#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
MEGF6	1953	hgsc.bcm.edu	37	1	3425655	3425655	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:3425655C>T	ENST00000356575.4	-	12	1738	c.1512G>A	c.(1510-1512)acG>acA	p.T504T	MEGF6_ENST00000294599.4_Silent_p.T399T	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	504						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		TCTCTGTGAGCGTGTGTTCGC	0.672																																					p.T504T	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G1512A						.						15.0	18.0	17.0					1																	3425655		1958	4117	6075	SO:0001819	synonymous_variant	1953	exon12			TGTGAGCGTGTGT	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.1512G>A	chr1.hg19:g.3425655C>T		114.0	0.0		138.0	41.0	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	hg19	CCDS41237.1																																																																																			.	.		0.672	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
COL16A1	1307	hgsc.bcm.edu	37	1	32158742	32158742	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:32158742T>A	ENST00000373672.3	-	13	1538	c.1022A>T	c.(1021-1023)gAg>gTg	p.E341V	COL16A1_ENST00000271069.6_Missense_Mutation_p.E341V|COL16A1_ENST00000373668.3_Missense_Mutation_p.E341V	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	341	Nonhelical region 10 (NC10).				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CAGGCCCCGCTCACCTTTCCC	0.632																																					p.E341V	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A1022T						.						35.0	37.0	37.0					1																	32158742		1928	4122	6050	SO:0001583	missense	1307	exon13			CCCCGCTCACCTT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1022A>T	chr1.hg19:g.32158742T>A	ENSP00000362776:p.Glu341Val	125.0	0.0		113.0	18.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497511	0.44455	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668;ENST00000373667	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	4.92	4.92	0.64577	.	0.150748	0.41938	D	0.000790	D	0.93223	0.7841	M	0.62266	1.93	0.38037	D	0.93533	P;P;P	0.49185	0.92;0.7;0.801	B;B;P	0.48704	0.341;0.383;0.587	D	0.94418	0.7638	10	0.62326	D	0.03	.	12.3899	0.55352	0.0:0.0:0.0:1.0	.	341;341;341	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	V	341;341;341;60	ENSP00000362776:E341V;ENSP00000271069:E341V;ENSP00000362772:E341V;ENSP00000362771:E60V	ENSP00000271069:E341V	E	-	2	0	COL16A1	31931329	1.000000	0.71417	0.965000	0.40720	0.658000	0.38924	4.988000	0.63863	1.996000	0.58369	0.379000	0.24179	GAG	.	.		0.632	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
CSMD2	114784	hgsc.bcm.edu	37	1	34498286	34498286	+	Silent	SNP	T	T	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:34498286T>G	ENST00000373381.4	-	3	602	c.426A>C	c.(424-426)ccA>ccC	p.P142P		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	102	Sushi 1. {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)				CAATGGTGGCTGGCAGCTGAA	0.527																																					p.P102P		Atlas-SNP	.											.	CSMD2	946	.	0			c.A306C						.						79.0	62.0	68.0					1																	34498286		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon3			GGTGGCTGGCAGC	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.426A>C	chr1.hg19:g.34498286T>G		83.0	0.0		93.0	12.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.527	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
CNN3	1266	hgsc.bcm.edu	37	1	95364951	95364951	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:95364951C>T	ENST00000370206.4	-	6	1007	c.624G>A	c.(622-624)atG>atA	p.M208I	CNN3_ENST00000394202.4_Missense_Mutation_p.M162I|CNN3_ENST00000538964.1_Missense_Mutation_p.M208I|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000545882.1_Missense_Mutation_p.M167I	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	208					actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		TATTAGTGCCCATCTGCAGAC	0.408																																					p.M208I		Atlas-SNP	.											.	CNN3	23	.	0			c.G624A						.						131.0	123.0	126.0					1																	95364951		2203	4300	6503	SO:0001583	missense	1266	exon6			AGTGCCCATCTGC	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.624G>A	chr1.hg19:g.95364951C>T	ENSP00000359225:p.Met208Ile	128.0	0.0		67.0	15.0	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Missense_Mutation	SNP	ENST00000370206.4	hg19	CCDS30775.1	.	.	.	.	.	.	.	.	.	.	C	31	5.069592	0.93950	.	.	ENSG00000117519	ENST00000370206;ENST00000538964;ENST00000394202;ENST00000545882;ENST00000415017	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.81069	0.4746	M	0.93978	3.48	0.80722	D	1	D;D	0.71674	0.998;0.963	D;D	0.69824	0.944;0.966	D	0.84795	0.0781	10	0.72032	D	0.01	-15.6579	20.2279	0.98344	0.0:1.0:0.0:0.0	.	162;208	F8WA86;Q15417	.;CNN3_HUMAN	I	208;208;162;167;167	ENSP00000359225:M208I;ENSP00000437665:M208I;ENSP00000377752:M162I;ENSP00000440081:M167I;ENSP00000401452:M167I	ENSP00000359225:M208I	M	-	3	0	CNN3	95137539	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.778000	0.95560	0.655000	0.94253	ATG	.	.		0.408	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839	
FNDC7	163479	hgsc.bcm.edu	37	1	109273448	109273448	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:109273448C>T	ENST00000370017.3	+	9	2054	c.1777C>T	c.(1777-1779)Ctc>Ttc	p.L593F	FNDC7_ENST00000271311.2_Missense_Mutation_p.L594F	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	593	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		AAACCACTGCCTCCTAGGATG	0.468																																					p.L593F		Atlas-SNP	.											.	FNDC7	113	.	0			c.C1777T						.						166.0	132.0	144.0					1																	109273448		2203	4300	6503	SO:0001583	missense	163479	exon9			CACTGCCTCCTAG		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1777C>T	chr1.hg19:g.109273448C>T	ENSP00000359034:p.Leu593Phe	106.0	0.0		98.0	18.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.1|20.1	3.935704|3.935704	0.73442|0.73442	.|.	.|.	ENSG00000143107|ENSG00000143107	ENST00000370017;ENST00000271311|ENST00000445274	D;D|.	0.99051|.	-5.37;-5.37|.	6.05|6.05	3.97|3.97	0.46021|0.46021	Fibronectin, type III (3);|.	0.195956|.	0.46442|.	D|.	0.000290|.	T|T	0.63105|0.63105	0.2483|0.2483	M|M	0.63843|0.63843	1.955|1.955	0.46279|0.46279	D|D	0.998968|0.998968	D;D|.	0.58620|.	0.983;0.969|.	P;P|.	0.59595|.	0.86;0.73|.	T|T	0.64685|0.64685	-0.6349|-0.6349	10|5	0.44086|.	T|.	0.13|.	-16.7176|-16.7176	16.7121|16.7121	0.85388|0.85388	0.2468:0.7532:0.0:0.0|0.2468:0.7532:0.0:0.0	.|.	594;593|.	Q5VTL7;E9PAZ5|.	FNDC7_HUMAN;.|.	F|L	593;594|368	ENSP00000359034:L593F;ENSP00000271311:L594F|.	ENSP00000271311:L594F|.	L|P	+|+	1|2	0|0	FNDC7|FNDC7	109074971|109074971	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.941000|0.941000	0.58515|0.58515	5.661000|5.661000	0.68025|0.68025	1.530000|1.530000	0.49136|0.49136	0.655000|0.655000	0.94253|0.94253	CTC|CCT	.	.		0.468	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
DCLRE1B	64858	hgsc.bcm.edu	37	1	114454510	114454510	+	Silent	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:114454510A>G	ENST00000369563.3	+	4	1742	c.1296A>G	c.(1294-1296)tcA>tcG	p.S432S	DCLRE1B_ENST00000466480.1_Intron	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	432					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		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)		TGGGATTTTCAGTGCACTTAA	0.463								Other identified genes with known or suspected DNA repair function																													p.S432S		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.A1296G						.						171.0	189.0	183.0					1																	114454510		2203	4300	6503	SO:0001819	synonymous_variant	64858	exon4			ATTTTCAGTGCAC	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"""APOLLO"", ""PSO2 homolog (S. cerevisiae)"""	609683	"""DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"""				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.1296A>G	chr1.hg19:g.114454510A>G		117.0	0.0		102.0	18.0	NM_022836	Q9H9E5	Silent	SNP	ENST00000369563.3	hg19	CCDS866.1																																																																																			.	.		0.463	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836	
LRRC71	149499	hgsc.bcm.edu	37	1	156901780	156901780	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:156901780A>G	ENST00000337428.7	+	13	1556	c.1402A>G	c.(1402-1404)Atg>Gtg	p.M468V	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	468										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						GAAAGTTTTCATGCCTGGGAA	0.552																																					p.M468V		Atlas-SNP	.											.	LRRC71	33	.	0			c.A1402G						.						78.0	83.0	81.0					1																	156901780		2046	4181	6227	SO:0001583	missense	149499	exon13			GTTTTCATGCCTG	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1402A>G	chr1.hg19:g.156901780A>G	ENSP00000336661:p.Met468Val	210.0	0.0		187.0	16.0	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	hg19	CCDS44249.1	.	.	.	.	.	.	.	.	.	.	A	9.998	1.232562	0.22626	.	.	ENSG00000160838	ENST00000337428	T	0.17854	2.25	5.68	-1.36	0.09085	.	0.216602	0.32819	N	0.005616	T	0.03348	0.0097	L	0.27053	0.805	0.23483	N	0.997586	B;B	0.24920	0.01;0.114	B;B	0.27262	0.004;0.078	T	0.37384	-0.9708	10	0.48119	T	0.1	-32.5944	6.0254	0.19652	0.2605:0.2118:0.0:0.5277	.	468;254	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	V	468	ENSP00000336661:M468V	ENSP00000336661:M468V	M	+	1	0	LRRC71	155168404	0.997000	0.39634	0.999000	0.59377	0.949000	0.60115	0.329000	0.19698	0.046000	0.15833	-0.490000	0.04691	ATG	.	.		0.552	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
DDR2	4921	hgsc.bcm.edu	37	1	162688873	162688873	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:162688873T>C	ENST00000367922.3	+	4	458	c.20T>C	c.(19-21)aTg>aCg	p.M7T	DDR2_ENST00000367921.3_Missense_Mutation_p.M7T	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	7					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	ATTCCCAGAATGCTCTTGGTG	0.448																																					p.M7T	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											.	DDR2	228	.	0			c.T20C						.						205.0	178.0	187.0					1																	162688873		2203	4300	6503	SO:0001583	missense	4921	exon4			CCAGAATGCTCTT	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.20T>C	chr1.hg19:g.162688873T>C	ENSP00000356899:p.Met7Thr	118.0	0.0		64.0	15.0	NM_001014796	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	hg19	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.611739	0.28712	.	.	ENSG00000162733	ENST00000446985;ENST00000415555;ENST00000542391;ENST00000367922;ENST00000367921	D;D;D;D	0.97688	-4.22;-4.49;-1.67;-1.67	4.25	3.12	0.35913	.	1.126930	0.06488	N	0.734009	D	0.91307	0.7259	L	0.36672	1.1	0.25662	N	0.985988	B	0.02656	0.0	B	0.06405	0.002	D	0.84515	0.0624	9	0.62326	D	0.03	.	6.3202	0.21213	0.0:0.1125:0.0:0.8875	.	7	Q16832	DDR2_HUMAN	T	7	ENSP00000400309:M7T;ENSP00000391310:M7T;ENSP00000356899:M7T;ENSP00000356898:M7T	ENSP00000356898:M7T	M	+	2	0	DDR2	160955497	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	1.360000	0.34125	0.796000	0.33947	0.383000	0.25322	ATG	.	.		0.448	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
MFSD4	148808	hgsc.bcm.edu	37	1	205568282	205568282	+	Silent	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:205568282T>C	ENST00000367147.4	+	9	1485	c.1392T>C	c.(1390-1392)taT>taC	p.Y464Y	MFSD4_ENST00000478555.1_3'UTR|MFSD4_ENST00000536357.1_Silent_p.Y377Y|MFSD4_ENST00000539267.1_Nonstop_Mutation_p.*441Q	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	464					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			AGGGCAGCTATAGTTTCCTGG	0.483																																					p.Y464Y		Atlas-SNP	.											.	MFSD4	46	.	0			c.T1392C						.						438.0	386.0	404.0					1																	205568282		2203	4300	6503	SO:0001819	synonymous_variant	148808	exon9			CAGCTATAGTTTC	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.1392T>C	chr1.hg19:g.205568282T>C		369.0	0.0		317.0	73.0	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Silent	SNP	ENST00000367147.4	hg19	CCDS1455.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.215492	0.39102	.	.	ENSG00000174514	ENST00000539267	.	.	.	5.64	-3.36	0.04913	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.5828	15.7076	0.77598	0.0:0.817:0.0:0.183	.	.	.	.	Q	441	.	.	X	+	1	0	MFSD4	203834905	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	0.873000	0.28052	-0.496000	0.06650	-0.376000	0.06991	TAG	.	.		0.483	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644	
OBSCN	84033	hgsc.bcm.edu	37	1	228461239	228461239	+	Intron	SNP	C	C	A	rs189809636	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:228461239C>A	ENST00000422127.1	+	18	5181				RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Intron|RP5-1139B12.3_ENST00000602529.1_RNA|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000570156.2_Missense_Mutation_p.H2085N|OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000359599.6_Missense_Mutation_p.H557N	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)				CTTCCGCCTGCACGTGGCAGG	0.632																																					p.H2085N		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	.	0			c.C6253A						.						29.0	39.0	36.0					1																	228461239		2111	4208	6319	SO:0001627	intron_variant	84033	exon21			CGCCTGCACGTGG	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.5138-232C>A	chr1.hg19:g.228461239C>A		224.0	0.0		156.0	21.0	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	.	.	.	.	.	.	.	.	.	.	C	1.065	-0.671828	0.03403	.	.	ENSG00000154358	ENST00000359599	T	0.04502	3.61	4.52	1.53	0.23141	.	.	.	.	.	T	0.02193	0.0068	N	0.02865	-0.47	0.80722	D	1	.	.	.	.	.	.	T	0.57165	-0.7858	7	0.17832	T	0.49	.	8.1064	0.30887	0.0843:0.3182:0.5975:0.0	.	.	.	.	N	557	ENSP00000352613:H557N	ENSP00000352613:H557N	H	+	1	0	OBSCN	226527862	0.000000	0.05858	0.240000	0.24138	0.057000	0.15508	-1.203000	0.03019	0.140000	0.18849	-0.502000	0.04539	CAC	.	C|0.995;T|0.005		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ZNF496	84838	hgsc.bcm.edu	37	1	247464447	247464447	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:247464447C>A	ENST00000294753.4	-	9	1602	c.1138G>T	c.(1138-1140)Gag>Tag	p.E380*	ZNF496_ENST00000366498.2_Nonsense_Mutation_p.E416*|ZNF496_ENST00000462139.1_5'UTR	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	380					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			CGCTGCTTCTCTGTGGGGCTC	0.632																																					p.E380X		Atlas-SNP	.											ZNF496,right_lower_lobe,carcinoma,0,1	ZNF496	80	.	0			c.G1138T						.						31.0	38.0	35.0					1																	247464447		2203	4296	6499	SO:0001587	stop_gained	84838	exon9			GCTTCTCTGTGGG	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.1138G>T	chr1.hg19:g.247464447C>A	ENSP00000294753:p.Glu380*	190.0	0.0		154.0	47.0	NM_032752	Q8TBS2	Nonsense_Mutation	SNP	ENST00000294753.4	hg19	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	C	37	6.432110	0.97564	.	.	ENSG00000162714	ENST00000294753;ENST00000366498	.	.	.	3.88	1.99	0.26369	.	0.757625	0.11666	N	0.541327	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-10.814	5.0192	0.14352	0.0:0.6497:0.0:0.3503	.	.	.	.	X	380;416	.	ENSP00000294753:E380X	E	-	1	0	ZNF496	245531070	0.001000	0.12720	0.022000	0.16811	0.021000	0.10359	1.225000	0.32551	0.983000	0.38602	0.591000	0.81541	GAG	.	.		0.632	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
