62597492	62597583	+	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-	rs200518817|rs376642783|rs540039560|rs200940725|rs371234637|rs139142804|rs146666443	byFrequency	TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr20:62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	ENST00000450537.1	-	5	1005_1095	c.945_1035delAGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC	c.(943-1035)agagggaggaacagtggtaagaaaaggtatgggggctcgtcccaggtcggggaggaacagtggtaagaaaaggtatgggggctcgtcccaggt>ag	p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs	ZNF512B_ENST00000217130.3_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs|ZNF512B_ENST00000369888.1_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAA	0.575																																					p.338_345del		Pindel	.											.	ZNF512B	72	.	0			c.1012_1034del						.																																			SO:0001630	splice_region_variant	57473	exon5			.	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1034+1AGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC>-	chr20.hg19:g.62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT		0.0	0.0		121.0	11.0	NM_020713	Q08AK9|Q9ULM4	Frame_Shift_Del	DEL	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.575	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	Frame_Shift_Del
SCFD1	23256	hgsc.bcm.edu	37	14	31107344	31107345	+	Frame_Shift_Ins	INS	-	-	ACTAT			TCGA-BD-A3EP-01A-11D-A22F-10	TCGA-BD-A3EP-11A-12D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cd66ad6-837c-48db-b3a9-ed3e2558eef5	631a4a75-d468-41a0-9bf7-693499a63901	g.chr14:31107344_31107345insACTAT	ENST00000458591.2	+	5	553_554	c.326_327insACTAT	c.(325-330)caactafs	p.-111fs	SCFD1_ENST00000421551.3_Frame_Shift_Ins_p.-52fs|SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000544052.2_Frame_Shift_Ins_p.-44fs|SCFD1_ENST00000396629.2_Frame_Shift_Ins_p.-19fs	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1						post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		CTTCGAAATCAACTATATGAAT	0.287																																					p.Q109fs		Pindel	.											.	SCFD1	43	.	0			c.326_327insACTAT						.																																			SO:0001589	frameshift_variant	23256	exon5			.	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.327_331dupACTAT	chr14.hg19:g.31107345_31107349dupACTAT	ENSP00000390783:p.Tyr111fs	0.0	0.0		210.0	40.0	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Frame_Shift_Ins	INS	ENST00000458591.2	hg19	CCDS9639.1																																																																																			.	.		0.287	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