TRIM58	25893	hgsc.bcm.edu	37	1	248039390	248039390	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr1:248039390G>A	ENST00000366481.3	+	6	1108	c.1060G>A	c.(1060-1062)Gaa>Aaa	p.E354K	OR2W3_ENST00000537741.1_Intron	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	354	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCTGGTGGGAGAAGGAGCAGA	0.572																																					p.E354K		Atlas-SNP	.											.	TRIM58	143	.	0			c.G1060A						.						110.0	100.0	103.0					1																	248039390		2203	4300	6503	SO:0001583	missense	25893	exon6			GTGGGAGAAGGAG	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	24150	protein-coding gene	gene with protein product			"""tripartite motif-containing 58"""				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.1060G>A	chr1.hg19:g.248039390G>A	ENSP00000355437:p.Glu354Lys	206.0	0.0		193.0	11.0	NM_015431	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	hg19	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	G	9.325	1.058964	0.19987	.	.	ENSG00000162722	ENST00000366481	T	0.61040	0.14	4.05	3.12	0.35913	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.828799	0.10839	N	0.628397	T	0.43255	0.1239	L	0.28054	0.825	0.80722	D	1	B	0.06786	0.001	B	0.12837	0.008	T	0.18618	-1.0331	10	0.23891	T	0.37	.	10.462	0.44585	0.0976:0.0:0.9024:0.0	.	354	Q8NG06	TRI58_HUMAN	K	354	ENSP00000355437:E354K	ENSP00000355437:E354K	E	+	1	0	TRIM58	246106013	1.000000	0.71417	0.089000	0.20774	0.062000	0.15995	5.895000	0.69814	1.288000	0.44600	0.650000	0.86243	GAA	.	.		0.572	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431	
CNTNAP5	129684	hgsc.bcm.edu	37	2	125555776	125555776	+	Silent	SNP	A	A	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:125555776A>T	ENST00000431078.1	+	19	3457	c.3093A>T	c.(3091-3093)acA>acT	p.T1031T		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1031	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTATTTACACAGATTCAGCTC	0.438																																					p.T1031T		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.A3093T						.						148.0	142.0	144.0					2																	125555776		1946	4150	6096	SO:0001819	synonymous_variant	129684	exon19			TTACACAGATTCA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.3093A>T	chr2.hg19:g.125555776A>T		243.0	0.0		199.0	53.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.		0.438	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
IWS1	55677	hgsc.bcm.edu	37	2	128247424	128247424	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:128247424G>A	ENST00000295321.4	-	11	2402	c.2143C>T	c.(2143-2145)Cga>Tga	p.R715*	AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	715	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		ATTCTTCGTCGTTGAGGCATC	0.413																																					p.R715X		Atlas-SNP	.											.	IWS1	61	.	0			c.C2143T						.						401.0	344.0	363.0					2																	128247424		2203	4300	6503	SO:0001587	stop_gained	55677	exon11			TTCGTCGTTGAGG	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2143C>T	chr2.hg19:g.128247424G>A	ENSP00000295321:p.Arg715*	348.0	0.0		268.0	41.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Nonsense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	G	39	7.512099	0.98329	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	.	.	.	5.03	3.16	0.36331	.	0.133236	0.50627	D	0.000119	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.7877	13.711	0.62667	0.0:0.0:0.7186:0.2814	.	.	.	.	X	715;668	.	ENSP00000295321:R715X	R	-	1	2	IWS1	127963894	1.000000	0.71417	0.989000	0.46669	0.943000	0.58893	2.581000	0.46077	0.480000	0.27534	0.563000	0.77884	CGA	.	.		0.413	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
MYO3B	140469	hgsc.bcm.edu	37	2	171259467	171259467	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:171259467C>G	ENST00000408978.4	+	19	2382	c.2239C>G	c.(2239-2241)Cag>Gag	p.Q747E	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.Q747E|MYO3B_ENST00000334231.6_Missense_Mutation_p.Q756E	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	747	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGAGCAAATCCAGTACTATTT	0.413																																					p.Q747E		Atlas-SNP	.											.	MYO3B	320	.	0			c.C2239G						.						125.0	114.0	117.0					2																	171259467		1872	4107	5979	SO:0001583	missense	140469	exon19			CAAATCCAGTACT		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2239C>G	chr2.hg19:g.171259467C>G	ENSP00000386213:p.Gln747Glu	126.0	0.0		102.0	16.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.879044	0.91740	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	6.02	6.02	0.97574	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93446	0.7909	H	0.98629	4.285	0.80722	D	1	D;D;D	0.76494	0.982;0.999;0.997	D;D;D	0.72075	0.91;0.975;0.976	D	0.95115	0.8241	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	747;747;747	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	E	747;747;746;756;756	ENSP00000386497:Q747E;ENSP00000386213:Q747E;ENSP00000446237:Q756E;ENSP00000335100:Q756E	ENSP00000314213:Q746E	Q	+	1	0	MYO3B	170967713	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.788000	0.85771	2.865000	0.98341	0.655000	0.94253	CAG	.	.		0.413	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
UNC80	285175	hgsc.bcm.edu	37	2	210699734	210699734	+	Splice_Site	SNP	A	A	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr2:210699734A>T	ENST00000439458.1	+	18	3121	c.3041A>T	c.(3040-3042)cAc>cTc	p.H1014L	UNC80_ENST00000272845.6_Splice_Site_p.H1009L	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1014					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						ACTCCAGAGCAGTAAGTAGCG	0.483																																					p.H1014L		Atlas-SNP	.											.	UNC80	280	.	0			c.A3041T						.						172.0	153.0	159.0					2																	210699734		692	1591	2283	SO:0001630	splice_region_variant	285175	exon18			CAGAGCAGTAAGT	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.3041+1A>T	chr2.hg19:g.210699734A>T		62.0	0.0		19.0	6.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	hg19	CCDS46504.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983462	0.74474	.	.	ENSG00000144406	ENST00000439458;ENST00000272845	T;T	0.32753	1.44;1.44	6.07	6.07	0.98685	.	0.250986	0.39834	N	0.001255	T	0.38081	0.1027	N	0.22421	0.69	0.80722	D	1	D	0.53462	0.96	D	0.64237	0.923	T	0.09271	-1.0682	10	0.12103	T	0.63	-15.2115	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1014	Q8N2C7	UNC80_HUMAN	L	1014;1009	ENSP00000391088:H1014L;ENSP00000272845:H1009L	ENSP00000272845:H1009L	H	+	2	0	UNC80	210407979	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.027000	0.88791	2.326000	0.78906	0.533000	0.62120	CAC	.	.		0.483	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	Missense_Mutation
NUP210	23225	hgsc.bcm.edu	37	3	13383318	13383318	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:13383318T>A	ENST00000254508.5	-	23	3240	c.3158A>T	c.(3157-3159)cAg>cTg	p.Q1053L	NUP210_ENST00000485755.1_5'Flank	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1053					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TAGACTGGTCTGGCCGATGGC	0.522																																					p.Q1053L		Atlas-SNP	.											.	NUP210	182	.	0			c.A3158T						.						151.0	126.0	134.0					3																	13383318		2203	4300	6503	SO:0001583	missense	23225	exon23			CTGGTCTGGCCGA	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3158A>T	chr3.hg19:g.13383318T>A	ENSP00000254508:p.Gln1053Leu	217.0	0.0		193.0	57.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.482924	0.63962	.	.	ENSG00000132182	ENST00000254508	T	0.04917	3.53	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.13602	-1.0503	10	0.02654	T	1	-17.7609	14.8389	0.70209	0.0:0.0:0.0:1.0	.	1053	Q8TEM1	PO210_HUMAN	L	1053	ENSP00000254508:Q1053L	ENSP00000254508:Q1053L	Q	-	2	0	NUP210	13358318	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	7.073000	0.76784	2.147000	0.66899	0.455000	0.32223	CAG	.	.		0.522	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
SCN5A	6331	hgsc.bcm.edu	37	3	38645542	38645542	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:38645542C>T	ENST00000333535.4	-	12	1700	c.1551G>A	c.(1549-1551)agG>agA	p.R517R	SCN5A_ENST00000425664.1_Silent_p.R517R|SCN5A_ENST00000451551.2_Silent_p.R517R|SCN5A_ENST00000413689.1_Silent_p.R517R|SCN5A_ENST00000423572.2_Silent_p.R517R|SCN5A_ENST00000414099.2_Silent_p.R517R|SCN5A_ENST00000455624.2_Silent_p.R517R|SCN5A_ENST00000443581.1_Silent_p.R517R|SCN5A_ENST00000450102.2_Silent_p.R517R|SCN5A_ENST00000449557.2_Silent_p.R517R			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	517					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	TCATAGAAGTCCTGCTGAGGC	0.537																																					p.R517R		Atlas-SNP	.											.	SCN5A	634	.	0			c.G1551A						.						27.0	28.0	28.0					3																	38645542		2040	4209	6249	SO:0001819	synonymous_variant	6331	exon12			AGAAGTCCTGCTG	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1551G>A	chr3.hg19:g.38645542C>T		101.0	0.0		107.0	16.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	hg19	CCDS46796.1																																																																																			.	.		0.537	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
SCN11A	11280	hgsc.bcm.edu	37	3	38991632	38991632	+	Silent	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:38991632T>A	ENST00000302328.3	-	1	420	c.222A>T	c.(220-222)atA>atT	p.I74I	SCN11A_ENST00000444237.2_Silent_p.I74I|SCN11A_ENST00000450244.1_Silent_p.I74I|SCN11A_ENST00000456224.3_Silent_p.I74I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	74					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)	GAGGCTTTCCTATGAGCTCAC	0.562																																					p.I74I		Atlas-SNP	.											.	SCN11A	296	.	0			c.A222T						.						100.0	102.0	101.0					3																	38991632		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon1			CTTTCCTATGAGC	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.222A>T	chr3.hg19:g.38991632T>A		170.0	0.0		152.0	26.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.		0.562	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
POLQ	10721	hgsc.bcm.edu	37	3	121179064	121179064	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:121179064C>A	ENST00000264233.5	-	25	7113	c.6985G>T	c.(6985-6987)Gct>Tct	p.A2329S		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2329					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GAGTAGTCAGCAGCCAGTATT	0.398								DNA polymerases (catalytic subunits)																													p.A2329S	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G6985T						.						75.0	71.0	72.0					3																	121179064		2203	4300	6503	SO:0001583	missense	10721	exon25			AGTCAGCAGCCAG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6985G>T	chr3.hg19:g.121179064C>A	ENSP00000264233:p.Ala2329Ser	159.0	0.0		155.0	24.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.047027	0.93740	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.97352	-4.35	5.6	5.6	0.85130	DNA-directed DNA polymerase, family A, palm domain (2);	0.111909	0.64402	D	0.000011	D	0.98501	0.9500	M	0.79693	2.465	0.44908	D	0.997926	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.99338	1.0911	10	0.72032	D	0.01	.	19.6126	0.95616	0.0:1.0:0.0:0.0	.	2329;1501	O75417;O75417-2	DPOLQ_HUMAN;.	S	1952;2329;2465	ENSP00000264233:A2329S	ENSP00000264233:A2329S	A	-	1	0	POLQ	122661754	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.172000	0.77604	2.630000	0.89119	0.591000	0.81541	GCT	.	.		0.398	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MGLL	11343	hgsc.bcm.edu	37	3	127413989	127413989	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:127413989C>T	ENST00000434178.2	-	7	1511	c.615G>A	c.(613-615)ctG>ctA	p.L205L	MGLL_ENST00000265052.5_Silent_p.L215L|MGLL_ENST00000398104.1_Silent_p.L205L|MGLL_ENST00000398101.3_Silent_p.L179L|MGLL_ENST00000453507.2_Silent_p.L185L|MGLL_ENST00000476682.1_5'UTR			Q99685	MGLL_HUMAN	monoglyceride lipase	205					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						AGCACACCTTCAGCCCTGCCC	0.612																																					p.L215L		Atlas-SNP	.											.	MGLL	19	.	0			c.G645A						.						49.0	54.0	52.0					3																	127413989		2067	4195	6262	SO:0001819	synonymous_variant	11343	exon7			CACCTTCAGCCCT	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.615G>A	chr3.hg19:g.127413989C>T		232.0	0.0		165.0	36.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	hg19	CCDS43148.1																																																																																			.	.		0.612	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
WDR49	151790	hgsc.bcm.edu	37	3	167277892	167277892	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:167277892T>A	ENST00000308378.3	-	5	916	c.611A>T	c.(610-612)gAg>gTg	p.E204V	WDR49_ENST00000453925.2_Missense_Mutation_p.E257V|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.E29V	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	204										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						AAGCCGAGTCTCATTTGCATC	0.448																																					p.E204V		Atlas-SNP	.											.	WDR49	188	.	0			c.A611T						.						189.0	172.0	178.0					3																	167277892		2203	4300	6503	SO:0001583	missense	151790	exon5			CGAGTCTCATTTG	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.611A>T	chr3.hg19:g.167277892T>A	ENSP00000311343:p.Glu204Val	222.0	0.0		152.0	44.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.514|9.514	1.106465|1.106465	0.20632|0.20632	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925;ENST00000466760|ENST00000472600	T;T;T;T|.	0.60424|.	1.51;1.22;2.09;0.19|.	4.94|4.94	3.77|3.77	0.43336|0.43336	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.308110|.	0.34700|.	N|.	0.003745|.	T|.	0.50034|.	0.1592|.	L|L	0.52905|0.52905	1.665|1.665	0.26302|0.26302	N|N	0.977969|0.977969	P;P|.	0.50369|.	0.934;0.829|.	P;P|.	0.47346|.	0.541;0.544|.	T|.	0.38520|.	-0.9657|.	10|.	0.72032|.	D|.	0.01|.	.|.	11.3497|11.3497	0.49581|0.49581	0.0:0.0:0.1526:0.8474|0.0:0.0:0.1526:0.8474	.|.	257;204|.	E7EQK3;Q8IV35|.	.;WDR49_HUMAN|.	V|X	204;29;257;97|269	ENSP00000311343:E204V;ENSP00000420508:E29V;ENSP00000410863:E257V;ENSP00000418718:E97V|.	ENSP00000311343:E204V|.	E|R	-|-	2|1	0|2	WDR49|WDR49	168760586|168760586	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.483000|0.483000	0.33249|0.33249	2.697000|2.697000	0.47060|0.47060	0.839000|0.839000	0.34971|0.34971	-0.338000|-0.338000	0.08134|0.08134	GAG|AGA	.	.		0.448	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
LAMTOR3	8649	hgsc.bcm.edu	37	4	100808468	100808468	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:100808468C>A	ENST00000499666.2	-	4	280	c.88G>T	c.(88-90)Gta>Tta	p.V30L	LAMTOR3_ENST00000226522.8_Missense_Mutation_p.V30L|LAMTOR3_ENST00000515100.1_5'UTR	NM_001243736.1|NM_021970.3	NP_001230665.1|NP_068805.1	Q9UHA4	LTOR3_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	30					cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Ragulator complex (GO:0071986)				endometrium(1)|large_intestine(1)|lung(1)	3						ATAACAGGTACTCCATCTCTA	0.289																																					p.V30L		Atlas-SNP	.											.	LAMTOR3	6	.	0			c.G88T						.						54.0	50.0	51.0					4																	100808468		2202	4296	6498	SO:0001583	missense	8649	exon4			CAGGTACTCCATC	AF201947	CCDS3652.1, CCDS58920.1	4q24-q26	2012-02-28	2011-02-15	2011-02-15	ENSG00000109270	ENSG00000109270			15606	protein-coding gene	gene with protein product	"""MEK partner 1"""	603296	"""mitogen-activated protein kinase kinase 1 interacting protein 1"", ""MAPK scaffold protein 1"""	MAP2K1IP1, MAPKSP1		9733512, 15016825	Standard	NM_021970		Approved	MP1, MAPBP, Ragulator3	uc003hvg.2	Q9UHA4	OTTHUMG00000131050	ENST00000499666.2:c.88G>T	chr4.hg19:g.100808468C>A	ENSP00000424183:p.Val30Leu	214.0	0.0		143.0	42.0	NM_021970	B2R4A1|J3KMX4|Q9H364	Missense_Mutation	SNP	ENST00000499666.2	hg19	CCDS3652.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571581	0.65765	.	.	ENSG00000109270	ENST00000499666;ENST00000226522	.	.	.	4.72	4.72	0.59763	.	0.122073	0.56097	D	0.000040	T	0.72843	0.3511	M	0.87827	2.91	0.80722	D	1	B;B	0.28208	0.203;0.008	B;B	0.26864	0.074;0.009	T	0.76990	-0.2754	9	0.87932	D	0	.	18.0646	0.89387	0.0:1.0:0.0:0.0	.	30;30	Q53FH6;Q9UHA4	.;LTOR3_HUMAN	L	30	.	ENSP00000226522:V30L	V	-	1	0	LAMTOR3	101027491	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.137000	0.77295	2.343000	0.79666	0.467000	0.42956	GTA	.	.		0.289	LAMTOR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253698.2	NM_021970	
PDCD6	10016	hgsc.bcm.edu	37	5	306821	306821	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:306821G>C	ENST00000264933.4	+	4	413	c.313G>C	c.(313-315)Gac>Cac	p.D105H	AHRR_ENST00000505113.1_Intron|PDCD6_ENST00000511482.1_3'UTR|PDCD6_ENST00000505221.1_Intron|AHRR_ENST00000512529.1_Intron|AHRR_ENST00000316418.5_Intron|PDCD6_ENST00000507528.1_Missense_Mutation_p.D105H	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	105	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			GTACGACCGGGACAACTCCGG	0.542																																					p.D105H		Atlas-SNP	.											.	PDCD6	24	.	0			c.G313C						.						148.0	120.0	129.0					5																	306821		2203	4300	6503	SO:0001583	missense	10016	exon4			GACCGGGACAACT	AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"""EF-hand domain containing"""	8765	protein-coding gene	gene with protein product	"""apoptosis-linked gene-2"""	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.313G>C	chr5.hg19:g.306821G>C	ENSP00000264933:p.Asp105His	184.0	0.0		220.0	30.0	NM_001267556	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	hg19	CCDS3854.1	.	.	.	.	.	.	.	.	.	.	g	18.39	3.612557	0.66672	.	.	ENSG00000249915	ENST00000264933;ENST00000507528	T;T	0.46063	0.88;0.88	5.53	5.53	0.82687	EF-hand-like domain (1);	.	.	.	.	T	0.80166	0.4573	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88520	0.3095	9	0.87932	D	0	.	16.9576	0.86263	0.0:0.0:1.0:0.0	.	105;105	Q2YDC2;O75340	.;PDCD6_HUMAN	H	105	ENSP00000264933:D105H;ENSP00000423815:D105H	ENSP00000264933:D105H	D	+	1	0	PDCD6	359821	1.000000	0.71417	1.000000	0.80357	0.178000	0.23041	8.839000	0.92120	2.599000	0.87857	0.650000	0.86243	GAC	.	.		0.542	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232	
EXOC3	11336	hgsc.bcm.edu	37	5	464493	464493	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:464493A>G	ENST00000512944.1	+	10	1931	c.1742A>G	c.(1741-1743)aAc>aGc	p.N581S	CTD-2228K2.5_ENST00000510714.1_5'Flank|EXOC3_ENST00000315013.5_Missense_Mutation_p.N581S	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	592					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GACTATTTCAACGATTTTGCC	0.443																																					p.N581S		Atlas-SNP	.											.	EXOC3	54	.	0			c.A1742G						.						147.0	149.0	149.0					5																	464493		1961	4130	6091	SO:0001583	missense	11336	exon10			ATTTCAACGATTT	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"""SEC6-like 1 (S. cerevisiae)"""	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.1742A>G	chr5.hg19:g.464493A>G	ENSP00000425587:p.Asn581Ser	85.0	0.0		74.0	7.0	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Missense_Mutation	SNP	ENST00000512944.1	hg19	CCDS54830.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.748380	0.49257	.	.	ENSG00000180104	ENST00000512944;ENST00000315013;ENST00000340158	T;T	0.06608	3.28;3.28	4.92	3.75	0.43078	.	0.046651	0.85682	N	0.000000	T	0.05456	0.0144	L	0.45137	1.4	0.58432	D	0.999999	B	0.02656	0.0	B	0.12156	0.007	T	0.21484	-1.0244	10	0.07813	T	0.8	-28.488	9.0643	0.36453	0.911:0.0:0.089:0.0	.	592	O60645	EXOC3_HUMAN	S	581;581;476	ENSP00000425587:N581S;ENSP00000323377:N581S	ENSP00000323377:N581S	N	+	2	0	EXOC3	517493	1.000000	0.71417	0.845000	0.33349	0.611000	0.37282	4.533000	0.60615	0.829000	0.34733	0.533000	0.62120	AAC	.	.		0.443	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277	
MAP1B	4131	hgsc.bcm.edu	37	5	71491475	71491475	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:71491475T>C	ENST00000296755.7	+	5	2591	c.2293T>C	c.(2293-2295)Tct>Cct	p.S765P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	765	Lys-rich (highly basic, contains many KKEE and KKEI/V repeats).				axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GAAGGAAGAGTCTGTCAAGAA	0.443																																					p.S765P	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T2293C						.						78.0	85.0	83.0					5																	71491475		2203	4300	6503	SO:0001583	missense	4131	exon5			GAAGAGTCTGTCA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2293T>C	chr5.hg19:g.71491475T>C	ENSP00000296755:p.Ser765Pro	116.0	0.0		82.0	12.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.552924	0.00138	.	.	ENSG00000131711	ENST00000296755	T	0.25579	1.79	5.63	-9.33	0.00639	.	0.731439	0.13093	N	0.414380	T	0.07818	0.0196	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12967	-1.0527	10	0.21014	T	0.42	2.3708	5.3613	0.16089	0.0741:0.185:0.2202:0.5208	.	639;765	A2BDK6;P46821	.;MAP1B_HUMAN	P	765	ENSP00000296755:S765P	ENSP00000296755:S765P	S	+	1	0	MAP1B	71527231	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-4.608000	0.00209	-2.962000	0.00289	-1.139000	0.01908	TCT	.	.		0.443	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111600669	111600669	+	Missense_Mutation	SNP	C	C	A	rs370791654		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:111600669C>A	ENST00000261486.5	-	6	754	c.478G>T	c.(478-480)Gta>Tta	p.V160L		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	160	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TACTCAGATACATATCCTGCA	0.338																																					p.V160L		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.G478T						.						167.0	153.0	157.0					5																	111600669		1826	4095	5921	SO:0001583	missense	64097	exon6			CAGATACATATCC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.478G>T	chr5.hg19:g.111600669C>A	ENSP00000261486:p.Val160Leu	75.0	0.0		85.0	13.0	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368726	0.82463	.	.	ENSG00000129595	ENST00000261486	T	0.68903	-0.36	5.46	5.46	0.80206	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.64402	D	0.000001	T	0.71409	0.3336	N	0.17723	0.515	0.40048	D	0.975742	D	0.89917	1.0	D	0.85130	0.997	T	0.71724	-0.4506	10	0.34782	T	0.22	.	18.0769	0.89430	0.0:1.0:0.0:0.0	.	160	Q9HCS5	E41LA_HUMAN	L	160	ENSP00000261486:V160L	ENSP00000261486:V160L	V	-	1	0	EPB41L4A	111628568	0.999000	0.42202	0.840000	0.33206	0.687000	0.40016	4.437000	0.59955	2.568000	0.86640	0.650000	0.86243	GTA	.	.		0.338	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
YTHDC2	64848	hgsc.bcm.edu	37	5	112899131	112899131	+	Missense_Mutation	SNP	T	T	C	rs559215760	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:112899131T>C	ENST00000161863.4	+	19	2597	c.2384T>C	c.(2383-2385)aTg>aCg	p.M795T		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	795					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GATTTTCTTATGAAAGCTCCT	0.313													T|||	2	0.000399361	0.0	0.0	5008	,	,		14416	0.002		0.0	False		,,,				2504	0.0				p.M795T		Atlas-SNP	.											.	YTHDC2	118	.	0			c.T2384C						.						73.0	75.0	74.0					5																	112899131		2202	4300	6502	SO:0001583	missense	64848	exon19			TTCTTATGAAAGC	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2384T>C	chr5.hg19:g.112899131T>C	ENSP00000161863:p.Met795Thr	104.0	0.0		124.0	17.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	T	5.363	0.252250	0.10185	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.02395	4.31	5.31	5.31	0.75309	.	0.143832	0.64402	D	0.000004	T	0.02156	0.0067	N	0.05124	-0.11	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.59129	-0.7512	10	0.39692	T	0.17	.	15.2608	0.73621	0.0:0.0:0.0:1.0	.	795	Q9H6S0	YTDC2_HUMAN	T	795;705	ENSP00000161863:M795T	ENSP00000161863:M795T	M	+	2	0	YTHDC2	112927030	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.975000	0.56859	2.020000	0.59435	0.523000	0.50628	ATG	.	.		0.313	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
GRAMD3	65983	hgsc.bcm.edu	37	5	125821443	125821443	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:125821443A>G	ENST00000285689.3	+	11	1497	c.1036A>G	c.(1036-1038)Att>Gtt	p.I346V	RP11-517I3.1_ENST00000512500.1_RNA|GRAMD3_ENST00000502348.1_Missense_Mutation_p.I237V|GRAMD3_ENST00000515200.1_Missense_Mutation_p.I324V|GRAMD3_ENST00000511134.1_Missense_Mutation_p.I330V|GRAMD3_ENST00000544396.1_Missense_Mutation_p.I242V|GRAMD3_ENST00000513040.1_Missense_Mutation_p.I361V|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000543198.1_Missense_Mutation_p.I324V|GRAMD3_ENST00000542322.1_Missense_Mutation_p.I354V	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	346						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		GCTTCACCATATTCTTATATT	0.348																																					p.I361V		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A1081G						.						121.0	110.0	114.0					5																	125821443		2203	4300	6503	SO:0001583	missense	65983	exon11			CACCATATTCTTA	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.1036A>G	chr5.hg19:g.125821443A>G	ENSP00000285689:p.Ile346Val	52.0	0.0		39.0	6.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.38|10.38	1.334276|1.334276	0.24253|0.24253	.|.	.|.	ENSG00000155324|ENSG00000155324	ENST00000543367|ENST00000513040;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	.|T;T;T;T;T;T;T;T	.|0.34472	.|1.36;1.38;1.43;1.38;1.47;1.45;1.47;1.42	5.94|5.94	3.53|3.53	0.40419|0.40419	.|.	0.227191|0.227191	0.45126|0.45126	D|N	0.000396|0.000396	T|T	0.31918|0.31918	0.0812|0.0812	M|M	0.65975|0.65975	2.015|2.015	0.33672|0.33672	D|D	0.611053|0.611053	.|B;B;B;B;B	.|0.28900	.|0.151;0.028;0.145;0.227;0.151	.|B;B;B;B;B	.|0.27887	.|0.036;0.015;0.026;0.084;0.036	T|T	0.35943|0.35943	-0.9768|-0.9768	7|10	0.42905|0.22109	T|T	0.14|0.4	.|.	7.5781|7.5781	0.27948|0.27948	0.7867:0.1415:0.0719:0.0|0.7867:0.1415:0.0719:0.0	.|.	.|330;242;354;361;346	.|B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.|.;.;.;.;GRAM3_HUMAN	M|V	281|361;346;324;354;242;324;237;330	.|ENSP00000426120:I361V;ENSP00000285689:I346V;ENSP00000426143:I324V;ENSP00000441876:I354V;ENSP00000444049:I242V;ENSP00000442902:I324V;ENSP00000427596:I237V;ENSP00000426088:I330V	ENSP00000445954:I281M|ENSP00000285689:I346V	I|I	+|+	3|1	3|0	GRAMD3|GRAMD3	125849342|125849342	0.662000|0.662000	0.27439|0.27439	0.997000|0.997000	0.53966|0.53966	0.256000|0.256000	0.26092|0.26092	0.989000|0.989000	0.29629|0.29629	0.487000|0.487000	0.27698|0.27698	-0.379000|-0.379000	0.06801|0.06801	ATA|ATT	.	.		0.348	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
HSPA4	3308	hgsc.bcm.edu	37	5	132400692	132400692	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:132400692C>T	ENST00000304858.2	+	2	417	c.128C>T	c.(127-129)cCt>cTt	p.P43L		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	43					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTTTTGGTCCTAAGAATCGT	0.348																																					p.P43L	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.C128T						.						189.0	190.0	189.0					5																	132400692		2203	4300	6503	SO:0001583	missense	3308	exon2			TTGGTCCTAAGAA	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.128C>T	chr5.hg19:g.132400692C>T	ENSP00000302961:p.Pro43Leu	183.0	0.0		209.0	32.0	NM_002154	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	hg19	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542968	0.65198	.	.	ENSG00000170606	ENST00000304858;ENST00000321956;ENST00000537974	T	0.01034	5.42	5.69	5.69	0.88448	.	0.160713	0.56097	D	0.000029	T	0.02012	0.0063	L	0.61218	1.895	0.80722	D	1	B	0.23442	0.085	B	0.22152	0.038	T	0.60707	-0.7210	10	0.35671	T	0.21	-3.324	19.8209	0.96592	0.0:1.0:0.0:0.0	.	43	P34932	HSP74_HUMAN	L	43	ENSP00000302961:P43L	ENSP00000302961:P43L	P	+	2	0	HSPA4	132428591	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.473000	0.81007	2.688000	0.91661	0.650000	0.86243	CCT	.	.		0.348	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
PCDHGB7	56099	hgsc.bcm.edu	37	5	140798233	140798233	+	Silent	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:140798233G>A	ENST00000398594.2	+	1	807	c.807G>A	c.(805-807)caG>caA	p.Q269Q	PCDHGA8_ENST00000398604.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	269	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACTGACCAGGACGAGGGCA	0.522																																					p.Q269Q		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G807A						.						56.0	58.0	57.0					5																	140798233		2053	4195	6248	SO:0001819	synonymous_variant	56099	exon1			TGACCAGGACGAG	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.807G>A	chr5.hg19:g.140798233G>A		37.0	0.0		41.0	5.0	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	hg19	CCDS47293.1																																																																																			.	.		0.522	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
ARHGAP26	23092	hgsc.bcm.edu	37	5	142435642	142435642	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr5:142435642A>T	ENST00000274498.4	+	16	1801	c.1423A>T	c.(1423-1425)Aaa>Taa	p.K475*	ARHGAP26_ENST00000378004.3_Nonsense_Mutation_p.K475*	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	475	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTTTCATCAAAGCAGCAAG	0.338																																					p.K475X		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A1423T						.						161.0	156.0	158.0					5																	142435642		2203	4300	6503	SO:0001587	stop_gained	23092	exon16			TTCATCAAAGCAG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"""Rho GTPase activating proteins"""	17073	protein-coding gene	gene with protein product	"""GTPase regulator associated with the focal adhesion kinase pp125"""	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1423A>T	chr5.hg19:g.142435642A>T	ENSP00000274498:p.Lys475*	59.0	0.0		51.0	8.0	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Nonsense_Mutation	SNP	ENST00000274498.4	hg19	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	A	44	10.908573	0.99487	.	.	ENSG00000145819	ENST00000274498;ENST00000378004;ENST00000418668	.	.	.	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	16.2666	0.82588	1.0:0.0:0.0:0.0	.	.	.	.	X	475;475;48	.	ENSP00000274498:K475X	K	+	1	0	ARHGAP26	142415835	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.136000	0.89610	2.320000	0.78422	0.528000	0.53228	AAA	.	.		0.338	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	
GRM4	2914	hgsc.bcm.edu	37	6	34029743	34029743	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr6:34029743T>A	ENST00000538487.2	-	4	1242	c.799A>T	c.(799-801)Aag>Tag	p.K267*	GRM4_ENST00000544773.2_Nonsense_Mutation_p.K98*|GRM4_ENST00000374181.4_Nonsense_Mutation_p.K267*|GRM4_ENST00000455714.2_Nonsense_Mutation_p.K127*|GRM4_ENST00000535756.1_Nonsense_Mutation_p.K134*|GRM4_ENST00000374177.3_Nonsense_Mutation_p.K198*|GRM4_ENST00000609222.1_Nonsense_Mutation_p.K134*|GRM4_ENST00000545715.1_5'UTR	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	267					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CGGATGATCTTGTCGAACTCG	0.637																																					p.K267X		Atlas-SNP	.											.	GRM4	317	.	0			c.A799T						.						138.0	118.0	125.0					6																	34029743		2203	4300	6503	SO:0001587	stop_gained	2914	exon4			TGATCTTGTCGAA	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.799A>T	chr6.hg19:g.34029743T>A	ENSP00000440556:p.Lys267*	214.0	0.0		170.0	55.0	NM_001256811	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Nonsense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	T	37	6.533798	0.97641	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	.	.	.	4.01	4.01	0.46588	.	0.145987	0.45126	D	0.000398	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9967	0.58650	0.0:0.0:0.0:1.0	.	.	.	.	X	267;198;134;98;267;127	.	ENSP00000363292:K198X	K	-	1	0	GRM4	34137721	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.790000	0.85794	1.799000	0.52666	0.433000	0.28618	AAG	.	.		0.637	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
PRSS35	167681	hgsc.bcm.edu	37	6	84233541	84233541	+	Silent	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr6:84233541C>A	ENST00000369700.3	+	2	558	c.381C>A	c.(379-381)acC>acA	p.T127T	PRSS35_ENST00000536636.1_Silent_p.T127T	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	127	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		TGTATGGCACCGACAGCAGGT	0.463																																					p.T127T		Atlas-SNP	.											.	PRSS35	60	.	0			c.C381A						.						94.0	88.0	90.0					6																	84233541		2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			TGGCACCGACAGC	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.381C>A	chr6.hg19:g.84233541C>A		210.0	0.0		157.0	10.0	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	hg19	CCDS4999.1																																																																																			.	.		0.463	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
MTFR2	113115	hgsc.bcm.edu	37	6	136562631	136562631	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr6:136562631C>G	ENST00000420702.1	-	5	854	c.465G>C	c.(463-465)caG>caC	p.Q155H	MTFR2_ENST00000451457.2_Missense_Mutation_p.Q155H	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	155					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											TTGCTGCAATCTGAGAGCGAA	0.358																																					p.Q155H		Atlas-SNP	.											.	.	.	.	0			c.G465C						.						98.0	91.0	94.0					6																	136562631		2203	4300	6503	SO:0001583	missense	113115	exon5			TGCAATCTGAGAG	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.465G>C	chr6.hg19:g.136562631C>G	ENSP00000395232:p.Gln155His	155.0	0.0		149.0	10.0	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	hg19	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568702	0.65651	.	.	ENSG00000146410	ENST00000451457;ENST00000420702;ENST00000418509	T;T;T	0.70282	-0.47;-0.47;-0.47	5.59	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.80691	0.4671	M	0.87547	2.89	0.49051	D	0.999746	D	0.89917	1.0	D	0.97110	1.0	D	0.84097	0.0393	10	0.87932	D	0	-12.3202	9.8347	0.40963	0.0:0.8405:0.0:0.1595	.	155	Q6P444	FA54A_HUMAN	H	155;155;112	ENSP00000407010:Q155H;ENSP00000395232:Q155H;ENSP00000410861:Q112H	ENSP00000410861:Q112H	Q	-	3	2	FAM54A	136604324	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.406000	0.34646	1.367000	0.46095	0.462000	0.41574	CAG	.	.		0.358	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
INTS1	26173	hgsc.bcm.edu	37	7	1529320	1529320	+	Splice_Site	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:1529320T>A	ENST00000404767.3	-	17	2251		c.e17-2		INTS1_ENST00000389470.4_Splice_Site	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1						inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GGCTGGTACCTGGAAGGCAGG	0.677																																					.		Atlas-SNP	.											.	INTS1	145	.	0			c.2166-2A>T						.						27.0	30.0	29.0					7																	1529320		2032	4159	6191	SO:0001630	splice_region_variant	26173	exon18			GGTACCTGGAAGG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.2166-2A>T	chr7.hg19:g.1529320T>A		79.0	0.0		65.0	9.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Splice_Site	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.740938	0.49151	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4533	0.75294	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	INTS1	1495846	1.000000	0.71417	0.937000	0.37676	0.268000	0.26511	7.512000	0.81728	2.051000	0.60960	0.529000	0.55759	.	.	.		0.677	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		Intron
COL1A2	1278	hgsc.bcm.edu	37	7	94057038	94057038	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:94057038C>A	ENST00000297268.6	+	49	3838	c.3367C>A	c.(3367-3369)Cgc>Agc	p.R1123S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1123				Missing (in Ref. 17; CAA23761). {ECO:0000305}.	blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TGACCAGCCTCGCTCAGCACC	0.552										HNSCC(75;0.22)																											p.R1123S		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3367A						.						98.0	97.0	98.0					7																	94057038		2203	4300	6503	SO:0001583	missense	1278	exon49			CAGCCTCGCTCAG	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3367C>A	chr7.hg19:g.94057038C>A	ENSP00000297268:p.Arg1123Ser	123.0	0.0		87.0	26.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.145829	0.37923	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89196	-2.48	5.71	5.71	0.89125	.	0.000000	0.56097	D	0.000040	D	0.87204	0.6119	N	0.11427	0.14	0.32726	N	0.509689	D	0.60160	0.987	D	0.67725	0.953	D	0.84882	0.0831	10	0.17369	T	0.5	.	15.7376	0.77859	0.0:1.0:0.0:0.0	.	1123	P08123	CO1A2_HUMAN	S	1123;1124	ENSP00000297268:R1123S	ENSP00000297268:R1123S	R	+	1	0	COL1A2	93894974	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.549000	0.53681	2.873000	0.98535	0.561000	0.74099	CGC	.	.		0.552	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
LRWD1	222229	hgsc.bcm.edu	37	7	102113247	102113247	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:102113247C>T	ENST00000292616.5	+	14	1951	c.1799C>T	c.(1798-1800)aCa>aTa	p.T600I	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	600					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						CAGGCCCCCACACAGGTACTG	0.667																																					p.T600I		Atlas-SNP	.											.	LRWD1	41	.	0			c.C1799T						.						25.0	27.0	27.0					7																	102113247		2203	4299	6502	SO:0001583	missense	222229	exon14			CCCCCACACAGGT	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1799C>T	chr7.hg19:g.102113247C>T	ENSP00000292616:p.Thr600Ile	110.0	0.0		141.0	6.0	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	hg19	CCDS34715.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.550|8.550	0.875249|0.875249	0.17395|0.17395	.|.	.|.	ENSG00000161036|ENSG00000161036	ENST00000488689;ENST00000468175|ENST00000292616	.|T	.|0.62498	.|0.02	4.85|4.85	1.8|1.8	0.24995|0.24995	.|.	.|0.144056	.|0.64402	.|D	.|0.000006	T|T	0.66703|0.66703	0.2816|0.2816	M|M	0.61703|0.61703	1.905|1.905	0.20489|0.20489	N|N	0.999896|0.999896	.|D	.|0.60160	.|0.987	.|P	.|0.55871	.|0.786	T|T	0.57871|0.57871	-0.7736|-0.7736	5|10	.|0.62326	.|D	.|0.03	-6.3954|-6.3954	8.4157|8.4157	0.32670|0.32670	0.0:0.6243:0.2923:0.0835|0.0:0.6243:0.2923:0.0835	.|.	.|600	.|Q9UFC0	.|LRWD1_HUMAN	Y|I	211;186|600	.|ENSP00000292616:T600I	.|ENSP00000292616:T600I	H|T	+|+	1|2	0|0	LRWD1|LRWD1	101900252|101900252	0.000000|0.000000	0.05858|0.05858	0.033000|0.033000	0.17914|0.17914	0.113000|0.113000	0.19764|0.19764	0.329000|0.329000	0.19698|0.19698	0.730000|0.730000	0.32425|0.32425	0.561000|0.561000	0.74099|0.74099	CAC|ACA	.	.		0.667	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
CFTR	1080	hgsc.bcm.edu	37	7	117243675	117243675	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:117243675T>A	ENST00000003084.6	+	17	2879	c.2747T>A	c.(2746-2748)tTt>tAt	p.F916Y	CFTR_ENST00000454343.1_Missense_Mutation_p.F855Y|AC000111.6_ENST00000456270.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	916	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TATTATGTGTTTTACATTTAC	0.408									Cystic Fibrosis																												p.F916Y		Atlas-SNP	.											.	CFTR	171	.	0			c.T2747A						.						219.0	186.0	197.0					7																	117243675		2203	4300	6503	SO:0001583	missense	1080	exon17	Familial Cancer Database	CF	ATGTGTTTTACAT	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2747T>A	chr7.hg19:g.117243675T>A	ENSP00000003084:p.Phe916Tyr	243.0	0.0		118.0	11.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	hg19	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416019	0.83449	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.94576	-3.46;-3.46;-3.46	5.82	5.82	0.92795	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.294147	0.42682	D	0.000666	D	0.95143	0.8426	M	0.72118	2.19	0.42193	D	0.991737	P	0.34412	0.453	B	0.42959	0.403	D	0.95242	0.8352	10	0.72032	D	0.01	-7.0964	16.179	0.81887	0.0:0.0:0.0:1.0	.	916	P13569	CFTR_HUMAN	Y	916;855;886	ENSP00000003084:F916Y;ENSP00000403677:F855Y;ENSP00000389119:F886Y	ENSP00000003084:F916Y	F	+	2	0	CFTR	117030911	1.000000	0.71417	0.943000	0.38184	0.506000	0.33950	7.990000	0.88215	2.232000	0.73038	0.477000	0.44152	TTT	.	.		0.408	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
CTTNBP2	83992	hgsc.bcm.edu	37	7	117432538	117432538	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:117432538G>A	ENST00000160373.3	-	4	803	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	238					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AGCTGTTCCCGCTCAGTGTCA	0.453																																					p.R238W		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C712T						.						130.0	106.0	114.0					7																	117432538		2203	4300	6503	SO:0001583	missense	83992	exon4			GTTCCCGCTCAGT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.712C>T	chr7.hg19:g.117432538G>A	ENSP00000160373:p.Arg238Trp	233.0	0.0		232.0	28.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.405680	0.42715	.	.	ENSG00000077063	ENST00000160373	T	0.77098	-1.07	5.77	1.35	0.21983	.	0.000000	0.85682	D	0.000000	D	0.89223	0.6654	M	0.90650	3.135	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.91072	0.4893	10	0.72032	D	0.01	-16.092	15.4882	0.75584	0.0:0.0:0.5666:0.4333	.	238	Q8WZ74	CTTB2_HUMAN	W	238	ENSP00000160373:R238W	ENSP00000160373:R238W	R	-	1	2	CTTNBP2	117219774	0.995000	0.38212	0.033000	0.17914	0.401000	0.30781	2.190000	0.42630	0.362000	0.24319	0.650000	0.86243	CGG	.	.		0.453	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
SLC13A4	26266	hgsc.bcm.edu	37	7	135377154	135377154	+	Silent	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:135377154A>G	ENST00000354042.4	-	11	1826	c.1137T>C	c.(1135-1137)acT>acC	p.T379T	C7orf73_ENST00000422968.1_3'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	379					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						AGAAAAATCCAGTCACCATTT	0.418																																					p.T379T		Atlas-SNP	.											.	SLC13A4	56	.	0			c.T1137C						.						57.0	64.0	61.0					7																	135377154		2203	4300	6503	SO:0001819	synonymous_variant	26266	exon11			AAATCCAGTCACC	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1137T>C	chr7.hg19:g.135377154A>G		86.0	0.0		81.0	17.0	NM_012450	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	hg19	CCDS5840.1																																																																																			.	.		0.418	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450	
TRIM24	8805	hgsc.bcm.edu	37	7	138239638	138239638	+	Missense_Mutation	SNP	G	G	A	rs201288398		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:138239638G>A	ENST00000343526.4	+	9	1672	c.1457G>A	c.(1456-1458)cGg>cAg	p.R486Q	TRIM24_ENST00000497516.1_Intron|TRIM24_ENST00000415680.2_Intron			O15164	TIF1A_HUMAN	tripartite motif containing 24	486					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						CAGGTGCAACGGAGGCCAGCA	0.517																																					p.R486Q	Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)	Atlas-SNP	.											.	TRIM24	131	.	0			c.G1457A						.						95.0	99.0	98.0					7																	138239638		2203	4300	6503	SO:0001583	missense	8805	exon9			TGCAACGGAGGCC	AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	11812	protein-coding gene	gene with protein product		603406	"""transcriptional intermediary factor 1"", ""tripartite motif-containing 24"""	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.1457G>A	chr7.hg19:g.138239638G>A	ENSP00000340507:p.Arg486Gln	244.0	0.0		129.0	11.0	NM_015905	A4D1R7|A4D1R8|O95854	Missense_Mutation	SNP	ENST00000343526.4	hg19	CCDS5847.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.256006	0.39896	.	.	ENSG00000122779	ENST00000343526;ENST00000536822	T	0.75154	-0.91	5.54	5.54	0.83059	.	0.269417	0.35585	N	0.003110	T	0.76666	0.4019	N	0.25144	0.715	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.70132	-0.4956	10	0.10902	T	0.67	-17.1036	19.0694	0.93126	0.0:0.0:1.0:0.0	.	486	O15164	TIF1A_HUMAN	Q	486;397	ENSP00000340507:R486Q	ENSP00000340507:R486Q	R	+	2	0	TRIM24	137890178	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.022000	0.64078	2.602000	0.87976	0.557000	0.71058	CGG	.	G|0.999;T|0.001		0.517	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905	
KDM7A	80853	hgsc.bcm.edu	37	7	139791731	139791731	+	Silent	SNP	C	C	T	rs376853003		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:139791731C>T	ENST00000397560.2	-	19	2701	c.2604G>A	c.(2602-2604)gcG>gcA	p.A868A	Y_RNA_ENST00000515919.1_RNA	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		868					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					TTATCTGGCACGCCCCCGAAG	0.493																																					p.A868A		Atlas-SNP	.											.	JHDM1D	54	.	0			c.G2604A						.	C		0,3824		0,0,1912	110.0	106.0	107.0		2604	-11.2	0.0	7		107	1,8249		0,1,4124	no	coding-synonymous	JHDM1D	NM_030647.1		0,1,6036	TT,TC,CC		0.0121,0.0,0.0083		868/942	139791731	1,12073	1912	4125	6037	SO:0001819	synonymous_variant	80853	exon19			CTGGCACGCCCCC																												ENST00000397560.2:c.2604G>A	chr7.hg19:g.139791731C>T		201.0	0.0		181.0	9.0	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Silent	SNP	ENST00000397560.2	hg19	CCDS43658.1																																																																																			.	.		0.493	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		
NOS3	4846	hgsc.bcm.edu	37	7	150708074	150708074	+	Splice_Site	SNP	G	G	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:150708074G>C	ENST00000297494.3	+	23	3341	c.2984G>C	c.(2983-2985)gGg>gCg	p.G995A	ATG9B_ENST00000494791.1_5'Flank|NOS3_ENST00000461406.1_Splice_Site_p.G789A|NOS3_ENST00000477227.1_3'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTCATCCGGGGGTAAGTGAGA	0.622																																					p.G995A		Atlas-SNP	.											.	NOS3	131	.	0			c.G2984C						.						36.0	34.0	35.0					7																	150708074		2203	4300	6503	SO:0001630	splice_region_variant	4846	exon23			TCCGGGGGTAAGT		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.2984+1G>C	chr7.hg19:g.150708074G>C		78.0	0.0		48.0	10.0	NM_000603	Q495E5	Missense_Mutation	SNP	ENST00000297494.3	hg19	CCDS5912.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.60|14.60	2.583779|2.583779	0.46006|0.46006	.|.	.|.	ENSG00000164867|ENSG00000164867	ENST00000297494;ENST00000461406|ENST00000475017	T;T|.	0.32023|.	1.47;1.47|.	4.61|4.61	4.61|4.61	0.57282|0.57282	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);|.	0.000000|.	0.56097|.	D|.	0.000031|.	T|T	0.33933|0.33933	0.0880|0.0880	N|N	0.03154|0.03154	-0.405|-0.405	0.80722|0.80722	D|D	1|1	B;B|.	0.19200|.	0.034;0.0|.	B;B|.	0.22601|.	0.04;0.002|.	T|T	0.24799|0.24799	-1.0150|-1.0150	10|5	0.35671|.	T|.	0.21|.	-5.9629|-5.9629	14.9693|14.9693	0.71220|0.71220	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	789;995|.	E7ESA7;P29474|.	.;NOS3_HUMAN|.	A|L	995;789|289	ENSP00000297494:G995A;ENSP00000417143:G789A|.	ENSP00000297494:G995A|.	G|V	+|+	2|1	0|0	NOS3|NOS3	150339007|150339007	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.720000|0.720000	0.41350|0.41350	5.241000|5.241000	0.65384|0.65384	2.377000|2.377000	0.81083|0.81083	0.491000|0.491000	0.48974|0.48974	GGG|GTC	.	.		0.622	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	Missense_Mutation
KMT2C	58508	hgsc.bcm.edu	37	7	151970873	151970873	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:151970873C>A	ENST00000262189.6	-	7	1147	c.929G>T	c.(928-930)tGt>tTt	p.C310F	KMT2C_ENST00000355193.2_Missense_Mutation_p.C310F	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	310					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.C310S(2)									TCCTGCAGCACAAGGATAATG	0.448																																					p.C310F		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	.	2	Substitution - Missense(2)	endometrium(2)	c.G929T						.						215.0	200.0	205.0					7																	151970873		2203	4300	6503	SO:0001583	missense	58508	exon7			GCAGCACAAGGAT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.929G>T	chr7.hg19:g.151970873C>A	ENSP00000262189:p.Cys310Phe	472.0	0.0		394.0	18.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366743	0.61513	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.94330	-3.4;-3.4	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.48767	D	0.000161	D	0.97907	0.9312	H	0.96460	3.825	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99379	1.0922	10	0.87932	D	0	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	310	Q8NEZ4	MLL3_HUMAN	F	310	ENSP00000262189:C310F;ENSP00000347325:C310F	ENSP00000262189:C310F	C	-	2	0	MLL3	151601806	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.752000	0.85141	2.423000	0.82170	0.650000	0.86243	TGT	.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
CSMD1	64478	hgsc.bcm.edu	37	8	2799992	2799992	+	Splice_Site	SNP	A	A	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:2799992A>C	ENST00000520002.1	-	70	11094		c.e70+1		CSMD1_ENST00000400186.3_Splice_Site|CSMD1_ENST00000602557.1_Splice_Site|CSMD1_ENST00000537824.1_Splice_Site|CSMD1_ENST00000542608.1_Splice_Site|CSMD1_ENST00000602723.1_Splice_Site			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1							integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTTCTGCAGTACCTGTGTTTG	0.428																																					.		Atlas-SNP	.											.	CSMD1	1469	.	0			c.10535+2T>G						.						48.0	47.0	47.0					8																	2799992		1888	4123	6011	SO:0001630	splice_region_variant	64478	exon70			TGCAGTACCTGTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10538+1T>G	chr8.hg19:g.2799992A>C		51.0	0.0		41.0	23.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Splice_Site	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	A	28.0	4.884016	0.91814	.	.	ENSG00000183117	ENST00000335551;ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8993	0.79359	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD1	2787399	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	9.023000	0.93683	2.150000	0.67090	0.523000	0.50628	.	.	.		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	Intron
CSMD1	64478	hgsc.bcm.edu	37	8	3443701	3443701	+	Silent	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:3443701T>C	ENST00000520002.1	-	10	1737	c.1182A>G	c.(1180-1182)acA>acG	p.T394T	CSMD1_ENST00000400186.3_Silent_p.T394T|CSMD1_ENST00000602557.1_Silent_p.T394T|CSMD1_ENST00000537824.1_Silent_p.T393T|CSMD1_ENST00000542608.1_Silent_p.T393T|CSMD1_ENST00000602723.1_Silent_p.T394T|CSMD1_ENST00000539096.1_Silent_p.T393T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	394	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CGAGCGTCTCTGTAACTCTCT	0.478																																					p.T393T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A1179G						.						47.0	46.0	46.0					8																	3443701		1928	4135	6063	SO:0001819	synonymous_variant	64478	exon9			CGTCTCTGTAACT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.1182A>G	chr8.hg19:g.3443701T>C		79.0	0.0		75.0	21.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19																																																																																				.	.		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CHRNB3	1142	hgsc.bcm.edu	37	8	42587427	42587427	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:42587427C>T	ENST00000289957.2	+	5	1105	c.977C>T	c.(976-978)tCc>tTc	p.S326F		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	326					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	AGATCTTCTTCCACGTACCAC	0.453																																					p.S326F		Atlas-SNP	.											.	CHRNB3	74	.	0			c.C977T						.						297.0	248.0	265.0					8																	42587427		2203	4300	6503	SO:0001583	missense	1142	exon5			CTTCTTCCACGTA	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1963	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 3 (neuronal)"""	118508	"""cholinergic receptor, nicotinic, beta polypeptide 3"""			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.977C>T	chr8.hg19:g.42587427C>T	ENSP00000289957:p.Ser326Phe	300.0	0.0		438.0	176.0	NM_000749	Q15827	Missense_Mutation	SNP	ENST00000289957.2	hg19	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	c	14.61	2.587081	0.46110	.	.	ENSG00000147432	ENST00000289957	T	0.71934	-0.61	5.85	5.85	0.93711	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.055024	0.64402	D	0.000001	D	0.83418	0.5250	M	0.79011	2.435	0.28985	N	0.888397	P	0.51057	0.941	D	0.65140	0.932	T	0.80348	-0.1420	10	0.87932	D	0	.	15.3155	0.74074	0.0:0.9317:0.0:0.0683	.	326	Q05901	ACHB3_HUMAN	F	326	ENSP00000289957:S326F	ENSP00000289957:S326F	S	+	2	0	CHRNB3	42706584	0.839000	0.29477	0.108000	0.21378	0.117000	0.20001	6.067000	0.71193	2.778000	0.95560	0.650000	0.86243	TCC	.	.		0.453	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1		
CRISPLD1	83690	hgsc.bcm.edu	37	8	75932132	75932132	+	Silent	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:75932132A>G	ENST00000262207.4	+	11	1623	c.1155A>G	c.(1153-1155)acA>acG	p.T385T	CRISPLD1_ENST00000523524.1_Silent_p.T197T|CRISPLD1_ENST00000517786.1_Silent_p.T199T	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	385					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)		p.V386fs*5(1)		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)			ATTCCTTCACAGTCTCTAAAG	0.323																																					p.T385T		Atlas-SNP	.											.,1	CRISPLD1	94	.	1	Insertion - Frameshift(1)	prostate(1)	c.A1155G						.						150.0	145.0	147.0					8																	75932132		2203	4300	6503	SO:0001819	synonymous_variant	83690	exon11			CTTCACAGTCTCT	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.1155A>G	chr8.hg19:g.75932132A>G		211.0	0.0		165.0	56.0	NM_031461	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	hg19	CCDS6219.1																																																																																			.	.		0.323	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461	
PMP2	5375	hgsc.bcm.edu	37	8	82357106	82357106	+	Silent	SNP	G	G	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:82357106G>C	ENST00000256103.2	-	2	328	c.192C>G	c.(190-192)tcC>tcG	p.S64S	PMP2_ENST00000519260.1_Intron|RP11-157I4.4_ENST00000524085.2_RNA	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	64					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			CTAGCTTGAAGGAGATTTCTG	0.393																																					p.S64S		Atlas-SNP	.											PMP2,right_lower_lobe,carcinoma,0,1	PMP2	21	.	0			c.C192G						.						138.0	137.0	137.0					8																	82357106		2203	4300	6503	SO:0001819	synonymous_variant	5375	exon2			CTTGAAGGAGATT	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"""Fatty acid binding protein family"""	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.192C>G	chr8.hg19:g.82357106G>C		117.0	0.0		104.0	13.0	NM_002677	Q6FHL4	Silent	SNP	ENST00000256103.2	hg19	CCDS6229.1																																																																																			.	.		0.393	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677	
ATP6V0D2	245972	hgsc.bcm.edu	37	8	87165053	87165053	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:87165053G>T	ENST00000285393.3	+	8	1042	c.900G>T	c.(898-900)atG>atT	p.M300I	CTD-3118D11.2_ENST00000522679.1_RNA|CTD-3118D11.2_ENST00000524253.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	300					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)			breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						AGGTACAAATGAATGTGCTGG	0.358																																					p.M300I		Atlas-SNP	.											ATP6V0D2,NS,carcinoma,0,1	ATP6V0D2	61	.	0			c.G900T						.						158.0	146.0	151.0					8																	87165053		2203	4300	6503	SO:0001583	missense	245972	exon8			ACAAATGAATGTG	AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"""ATPases / V-type"""	18266	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"""			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.900G>T	chr8.hg19:g.87165053G>T	ENSP00000285393:p.Met300Ile	84.0	0.0		64.0	21.0	NM_152565		Missense_Mutation	SNP	ENST00000285393.3	hg19	CCDS6241.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.852908	0.32699	.	.	ENSG00000147614	ENST00000285393	T	0.28454	1.61	6.06	5.16	0.70880	.	0.181318	0.51477	N	0.000092	T	0.20495	0.0493	N	0.16656	0.425	0.41711	D	0.989459	B	0.02656	0.0	B	0.08055	0.003	T	0.03433	-1.1037	10	0.33940	T	0.23	-3.548	13.4993	0.61445	0.0786:0.0:0.9214:0.0	.	300	Q8N8Y2	VA0D2_HUMAN	I	300	ENSP00000285393:M300I	ENSP00000285393:M300I	M	+	3	0	ATP6V0D2	87234169	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	5.454000	0.66651	1.481000	0.48307	-0.355000	0.07637	ATG	.	.		0.358	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565	
CNGB3	54714	hgsc.bcm.edu	37	8	87755800	87755800	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:87755800T>A	ENST00000320005.5	-	1	103	c.56A>T	c.(55-57)gAg>gTg	p.E19V	RP11-386D6.1_ENST00000519041.1_RNA|CNGB3_ENST00000519777.1_5'UTR	NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	19					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TTGTTCATTCTCATTGTTCTC	0.433																																					p.E19V		Atlas-SNP	.											.	CNGB3	176	.	0			c.A56T						.						316.0	263.0	281.0					8																	87755800		2203	4300	6503	SO:0001583	missense	54714	exon1			TCATTCTCATTGT	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.56A>T	chr8.hg19:g.87755800T>A	ENSP00000316605:p.Glu19Val	397.0	0.0		285.0	120.0	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	hg19	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.349232	0.61183	.	.	ENSG00000170289	ENST00000320005	T	0.31247	1.5	5.96	4.79	0.61399	.	0.741096	0.11364	N	0.571597	T	0.33644	0.0870	L	0.40543	1.245	0.09310	N	0.999992	D	0.58620	0.983	P	0.49140	0.601	T	0.13495	-1.0507	10	0.62326	D	0.03	.	9.1158	0.36758	0.0:0.0893:0.0:0.9107	.	19	Q9NQW8	CNGB3_HUMAN	V	19	ENSP00000316605:E19V	ENSP00000316605:E19V	E	-	2	0	CNGB3	87824916	0.024000	0.19004	0.048000	0.18961	0.022000	0.10575	1.538000	0.36094	1.042000	0.40150	-0.417000	0.06048	GAG	.	.		0.433	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
SNTB1	6641	hgsc.bcm.edu	37	8	121644855	121644855	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:121644855C>T	ENST00000395601.3	-	4	1239	c.825G>A	c.(823-825)acG>acA	p.T275T	SNTB1_ENST00000517992.1_Silent_p.T275T|SNTB1_ENST00000519177.1_5'UTR	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	275	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)		p.T275T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			TTAGGATCACCGTGTGCTTAG	0.532																																					p.T275T		Atlas-SNP	.											SNTB1,colon,NS,0,1	SNTB1	54	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G825A						.						112.0	102.0	105.0					8																	121644855		2203	4300	6503	SO:0001819	synonymous_variant	6641	exon3			GATCACCGTGTGC	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"""Pleckstrin homology (PH) domain containing"""	11168	protein-coding gene	gene with protein product	"""tax interaction protein 43"""	600026	"""syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"""	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.825G>A	chr8.hg19:g.121644855C>T		131.0	0.0		96.0	5.0	NM_021021	A8K9E0|O14912|Q4KMG8	Silent	SNP	ENST00000395601.3	hg19	CCDS6334.1																																																																																			.	.		0.532	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021	
ZHX1	11244	hgsc.bcm.edu	37	8	124266621	124266621	+	Silent	SNP	T	T	C	rs373764646		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr8:124266621T>C	ENST00000522655.1	-	3	2106	c.1566A>G	c.(1564-1566)tcA>tcG	p.S522S	ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000395571.3_Silent_p.S522S|ZHX1_ENST00000297857.2_Silent_p.S522S|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	522	Required for interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			GATTACTCTTTGAATTTCTCT	0.388																																					p.S522S		Atlas-SNP	.											.	ZHX1	89	.	0			c.A1566G						.						140.0	136.0	138.0					8																	124266621		2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			ACTCTTTGAATTT	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	12871	protein-coding gene	gene with protein product		604764	"""zinc-fingers and homeoboxes 1"""			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.1566A>G	chr8.hg19:g.124266621T>C		100.0	0.0		54.0	20.0	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	hg19	CCDS6342.1	.	.	.	.	.	.	.	.	.	.	T	4.702	0.130447	0.08981	.	.	ENSG00000165156	ENST00000520474	.	.	.	5.19	-3.42	0.04825	.	.	.	.	.	T	0.39091	0.1065	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38672	-0.9650	4	.	.	.	-11.7049	2.1581	0.03818	0.103:0.1917:0.1954:0.51	.	.	.	.	R	207	.	.	Q	-	2	0	ZHX1	124335802	0.111000	0.22076	0.997000	0.53966	0.989000	0.77384	-0.744000	0.04839	-0.144000	0.11314	-0.388000	0.06559	CAA	.	.		0.388	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1		
PRSS3	5646	hgsc.bcm.edu	37	9	33796749	33796749	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr9:33796749G>A	ENST00000361005.5	+	2	320	c.320G>A	c.(319-321)gGc>gAc	p.G107D	PRSS3_ENST00000379405.3_Missense_Mutation_p.G50D|PRSS3_ENST00000429677.3_Missense_Mutation_p.G43D|PRSS3_ENST00000342836.4_Missense_Mutation_p.G64D|RP11-133O22.6_ENST00000454429.2_RNA	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	107	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			TTCTGCGGTGGCTCCCTCATC	0.572																																					p.G107D		Atlas-SNP	.											.	PRSS3	79	.	0			c.G320A						.						125.0	128.0	127.0					9																	33796749		2203	4300	6503	SO:0001583	missense	5646	exon2			GCGGTGGCTCCCT		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.320G>A	chr9.hg19:g.33796749G>A	ENSP00000354280:p.Gly107Asp	229.0	0.0		174.0	21.0	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	hg19	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816339	0.50527	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	T;D;D;T;D	0.98280	-1.46;-1.53;-4.84;-1.46;-4.84	3.21	3.21	0.36854	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.99149	0.9706	H	0.98068	4.14	0.58432	D	0.999999	D;D;D	0.60575	0.958;0.988;0.958	P;P;P	0.59948	0.866;0.842;0.866	D	0.98834	1.0752	10	0.72032	D	0.01	.	12.3047	0.54895	0.0:0.0:1.0:0.0	.	50;107;64	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	D	107;62;64;43;50	ENSP00000354280:G107D;ENSP00000401249:G62D;ENSP00000340889:G64D;ENSP00000401828:G43D;ENSP00000368715:G50D	ENSP00000340889:G64D	G	+	2	0	PRSS3	33786749	1.000000	0.71417	0.928000	0.36995	0.040000	0.13550	8.524000	0.90579	1.538000	0.49270	0.306000	0.20318	GGC	.	.		0.572	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
DAB2IP	153090	hgsc.bcm.edu	37	9	124535287	124535287	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr9:124535287C>G	ENST00000408936.3	+	12	2662	c.2480C>G	c.(2479-2481)tCc>tGc	p.S827C	DAB2IP_ENST00000259371.2_Missense_Mutation_p.S799C|DAB2IP_ENST00000309989.1_Missense_Mutation_p.S703C			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	827	Necessary for interaction with AKT1.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						GCACCGCTCTCCTTCCAGAAC	0.706																																					p.S799C		Atlas-SNP	.											.	DAB2IP	150	.	0			c.C2396G						.						29.0	29.0	29.0					9																	124535287		2158	4217	6375	SO:0001583	missense	153090	exon12			CGCTCTCCTTCCA	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"""nGAP-like protein"", ""DOC-2/DAB2 interactive protein"", ""ASK-interacting protein"", ""ASK1-interacting protein 1"""	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.2480C>G	chr9.hg19:g.124535287C>G	ENSP00000386183:p.Ser827Cys	148.0	0.0		98.0	28.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	hg19		.	.	.	.	.	.	.	.	.	.	C	21.7	4.184906	0.78677	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.59018	0.2163	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.997;1.0	T	0.66011	-0.6029	10	0.87932	D	0	.	16.9563	0.86260	0.0:1.0:0.0:0.0	.	827;799	Q5VWQ8;G3XA90	DAB2P_HUMAN;.	C	799;827;736;703	ENSP00000259371:S799C;ENSP00000386183:S827C;ENSP00000362887:S736C;ENSP00000310827:S703C	ENSP00000259371:S799C	S	+	2	0	DAB2IP	123575108	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.409000	0.80053	2.317000	0.78254	0.462000	0.41574	TCC	.	.		0.706	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552	
GPR158	57512	hgsc.bcm.edu	37	10	25861801	25861801	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:25861801T>A	ENST00000376351.3	+	7	2097	c.1738T>A	c.(1738-1740)Tac>Aac	p.Y580N		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	580					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CCGCTGGGACTACATGACAGC	0.423																																					p.Y580N		Atlas-SNP	.											.	GPR158	255	.	0			c.T1738A						.						132.0	104.0	114.0					10																	25861801		2203	4300	6503	SO:0001583	missense	57512	exon7			TGGGACTACATGA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1738T>A	chr10.hg19:g.25861801T>A	ENSP00000365529:p.Tyr580Asn	201.0	0.0		102.0	17.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.625518	0.87560	.	.	ENSG00000151025	ENST00000376351	D	0.88354	-2.37	5.67	5.67	0.87782	GPCR, family 3, C-terminal (2);	0.098369	0.44483	D	0.000447	D	0.94909	0.8354	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95517	0.8591	10	0.72032	D	0.01	.	15.9002	0.79369	0.0:0.0:0.0:1.0	.	580	Q5T848	GP158_HUMAN	N	580	ENSP00000365529:Y580N	ENSP00000365529:Y580N	Y	+	1	0	GPR158	25901807	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.161000	0.67846	0.455000	0.32223	TAC	.	.		0.423	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
GDF2	2658	hgsc.bcm.edu	37	10	48413759	48413759	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:48413759G>A	ENST00000249598.1	-	2	1268	c.1109C>T	c.(1108-1110)cCg>cTg	p.P370L		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	370					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						GTGTTTCGTCGGCGTCACATC	0.587																																					p.P370L		Atlas-SNP	.											.	GDF2	77	.	0			c.C1109T						.						128.0	105.0	113.0					10																	48413759		2203	4300	6503	SO:0001583	missense	2658	exon2			TTCGTCGGCGTCA	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"""Endogenous ligands"""	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.1109C>T	chr10.hg19:g.48413759G>A	ENSP00000249598:p.Pro370Leu	162.0	0.0		141.0	18.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752802	0.69648	.	.	ENSG00000128802	ENST00000249598	D	0.88046	-2.33	5.62	5.62	0.85841	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.94115	0.8113	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94522	0.7728	10	0.87932	D	0	.	18.6283	0.91349	0.0:0.0:1.0:0.0	.	370	Q9UK05	GDF2_HUMAN	L	370	ENSP00000249598:P370L	ENSP00000249598:P370L	P	-	2	0	GDF2	48033765	1.000000	0.71417	0.336000	0.25522	0.329000	0.28539	9.710000	0.98732	2.652000	0.90054	0.585000	0.79938	CCG	.	.		0.587	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204	
KIF11	3832	hgsc.bcm.edu	37	10	94369152	94369152	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:94369152T>C	ENST00000260731.3	+	6	674	c.584T>C	c.(583-585)aTa>aCa	p.I195T		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	195	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGAGGAGTGATAATTAAAGGT	0.388																																					p.I195T	Colon(47;212 1003 2764 4062 8431)	Atlas-SNP	.											.	KIF11	58	.	0			c.T584C						.						174.0	188.0	183.0					10																	94369152		2203	4300	6503	SO:0001583	missense	3832	exon6			GAGTGATAATTAA	X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"""Kinesins"""	6388	protein-coding gene	gene with protein product		148760	"""kinesin-like 1"""	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.584T>C	chr10.hg19:g.94369152T>C	ENSP00000260731:p.Ile195Thr	91.0	0.0		60.0	9.0	NM_004523	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	hg19	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.886183	0.72410	.	.	ENSG00000138160	ENST00000260731	T	0.64991	-0.13	5.54	5.54	0.83059	Kinesin, motor domain (4);	0.107041	0.64402	D	0.000006	T	0.56307	0.1976	N	0.17631	0.505	0.58432	D	0.999995	P	0.39022	0.655	P	0.45377	0.478	T	0.59674	-0.7410	10	0.48119	T	0.1	.	15.8422	0.78857	0.0:0.0:0.0:1.0	.	195	P52732	KIF11_HUMAN	T	195	ENSP00000260731:I195T	ENSP00000260731:I195T	I	+	2	0	KIF11	94359132	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.796000	0.62496	2.323000	0.78572	0.528000	0.53228	ATA	.	.		0.388	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523	
HSPA12A	259217	hgsc.bcm.edu	37	10	118458224	118458224	+	Silent	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:118458224C>A	ENST00000369209.3	-	5	572	c.468G>T	c.(466-468)acG>acT	p.T156T		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	156						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		CATTTGCTGCCGTCAGGTCTG	0.493																																					p.T156T		Atlas-SNP	.											.	HSPA12A	81	.	0			c.G468T						.						142.0	135.0	137.0					10																	118458224		1949	4157	6106	SO:0001819	synonymous_variant	259217	exon5			TGCTGCCGTCAGG	AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"""Heat shock proteins / HSP70"""	19022	protein-coding gene	gene with protein product		610701	"""heat shock 70kD protein 12A"""			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.468G>T	chr10.hg19:g.118458224C>A		124.0	0.0		89.0	28.0	NM_025015		Silent	SNP	ENST00000369209.3	hg19	CCDS41569.1																																																																																			.	.		0.493	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015	
DMBT1	1755	hgsc.bcm.edu	37	10	124377713	124377713	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr10:124377713C>A	ENST00000338354.3	+	38	4791	c.4685C>A	c.(4684-4686)gCc>gAc	p.A1562D	DMBT1_ENST00000368956.2_Missense_Mutation_p.A934D|DMBT1_ENST00000359586.6_Missense_Mutation_p.A413D|DMBT1_ENST00000344338.3_Missense_Mutation_p.A1552D|DMBT1_ENST00000368955.3_Missense_Mutation_p.A1552D|DMBT1_ENST00000368909.3_Missense_Mutation_p.A1562D|DMBT1_ENST00000330163.4_Missense_Mutation_p.A934D			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1562	SRCR 12. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCAGGAAATGCCCAGTTTGGC	0.612																																					p.A1562D	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C4685A						.						160.0	164.0	163.0					10																	124377713		1960	4163	6123	SO:0001583	missense	1755	exon38			GAAATGCCCAGTT		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.4685C>A	chr10.hg19:g.124377713C>A	ENSP00000342210:p.Ala1562Asp	100.0	0.0		66.0	21.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	C	16.99	3.272970	0.59649	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	4.12	3.21	0.36854	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.760730	0.04550	U	0.389673	D	0.82719	0.5098	M	0.86028	2.79	0.37016	D	0.895959	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.91635	0.967;0.988;0.999;0.991;0.951;0.97	T	0.69495	-0.5130	10	0.72032	D	0.01	.	12.2281	0.54472	0.0:0.9153:0.0:0.0847	.	413;811;1691;934;1552;1562	F8WEF7;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;DMBT1_HUMAN	D	1562;1691;1562;1562;1562;1562;934;1552;934;934;1562;1552;934;413	ENSP00000342210:A1562D;ENSP00000343175:A1552D;ENSP00000327747:A934D;ENSP00000357905:A1562D;ENSP00000357951:A1552D;ENSP00000357952:A934D;ENSP00000352593:A413D	ENSP00000331522:A934D	A	+	2	0	DMBT1	124367703	0.981000	0.34729	0.061000	0.19648	0.427000	0.31564	2.975000	0.49281	0.862000	0.35528	0.549000	0.68633	GCC	.	.		0.612	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
SYT8	90019	hgsc.bcm.edu	37	11	1858034	1858034	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:1858034T>A	ENST00000381968.3	+	7	903	c.775T>A	c.(775-777)Tca>Aca	p.S259T	SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381911.1_5'Flank|TNNI2_ENST00000252898.7_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.S245T|TNNI2_ENST00000381906.1_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	259	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CGTGCCCAGCTCAGGCCGGCT	0.672																																					p.S259T		Atlas-SNP	.											.	SYT8	29	.	0			c.T775A						.						36.0	38.0	37.0					11																	1858034		2200	4298	6498	SO:0001583	missense	90019	exon7			CCCAGCTCAGGCC	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"""Synaptotagmins"""	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.775T>A	chr11.hg19:g.1858034T>A	ENSP00000371394:p.Ser259Thr	107.0	0.0		94.0	11.0	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	hg19	CCDS7726.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	9.247|9.247	1.039737|1.039737	0.19669|0.19669	.|.	.|.	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.07567	.|3.18;3.18	2.97|2.97	1.68|1.68	0.24146|0.24146	.|C2 membrane targeting protein (1);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	.|.	.|.	.|.	.|.	T|T	0.04452|0.04452	0.0122|0.0122	N|N	0.16708|0.16708	0.43|0.43	0.18873|0.18873	N|N	0.999988|0.999988	.|B;B	.|0.26483	.|0.15;0.15	.|B;B	.|0.17722	.|0.019;0.019	T|T	0.36065|0.36065	-0.9763|-0.9763	5|9	.|0.44086	.|T	.|0.13	.|.	3.5396|3.5396	0.07806|0.07806	0.4358:0.0:0.1724:0.3917|0.4358:0.0:0.1724:0.3917	.|.	.|259;245	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	H|T	257|259;245	.|ENSP00000371394:S259T;ENSP00000343691:S245T	.|ENSP00000343691:S245T	L|S	+|+	2|1	0|0	SYT8|SYT8	1814610|1814610	0.001000|0.001000	0.12720|0.12720	0.879000|0.879000	0.34478|0.34478	0.447000|0.447000	0.32167|0.32167	0.421000|0.421000	0.21280|0.21280	1.368000|1.368000	0.46115|0.46115	0.260000|0.260000	0.18958|0.18958	CTC|TCA	.	.		0.672	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
TNNT3	7140	hgsc.bcm.edu	37	11	1955638	1955638	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:1955638C>T	ENST00000397301.1	+	13	484	c.476C>T	c.(475-477)tCt>tTt	p.S159F	TNNT3_ENST00000446240.1_Missense_Mutation_p.S129F|TNNT3_ENST00000360603.3_Missense_Mutation_p.S142F|TNNT3_ENST00000381548.3_Missense_Mutation_p.S150F|TNNT3_ENST00000493234.1_3'UTR|TNNT3_ENST00000381589.3_Missense_Mutation_p.S146F|TNNT3_ENST00000381558.1_Missense_Mutation_p.S140F|TNNT3_ENST00000397304.2_Missense_Mutation_p.S129F|TNNT3_ENST00000278317.6_Missense_Mutation_p.S148F|TNNT3_ENST00000381549.3_Missense_Mutation_p.S140F|TNNT3_ENST00000381561.4_Missense_Mutation_p.S151F|TNNT3_ENST00000381579.3_Missense_Mutation_p.S140F			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	159					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		AAAGCTCTGTCTTCCATGGGA	0.592																																					p.S148F		Atlas-SNP	.											.	TNNT3	68	.	0			c.C443T						.						104.0	95.0	98.0					11																	1955638		2202	4298	6500	SO:0001583	missense	7140	exon12			CTCTGTCTTCCAT	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"""troponin-T3, skeletal, fast"""	600692	"""troponin T3, skeletal, fast"""			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	ENST00000397301.1:c.476C>T	chr11.hg19:g.1955638C>T	ENSP00000380468:p.Ser159Phe	82.0	0.0		92.0	14.0	NM_006757	A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Missense_Mutation	SNP	ENST00000397301.1	hg19		.	.	.	.	.	.	.	.	.	.	.	23.9	4.472056	0.84533	.	.	ENSG00000130595	ENST00000278317;ENST00000544980;ENST00000397309;ENST00000381561;ENST00000381548;ENST00000360603;ENST00000381549;ENST00000381589;ENST00000381579;ENST00000381557;ENST00000453458;ENST00000381563;ENST00000344578;ENST00000381558;ENST00000397301;ENST00000397304;ENST00000446240	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98996	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57;-5.31;-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	4.66	4.66	0.58398	.	0.115083	0.64402	D	0.000013	D	0.99351	0.9772	M	0.87971	2.92	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.992;0.992;0.992;0.994;0.997	D	0.98903	1.0777	10	0.87932	D	0	-24.9044	17.9291	0.88992	0.0:1.0:0.0:0.0	.	148;140;146;140;159	P45378-2;P45378-7;P45378-6;P45378-4;P45378	.;.;.;.;TNNT3_HUMAN	F	148;44;160;151;150;142;140;146;140;134;129;151;135;140;159;129;129	ENSP00000278317:S148F;ENSP00000370973:S151F;ENSP00000370960:S150F;ENSP00000353815:S142F;ENSP00000370961:S140F;ENSP00000371001:S146F;ENSP00000370991:S140F;ENSP00000370969:S134F;ENSP00000415614:S129F;ENSP00000370975:S151F;ENSP00000344870:S135F;ENSP00000370970:S140F;ENSP00000380468:S159F;ENSP00000380471:S129F;ENSP00000413203:S129F	ENSP00000278317:S148F	S	+	2	0	TNNT3	1912214	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.663000	0.68038	2.314000	0.78098	0.313000	0.20887	TCT	.	.		0.592	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757	
STK33	65975	hgsc.bcm.edu	37	11	8496345	8496345	+	Silent	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:8496345T>C	ENST00000447869.1	-	1	1026	c.108A>G	c.(106-108)ccA>ccG	p.P36P	STK33_ENST00000358872.3_Intron|STK33_ENST00000396672.1_Silent_p.P36P|STK33_ENST00000534493.1_5'UTR|STK33_ENST00000396673.1_Silent_p.P36P|STK33_ENST00000315204.1_Silent_p.P36P			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	36					protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CCACCAAAACTGGAGGAACCC	0.368																																					p.P36P		Atlas-SNP	.											.	STK33	147	.	0			c.A108G						.						135.0	138.0	137.0					11																	8496345		2201	4296	6497	SO:0001819	synonymous_variant	65975	exon3			CAAAACTGGAGGA	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.108A>G	chr11.hg19:g.8496345T>C		140.0	0.0		92.0	21.0	NM_030906	Q658S6|Q8NEF5	Silent	SNP	ENST00000447869.1	hg19	CCDS7789.1																																																																																			.	.		0.368	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
RBM14	10432	hgsc.bcm.edu	37	11	66384504	66384504	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:66384504G>T	ENST00000310137.4	+	1	452	c.313G>T	c.(313-315)Gtc>Ttc	p.V105F	RBM14_ENST00000409738.4_Missense_Mutation_p.V105F|RBM4_ENST00000503028.2_5'UTR|RBM14_ENST00000393979.3_Missense_Mutation_p.V105F|RBM14-RBM4_ENST00000412278.2_Missense_Mutation_p.V105F|RBM14-RBM4_ENST00000500635.2_Missense_Mutation_p.V105F|RNU4-39P_ENST00000362455.1_RNA|RBM4_ENST00000514361.3_Missense_Mutation_p.V105F|RBM14-RBM4_ENST00000511114.1_3'UTR|RBM14_ENST00000409372.1_Missense_Mutation_p.V105F|RBM14_ENST00000443702.1_Missense_Mutation_p.V105F	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	105	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CCGCGGACGCGTCATCGAGTG	0.662																																					p.V105F		Atlas-SNP	.											.	RBM14	59	.	0			c.G313T						.						43.0	51.0	48.0					11																	66384504		2159	4218	6377	SO:0001583	missense	10432	exon1			GGACGCGTCATCG	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.313G>T	chr11.hg19:g.66384504G>T	ENSP00000311747:p.Val105Phe	73.0	0.0		76.0	9.0	NM_001198837	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989364	0.93106	.	.	ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000248643;ENSG00000248643	ENST00000310137;ENST00000393979;ENST00000409372;ENST00000443702;ENST00000409738;ENST00000412278;ENST00000500635	T;T;T;T;T;T;T	0.79554	-1.28;-1.28;2.05;2.05;2.05;2.05;2.05	5.18	4.25	0.50352	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.256789	0.32563	N	0.005936	D	0.90995	0.7168	M	0.91768	3.24	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.992;1.0	D	0.92334	0.5876	10	0.87932	D	0	-11.3981	12.6918	0.56978	0.0:0.0:0.8335:0.1665	.	105;105;105;105	B0LM41;Q96PK6-2;Q2PYN1;Q96PK6	.;.;.;RBM14_HUMAN	F	105	ENSP00000311747:V105F;ENSP00000377548:V105F;ENSP00000386518:V105F;ENSP00000414650:V105F;ENSP00000386995:V105F;ENSP00000388552:V105F;ENSP00000421279:V105F	ENSP00000311747:V105F	V	+	1	0	RBM14;RBM14-RBM4	66141080	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.213000	0.77950	1.157000	0.42530	0.555000	0.69702	GTC	.	.		0.662	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328	
FOLR4	390243	hgsc.bcm.edu	37	11	94040391	94040391	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:94040391G>A	ENST00000440961.2	+	3	432	c.388G>A	c.(388-390)Gag>Aag	p.E130K		NM_001199206.1	NP_001186135.1	A6ND01	JUNO_HUMAN	folate receptor 4, delta (putative)	137					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						GGAGGACTGTGAGGAGTGGTG	0.567																																					p.E137K		Atlas-SNP	.											.	FOLR4	31	.	0			c.G409A						.						102.0	110.0	108.0					11																	94040391		2195	4292	6487	SO:0001583	missense	390243	exon3			GACTGTGAGGAGT			11q14	2014-07-23	2012-12-07		ENSG00000183560	ENSG00000183560			32565	protein-coding gene	gene with protein product		615737	"""folate receptor 4 (delta) homolog (mouse)"""			11111049, 24739963	Standard	NM_001199206		Approved	Folbp3, JUNO	uc021qou.1	A6ND01		ENST00000440961.2:c.388G>A	chr11.hg19:g.94040391G>A	ENSP00000416935:p.Glu130Lys	162.0	0.0		112.0	12.0	NM_001199206		Missense_Mutation	SNP	ENST00000440961.2	hg19		.	.	.	.	.	.	.	.	.	.	G	17.51	3.406533	0.62399	.	.	ENSG00000183560	ENST00000440961	T	0.76316	-1.01	4.67	1.75	0.24633	.	0.501919	0.22175	N	0.063598	T	0.74854	0.3771	M	0.77313	2.365	0.09310	N	1	P	0.40553	0.721	B	0.42030	0.373	T	0.66356	-0.5944	10	0.49607	T	0.09	-13.7692	5.5608	0.17142	0.1814:0.0:0.6554:0.1633	.	130	A6ND01-2	.	K	130	ENSP00000416935:E130K	ENSP00000416935:E130K	E	+	1	0	FOLR4	93680039	0.985000	0.35326	0.877000	0.34402	0.990000	0.78478	2.373000	0.44266	0.681000	0.31386	0.491000	0.48974	GAG	.	.		0.567	FOLR4-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000396420.1	NM_001080486	
C11orf87	399947	hgsc.bcm.edu	37	11	109294862	109294862	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr11:109294862C>A	ENST00000327419.6	+	2	906	c.503C>A	c.(502-504)cCg>cAg	p.P168Q	RP11-708B6.2_ENST00000532929.1_RNA|RP11-708B6.2_ENST00000532992.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	168						integral component of membrane (GO:0016021)		p.P168L(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						CCGCCTCCACCGCCAGCCTCC	0.652																																					p.P168Q		Atlas-SNP	.											C11orf87,rectum,carcinoma,0,2	C11orf87	37	.	1	Substitution - Missense(1)	large_intestine(1)	c.C503A						.						40.0	42.0	41.0					11																	109294862		2201	4298	6499	SO:0001583	missense	399947	exon2			CTCCACCGCCAGC	AB096240, BC035798	CCDS31672.1	11q22.3	2013-12-13	2013-12-13	2013-12-13	ENSG00000185742	ENSG00000185742			33788	protein-coding gene	gene with protein product	"""neuronal integral membrane protein 1"""					12477932	Standard	NM_207645		Approved	LOH11CR1A, LOC399947, NEURIM1	uc010rwb.2	Q6NUJ2		ENST00000327419.6:c.503C>A	chr11.hg19:g.109294862C>A	ENSP00000331581:p.Pro168Gln	71.0	0.0		64.0	19.0	NM_207645	B4E169	Missense_Mutation	SNP	ENST00000327419.6	hg19	CCDS31672.1	.	.	.	.	.	.	.	.	.	.	C	7.918	0.737911	0.15574	.	.	ENSG00000185742	ENST00000327419	.	.	.	3.42	0.388	0.16264	.	.	.	.	.	T	0.12050	0.0293	N	0.08118	0	0.23249	N	0.998049	B	0.30146	0.27	B	0.22386	0.039	T	0.19031	-1.0318	8	0.40728	T	0.16	-5.3732	3.1802	0.06582	0.186:0.4978:0.0:0.3162	.	168	Q6NUJ2	CK087_HUMAN	Q	168	.	ENSP00000331581:P168Q	P	+	2	0	C11orf87	108800072	0.000000	0.05858	0.934000	0.37439	0.983000	0.72400	0.007000	0.13174	0.095000	0.17434	-0.123000	0.14984	CCG	.	.		0.652	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645	
LHX5	64211	hgsc.bcm.edu	37	12	113901064	113901064	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr12:113901064G>T	ENST00000261731.3	-	5	1713	c.1140C>A	c.(1138-1140)agC>agA	p.S380R		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	380					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						CGCTGGTGCCGCTCATTGGGA	0.751																																					p.S380R		Atlas-SNP	.											.	LHX5	39	.	0			c.C1140A						.						3.0	6.0	5.0					12																	113901064		1712	3364	5076	SO:0001583	missense	64211	exon5			GGTGCCGCTCATT	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"""Homeoboxes / LIM class"""	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.1140C>A	chr12.hg19:g.113901064G>T	ENSP00000261731:p.Ser380Arg	20.0	0.0		34.0	14.0	NM_022363	Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	hg19	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462281	0.43736	.	.	ENSG00000089116	ENST00000261731	D	0.90900	-2.75	4.08	2.23	0.28157	.	0.269330	0.24856	N	0.035041	T	0.81823	0.4904	L	0.40543	1.245	0.45261	D	0.998267	P	0.45715	0.865	B	0.35971	0.215	T	0.74604	-0.3610	10	0.29301	T	0.29	.	7.7318	0.28791	0.2635:0.0:0.7365:0.0	.	380	Q9H2C1	LHX5_HUMAN	R	380	ENSP00000261731:S380R	ENSP00000261731:S380R	S	-	3	2	LHX5	112385447	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.399000	0.44495	0.324000	0.23333	-0.258000	0.10820	AGC	.	.		0.751	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363	
HNF1A	6927	hgsc.bcm.edu	37	12	121432040	121432040	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr12:121432040C>G	ENST00000257555.6	+	4	1013	c.787C>G	c.(787-789)Cgt>Ggt	p.R263G	HNF1A_ENST00000543427.1_Missense_Mutation_p.R146G|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Missense_Mutation_p.R263G|HNF1A_ENST00000402929.1_Missense_Mutation_p.R263G|HNF1A_ENST00000400024.2_Missense_Mutation_p.R263G|HNF1A_ENST00000541395.1_Missense_Mutation_p.R263G			P20823	HNF1A_HUMAN	HNF1 homeobox A	263	Interaction with DNA.		R -> C (in MODY3; expected to interfere with DNA binding). {ECO:0000269|PubMed:9287053}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R263C(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CACGGAGGTGCGTGTCTACAA	0.647									Hepatic Adenoma, Familial Clustering of																												p.R263G		Atlas-SNP	.											HNF1A,NS,other,-1,2	HNF1A	302	.	2	Substitution - Missense(2)	liver(2)	c.C787G	GRCh37	CM971458	HNF1A	M		.						41.0	40.0	40.0					12																	121432040		2203	4300	6503	SO:0001583	missense	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GAGGTGCGTGTCT	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.787C>G	chr12.hg19:g.121432040C>G	ENSP00000257555:p.Arg263Gly	111.0	0.0		61.0	5.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316878	0.81469	.	.	ENSG00000135100	ENST00000257555;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89	4.84	4.84	0.62591	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000003	D	0.96747	0.8938	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.997	D;D;D;D	0.81914	0.994;0.995;0.988;0.983	D	0.97136	0.9821	10	0.87932	D	0	-10.9955	13.6154	0.62105	0.1555:0.8445:0.0:0.0	.	263;263;263;263	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	G	263;263;263;263;146;263;263;263;263;263	ENSP00000257555:R263G;ENSP00000439721:R146G;ENSP00000443112:R263G;ENSP00000438804:R263G	ENSP00000257555:R263G	R	+	1	0	HNF1A	119916423	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.985000	0.49362	2.245000	0.73994	0.409000	0.27619	CGT	.	.		0.647	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
GOLGA3	2802	hgsc.bcm.edu	37	12	133384623	133384623	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr12:133384623C>A	ENST00000450791.2	-	4	1215	c.1032G>T	c.(1030-1032)atG>atT	p.M344I	GOLGA3_ENST00000456883.2_Missense_Mutation_p.M344I|GOLGA3_ENST00000204726.3_Missense_Mutation_p.M344I|GOLGA3_ENST00000545875.1_Missense_Mutation_p.M344I|GOLGA3_ENST00000537452.1_Missense_Mutation_p.M344I			Q08378	GOGA3_HUMAN	golgin A3	344					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GGCCGTTGACCATATAGGGGG	0.612																																					p.M344I		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G1032T						.						90.0	77.0	81.0					12																	133384623		2203	4300	6503	SO:0001583	missense	2802	exon5			GTTGACCATATAG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.1032G>T	chr12.hg19:g.133384623C>A	ENSP00000410378:p.Met344Ile	124.0	0.0		103.0	30.0	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	hg19	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	c	1.100	-0.661288	0.03454	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.73	4.83	0.62350	.	0.618093	0.17067	N	0.188325	T	0.19846	0.0477	L	0.36672	1.1	0.33105	D	0.539808	B;B;B	0.10296	0.003;0.001;0.002	B;B;B	0.11329	0.006;0.006;0.003	T	0.17623	-1.0363	10	0.21014	T	0.42	.	3.9634	0.09421	0.2206:0.6184:0.0:0.161	.	344;344;344	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	I	344	ENSP00000204726:M344I;ENSP00000410378:M344I;ENSP00000409303:M344I;ENSP00000442143:M344I;ENSP00000442603:M344I	ENSP00000204726:M344I	M	-	3	0	GOLGA3	131894696	0.964000	0.33143	0.048000	0.18961	0.006000	0.05464	0.276000	0.18716	2.707000	0.92482	0.645000	0.84053	ATG	.	.		0.612	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
UCHL3	7347	hgsc.bcm.edu	37	13	76140947	76140947	+	Silent	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr13:76140947G>A	ENST00000377595.3	+	4	330	c.300G>A	c.(298-300)ctG>ctA	p.L100L	RP11-29G8.3_ENST00000563635.1_RNA	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	100					protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		CAATTGGACTGATTCATGCTA	0.338																																					p.L100L		Atlas-SNP	.											.	UCHL3	9	.	0			c.G300A						.						130.0	124.0	126.0					13																	76140947		2203	4300	6503	SO:0001819	synonymous_variant	7347	exon4			TGGACTGATTCAT	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.300G>A	chr13.hg19:g.76140947G>A		102.0	0.0		54.0	8.0	NM_006002	B2R970|Q5TBK8|Q6IBE9	Silent	SNP	ENST00000377595.3	hg19	CCDS9453.1																																																																																			.	.		0.338	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002	
LRRC74A	145497	hgsc.bcm.edu	37	14	77311222	77311222	+	Silent	SNP	G	G	A	rs374431496		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr14:77311222G>A	ENST00000393774.3	+	7	829	c.705G>A	c.(703-705)ggG>ggA	p.G235G	C14orf166B_ENST00000450042.2_3'UTR	NM_194287.2	NP_919263.2														breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		ATGTAGGAGGGGAGCACCTGG	0.478																																					p.G235G	Ovarian(165;1056 1958 32571 36789 48728)	Atlas-SNP	.											.	C14orf166B	52	.	0			c.G705A						.	G		0,4406		0,0,2203	50.0	50.0	50.0		705	-7.4	0.0	14		50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C14orf166B	NM_194287.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		235/489	77311222	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	145497	exon7			AGGAGGGGAGCAC																												ENST00000393774.3:c.705G>A	chr14.hg19:g.77311222G>A		67.0	0.0		51.0	17.0	NM_194287		Silent	SNP	ENST00000393774.3	hg19	CCDS9853.2																																																																																			.	.		0.478	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1		
NRXN3	9369	hgsc.bcm.edu	37	14	79269978	79269978	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr14:79269978G>A	ENST00000554719.1	+	6	1432	c.941G>A	c.(940-942)aGc>aAc	p.S314N	NRXN3_ENST00000335750.5_Missense_Mutation_p.S314N	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	0					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TCCATCCTGAGCTATGATGGT	0.493																																					p.S314N		Atlas-SNP	.											.	NRXN3	342	.	0			c.G941A						.						178.0	134.0	149.0					14																	79269978		2203	4300	6503	SO:0001583	missense	9369	exon6			TCCTGAGCTATGA	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.941G>A	chr14.hg19:g.79269978G>A	ENSP00000451648:p.Ser314Asn	130.0	0.0		107.0	27.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	hg19	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831635	0.71258	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.80304	-1.36;-1.36	5.91	5.91	0.95273	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.207171	0.51477	D	0.000086	D	0.90147	0.6921	.	.	.	0.43338	D	0.995381	D;D	0.76494	0.996;0.999	D;D	0.73380	0.978;0.98	D	0.89074	0.3471	8	.	.	.	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	687;314	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	N	687;685;314;314	ENSP00000451648:S314N;ENSP00000338349:S314N	.	S	+	2	0	NRXN3	78339731	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	6.265000	0.72534	2.793000	0.96121	0.655000	0.94253	AGC	.	.		0.493	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250	
KIF26A	26153	hgsc.bcm.edu	37	14	104642658	104642658	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr14:104642658G>T	ENST00000423312.2	+	12	3533	c.3533G>T	c.(3532-3534)gGg>gTg	p.G1178V	KIF26A_ENST00000315264.7_Missense_Mutation_p.G1039V	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1178					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CCGTGCCCTGGGGAAGTGGCT	0.721																																					p.G1178V		Atlas-SNP	.											.	KIF26A	84	.	0			c.G3533T						.						8.0	10.0	9.0					14																	104642658		1708	3820	5528	SO:0001583	missense	26153	exon12			GCCCTGGGGAAGT	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.3533G>T	chr14.hg19:g.104642658G>T	ENSP00000388241:p.Gly1178Val	83.0	0.0		107.0	34.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	G	0.517	-0.863862	0.02590	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.78481	-1.18;-1.17	3.52	-1.71	0.08133	.	.	.	.	.	T	0.67748	0.2926	M	0.64404	1.975	0.09310	N	1	B	0.22003	0.063	B	0.14578	0.011	T	0.57004	-0.7885	9	0.48119	T	0.1	.	2.8448	0.05540	0.1081:0.4273:0.2229:0.2418	.	1178	Q9ULI4	KI26A_HUMAN	V	1178;1039	ENSP00000388241:G1178V;ENSP00000325452:G1039V	ENSP00000325452:G1039V	G	+	2	0	KIF26A	103712411	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-0.682000	0.05185	-0.127000	0.11661	-0.657000	0.03884	GGG	.	.		0.721	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
SLC12A1	6557	hgsc.bcm.edu	37	15	48500027	48500027	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:48500027T>A	ENST00000558405.1	+	1	125	c.111T>A	c.(109-111)gaT>gaA	p.D37E	SLC12A1_ENST00000330289.6_Missense_Mutation_p.D37E|SLC12A1_ENST00000396577.3_Missense_Mutation_p.D37E|SLC12A1_ENST00000561031.1_Missense_Mutation_p.D37E|SLC12A1_ENST00000380993.3_Missense_Mutation_p.D37E			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	37					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CAGCTGCAGATGACAATACTG	0.433																																					p.D37E		Atlas-SNP	.											.	SLC12A1	243	.	0			c.T111A						.						76.0	72.0	73.0					15																	48500027		2198	4297	6495	SO:0001583	missense	6557	exon2			TGCAGATGACAAT		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.111T>A	chr15.hg19:g.48500027T>A	ENSP00000453409:p.Asp37Glu	120.0	0.0		83.0	25.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.422|3.422	-0.117977|-0.117977	0.06838|0.06838	.|.	.|.	ENSG00000074803|ENSG00000074803	ENST00000380993;ENST00000396577;ENST00000330289|ENST00000546071	D;D;D|.	0.91180|.	-1.89;-1.89;-2.8|.	5.45|5.45	-4.87|-4.87	0.03123|0.03123	.|.	1.652850|.	0.03156|.	N|.	0.168601|.	T|T	0.19248|0.19248	0.0462|0.0462	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.0;0.009|.	B;B|.	0.12156|.	0.001;0.007|.	T|T	0.39292|0.39292	-0.9621|-0.9621	10|6	0.24483|0.56958	T|D	0.36|0.05	.|.	9.3696|9.3696	0.38246|0.38246	0.0:0.4299:0.2772:0.2929|0.0:0.4299:0.2772:0.2929	.|.	37;37|.	Q8IUN5;Q13621|.	.;S12A1_HUMAN|.	E|K	37|11	ENSP00000370381:D37E;ENSP00000379822:D37E;ENSP00000331550:D37E|.	ENSP00000331550:D37E|ENSP00000441148:M11K	D|M	+|+	3|2	2|0	SLC12A1|SLC12A1	46287319|46287319	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-0.804000|-0.804000	0.04535|0.04535	-0.488000|-0.488000	0.06726|0.06726	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.433	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
SHC4	399694	hgsc.bcm.edu	37	15	49135766	49135766	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:49135766C>T	ENST00000332408.4	-	10	1751	c.1323G>A	c.(1321-1323)ggG>ggA	p.G441G	SHC4_ENST00000537958.1_Silent_p.G155G|SHC4_ENST00000396535.3_Silent_p.G198G	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	441	CH1.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		GGGACTGCACCCCTCTTGGAT	0.388																																					p.G441G		Atlas-SNP	.											.	SHC4	70	.	0			c.G1323A						.						122.0	111.0	114.0					15																	49135766		2197	4295	6492	SO:0001819	synonymous_variant	399694	exon10			CTGCACCCCTCTT	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"""SH2 domain containing"""	16743	protein-coding gene	gene with protein product	"""rai-like protein"""						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1323G>A	chr15.hg19:g.49135766C>T		183.0	0.0		186.0	57.0	NM_203349	Q6UXQ3|Q8IYW3	Silent	SNP	ENST00000332408.4	hg19	CCDS10130.1																																																																																			.	.		0.388	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349	
UBE2Q2	92912	hgsc.bcm.edu	37	15	76165791	76165791	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:76165791A>G	ENST00000267938.4	+	5	852	c.470A>G	c.(469-471)tAt>tGt	p.Y157C	UBE2Q2_ENST00000338677.4_Missense_Mutation_p.Y157C|UBE2Q2_ENST00000561851.1_Missense_Mutation_p.Y141C|UBE2Q2_ENST00000569423.1_Missense_Mutation_p.Y122C	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	157	Glu-rich.				protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						TTAGATCACTATGAGATGAAG	0.313																																					p.Y157C		Atlas-SNP	.											.	UBE2Q2	26	.	0			c.A470G						.						71.0	71.0	71.0					15																	76165791		2197	4294	6491	SO:0001583	missense	92912	exon5			ATCACTATGAGAT	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"""Ubiquitin-conjugating enzymes E2"""	19248	protein-coding gene	gene with protein product		612501	"""ubiquitin-conjugating enzyme E2Q (putative) 2"""			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.470A>G	chr15.hg19:g.76165791A>G	ENSP00000267938:p.Tyr157Cys	183.0	0.0		130.0	20.0	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Missense_Mutation	SNP	ENST00000267938.4	hg19	CCDS10286.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.614236	0.46631	.	.	ENSG00000140367	ENST00000338677;ENST00000267938;ENST00000426727	.	.	.	4.41	4.41	0.53225	.	0.192041	0.44902	D	0.000401	T	0.60663	0.2286	M	0.67953	2.075	0.53688	D	0.999973	B;B;B;B	0.17465	0.022;0.01;0.009;0.012	B;B;B;B	0.17979	0.02;0.019;0.01;0.014	T	0.61997	-0.6947	9	0.51188	T	0.08	.	13.5368	0.61652	1.0:0.0:0.0:0.0	.	141;157;141;157	E9PHD0;C9JX13;B7Z3Q2;Q8WVN8	.;.;.;UB2Q2_HUMAN	C	157;157;141	.	ENSP00000267938:Y157C	Y	+	2	0	UBE2Q2	73952846	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.158000	0.94723	1.933000	0.56026	0.519000	0.50382	TAT	.	.		0.313	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469	
ACAN	176	hgsc.bcm.edu	37	15	89417182	89417182	+	Silent	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr15:89417182C>A	ENST00000561243.1	+	16	7443	c.7443C>A	c.(7441-7443)gtC>gtA	p.V2481V	ACAN_ENST00000352105.7_Intron|ACAN_ENST00000439576.2_Silent_p.V2481V|ACAN_ENST00000559004.1_Silent_p.V2443V			P16112	PGCA_HUMAN	aggrecan	2366					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGGGTTTGTCCAGCGCCACA	0.637																																					p.V2481V		Atlas-SNP	.											.	ACAN	220	.	0			c.C7443A						.						44.0	55.0	51.0					15																	89417182		2153	4241	6394	SO:0001819	synonymous_variant	176	exon17			GTTTGTCCAGCGC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.7443C>A	chr15.hg19:g.89417182C>A		107.0	0.0		95.0	9.0	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.637	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
KIF22	3835	hgsc.bcm.edu	37	16	29811026	29811026	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:29811026C>T	ENST00000160827.4	+	7	1108	c.1068C>T	c.(1066-1068)gtC>gtT	p.V356V	KIF22_ENST00000569382.2_Silent_p.V288V|KIF22_ENST00000400750.2_5'UTR|KIF22_ENST00000563263.1_3'UTR|KIF22_ENST00000400751.5_Silent_p.V288V|KIF22_ENST00000561482.1_Silent_p.V288V	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	356	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						TAGACACAGTCTCCGCACTCA	0.562																																					p.V356V		Atlas-SNP	.											.	KIF22	29	.	0			c.C1068T						.						58.0	42.0	47.0					16																	29811026		2197	4296	6493	SO:0001819	synonymous_variant	3835	exon7			CACAGTCTCCGCA	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"""Kinesins"""	6391	protein-coding gene	gene with protein product		603213	"""kinesin-like 4"""	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.1068C>T	chr16.hg19:g.29811026C>T		225.0	0.0		124.0	22.0	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Silent	SNP	ENST00000160827.4	hg19	CCDS10653.1																																																																																			.	.		0.562	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2		
CDH11	1009	hgsc.bcm.edu	37	16	65038624	65038624	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:65038624C>T	ENST00000268603.4	-	3	764	c.149G>A	c.(148-150)cGc>cAc	p.R50H	CDH11_ENST00000394156.3_Missense_Mutation_p.R50H|CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	50					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R50L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		ACGCTTGGAGCGCTGTAGCAC	0.642			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.R50H		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	CDH11_ENST00000394156,NS,carcinoma,-1,2	CDH11	260	.	1	Substitution - Missense(1)	lung(1)	c.G149A						.						55.0	44.0	48.0					16																	65038624		2202	4300	6502	SO:0001583	missense	1009	exon3			TTGGAGCGCTGTA	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.149G>A	chr16.hg19:g.65038624C>T	ENSP00000268603:p.Arg50His	109.0	0.0		95.0	19.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	C	36	5.617948	0.96649	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000536902	T;T	0.00585	6.39;6.39	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.02533	0.0077	L	0.58810	1.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.59193	-0.7500	10	0.87932	D	0	.	18.6407	0.91394	0.0:1.0:0.0:0.0	.	50;50	P55287-2;P55287	.;CAD11_HUMAN	H	50	ENSP00000268603:R50H;ENSP00000377711:R50H	ENSP00000268603:R50H	R	-	2	0	CDH11	63596125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.250000	0.78287	2.662000	0.90505	0.591000	0.81541	CGC	.	.		0.642	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
CDH11	1009	hgsc.bcm.edu	37	16	65038770	65038770	+	Start_Codon_SNP	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:65038770C>A	ENST00000268603.4	-	3	618	c.3G>T	c.(1-3)atG>atT	p.M1I	CDH11_ENST00000394156.3_Start_Codon_SNP_p.M1I|CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	1					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		AGTTCTCCTTCATTTTTGGTT	0.617			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.M1I		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.G3T						.						16.0	22.0	20.0					16																	65038770		2155	4232	6387	SO:0001582	initiator_codon_variant	1009	exon3			CTCCTTCATTTTT	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.3G>T	chr16.hg19:g.65038770C>A	ENSP00000268603:p.Met1Ile	178.0	0.0		133.0	31.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.474059	0.43942	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000536902	T;T	0.55413	0.59;0.52	5.47	5.47	0.80525	.	0.157945	0.56097	D	0.000026	T	0.49695	0.1572	.	.	.	0.80722	D	1	B;B	0.33807	0.426;0.028	B;B	0.32090	0.14;0.007	T	0.54470	-0.8289	9	0.87932	D	0	.	18.3184	0.90229	0.0:1.0:0.0:0.0	.	1;1	P55287-2;P55287	.;CAD11_HUMAN	I	1	ENSP00000268603:M1I;ENSP00000377711:M1I	ENSP00000268603:M1I	M	-	3	0	CDH11	63596271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.374000	0.59543	2.572000	0.86782	0.591000	0.81541	ATG	.	.		0.617	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	Missense_Mutation
WWP2	11060	hgsc.bcm.edu	37	16	69959360	69959360	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:69959360C>T	ENST00000359154.2	+	11	1308	c.1207C>T	c.(1207-1209)Ccc>Tcc	p.P403S	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Missense_Mutation_p.P403S|WWP2_ENST00000356003.2_Missense_Mutation_p.P403S|WWP2_ENST00000568684.1_5'UTR|WWP2_ENST00000542271.1_Missense_Mutation_p.P287S	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	403					cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGACCATGATCCCCTGGGCCC	0.522																																					p.P403S		Atlas-SNP	.											.	WWP2	88	.	0			c.C1207T						.						354.0	351.0	352.0					16																	69959360		2198	4300	6498	SO:0001583	missense	11060	exon11			CATGATCCCCTGG	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.1207C>T	chr16.hg19:g.69959360C>T	ENSP00000352069:p.Pro403Ser	129.0	0.0		157.0	40.0	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	hg19	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	C	35	5.547943	0.96488	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.31247	1.52;1.52;1.52;1.5	5.65	5.65	0.86999	WW/Rsp5/WWP (2);	0.096147	0.64402	D	0.000001	T	0.33847	0.0877	M	0.63428	1.95	0.80722	D	1	B	0.33103	0.397	B	0.28709	0.093	T	0.07404	-1.0774	9	.	.	.	.	19.7358	0.96202	0.0:1.0:0.0:0.0	.	403	O00308	WWP2_HUMAN	S	403;403;403;290;287	ENSP00000352069:P403S;ENSP00000396871:P403S;ENSP00000348283:P403S;ENSP00000445616:P287S	.	P	+	1	0	WWP2	68516861	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.802000	0.85969	2.660000	0.90430	0.557000	0.71058	CCC	.	.		0.522	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
FOXL1	2300	hgsc.bcm.edu	37	16	86612389	86612389	+	Silent	SNP	G	G	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr16:86612389G>C	ENST00000320241.3	+	1	275	c.60G>C	c.(58-60)ctG>ctC	p.L20L		NM_005250.2	NP_005241.1	Q12952	FOXL1_HUMAN	forkhead box L1	20					heart development (GO:0007507)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|Peyer's patch morphogenesis (GO:0061146)|proteoglycan biosynthetic process (GO:0030166)|regulation of Wnt signaling pathway (GO:0030111)|transcription, DNA-templated (GO:0006351)|visceral mesoderm-endoderm interaction involved in midgut development (GO:0007495)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(2)|prostate(3)|skin(1)|urinary_tract(1)	15						TGCTGTATCTGTACGGTCCCG	0.706																																					p.L20L	NSCLC(163;308 2020 10889 11476 18208)	Atlas-SNP	.											.	FOXL1	39	.	0			c.G60C						.						35.0	39.0	38.0					16																	86612389		2195	4295	6490	SO:0001819	synonymous_variant	2300	exon1			GTATCTGTACGGT	AF315075	CCDS10959.1	16q24	2014-07-15			ENSG00000176678	ENSG00000176678		"""Forkhead boxes"""	3817	protein-coding gene	gene with protein product		603252		FKHL11		7957066	Standard	NM_005250		Approved	FREAC7, FKH6	uc002fjr.3	Q12952	OTTHUMG00000137653	ENST00000320241.3:c.60G>C	chr16.hg19:g.86612389G>C		115.0	0.0		96.0	11.0	NM_005250	Q17RR1|Q9H242	Silent	SNP	ENST00000320241.3	hg19	CCDS10959.1																																																																																			.	.		0.706	FOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269105.2	NM_005250	
OR3A3	8392	hgsc.bcm.edu	37	17	3324438	3324438	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:3324438C>T	ENST00000291231.1	+	1	577	c.577C>T	c.(577-579)Ctc>Ttc	p.L193F		NM_012373.2	NP_036505.2	P47888	OR3A3_HUMAN	olfactory receptor, family 3, subfamily A, member 3	193				L -> V (in Ref. 7; AAA18351). {ECO:0000305}.	signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)	9						CCTCCCACAGCTCTTCCAGCT	0.552																																					p.L193F		Atlas-SNP	.											.	OR3A3	20	.	0			c.C577T						.						76.0	72.0	74.0					17																	3324438		2203	4297	6500	SO:0001583	missense	8392	exon1			CCACAGCTCTTCC	U04688	CCDS11025.1	17p13.3	2012-08-09			ENSG00000159961	ENSG00000159961		"""GPCR / Class A : Olfactory receptors"""	8284	protein-coding gene	gene with protein product				OR3A6, OR3A7, OR3A8P		8004088, 9500546	Standard	NM_012373		Approved	OR17-201, OR17-137, OR17-16	uc010vrd.2	P47888	OTTHUMG00000090649	ENST00000291231.1:c.577C>T	chr17.hg19:g.3324438C>T	ENSP00000291231:p.Leu193Phe	262.0	0.0		311.0	13.0	NM_012373	Q2VPE4|Q6IFM6|Q9P1Q4|Q9UBE7	Missense_Mutation	SNP	ENST00000291231.1	hg19	CCDS11025.1	.	.	.	.	.	.	.	.	.	.	.	13.48	2.248630	0.39797	.	.	ENSG00000159961	ENST00000291231	T	0.00231	8.49	2.52	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00580	0.0019	M	0.90759	3.145	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.43228	-0.9404	9	0.72032	D	0.01	.	5.1894	0.15201	0.2316:0.5421:0.2263:0.0	.	193	P47888	OR3A3_HUMAN	F	193	ENSP00000291231:L193F	ENSP00000291231:L193F	L	+	1	0	OR3A3	3271188	0.000000	0.05858	0.997000	0.53966	0.989000	0.77384	-0.558000	0.05978	1.692000	0.51112	0.650000	0.86243	CTC	.	.		0.552	OR3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207309.1		
TP53	7157	hgsc.bcm.edu	37	17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	rs28934571		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R249S	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	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (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.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(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)	TGAGGATGGGCCTCCGGTTCA	0.572		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.R249S	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_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155.0	113.0	127.0					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	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;	GATGGGCCTCCGG	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.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	211.0	0.0		203.0	103.0	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	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
MYH2	4620	hgsc.bcm.edu	37	17	10432947	10432947	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:10432947C>T	ENST00000245503.5	-	24	3435	c.3051G>A	c.(3049-3051)caG>caA	p.Q1017Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|MYH2_ENST00000397183.2_Silent_p.Q1017Q	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1017					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CCTCCTCTGCCTGCAGGTCAT	0.478																																					p.Q1017Q		Atlas-SNP	.											.	MYH2	390	.	0			c.G3051A						.						169.0	162.0	165.0					17																	10432947		2203	4297	6500	SO:0001819	synonymous_variant	4620	exon24			CTCTGCCTGCAGG		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.3051G>A	chr17.hg19:g.10432947C>T		335.0	0.0		362.0	166.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	hg19	CCDS11156.1																																																																																			.	.		0.478	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
NSRP1	84081	hgsc.bcm.edu	37	17	28511699	28511699	+	Silent	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:28511699A>G	ENST00000247026.5	+	7	747	c.684A>G	c.(682-684)ccA>ccG	p.P228P	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	228					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						ACAGAATACCACAAGAGAAAT	0.368																																					p.P228P		Atlas-SNP	.											.	NSRP1	49	.	0			c.A684G						.						60.0	59.0	59.0					17																	28511699		2203	4300	6503	SO:0001819	synonymous_variant	84081	exon7			AATACCACAAGAG	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.684A>G	chr17.hg19:g.28511699A>G		145.0	0.0		280.0	15.0	NM_032141	Q6FI71	Silent	SNP	ENST00000247026.5	hg19	CCDS11255.1																																																																																			.	.		0.368	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141	
OSBPL7	114881	hgsc.bcm.edu	37	17	45885990	45885990	+	Silent	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:45885990G>A	ENST00000007414.3	-	22	2525	c.2334C>T	c.(2332-2334)gcC>gcT	p.A778A	OSBPL7_ENST00000392507.3_Silent_p.A778A	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	778					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						TTCTCTTCTGGGCCTCAGCGG	0.597																																					p.A778A		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C2334T						.						258.0	230.0	240.0					17																	45885990		2203	4300	6503	SO:0001819	synonymous_variant	114881	exon22			CTTCTGGGCCTCA	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2334C>T	chr17.hg19:g.45885990G>A		305.0	0.0		237.0	33.0	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	hg19	CCDS11515.1																																																																																			.	.		0.597	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
SLC16A6	9120	hgsc.bcm.edu	37	17	66267772	66267772	+	Missense_Mutation	SNP	T	T	C	rs139961659		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:66267772T>C	ENST00000327268.4	-	6	693	c.529A>G	c.(529-531)Att>Gtt	p.I177V	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.I177V	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	177					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	CTCCAGCCAATGCGCTCCTTC	0.473																																					p.I177V		Atlas-SNP	.											.	SLC16A6	56	.	0			c.A529G						.	T	VAL/ILE,VAL/ILE,	1,4405	2.1+/-5.4	0,1,2202	44.0	43.0	44.0		529,529,	0.9	0.0	17	dbSNP_134	44	0,8600		0,0,4300	no	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	29,29,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,	177/524,177/524,	66267772	1,13005	2203	4300	6503	SO:0001583	missense	9120	exon6			AGCCAATGCGCTC	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.529A>G	chr17.hg19:g.66267772T>C	ENSP00000319991:p.Ile177Val	93.0	0.0		95.0	19.0	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	hg19	CCDS11675.1	.	.	.	.	.	.	.	.	.	.	T	8.162	0.789772	0.16258	2.27E-4	0.0	ENSG00000108932	ENST00000327268	T	0.36699	1.24	4.33	0.903	0.19296	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.248067	0.40469	N	0.001095	T	0.30947	0.0781	L	0.55834	1.745	0.26325	N	0.9776	B	0.20459	0.045	B	0.26693	0.072	T	0.26258	-1.0108	10	0.52906	T	0.07	.	7.6143	0.28148	0.0:0.2577:0.0:0.7423	.	177	O15403	MOT7_HUMAN	V	177	ENSP00000319991:I177V	ENSP00000319991:I177V	I	-	1	0	SLC16A6	63779367	0.998000	0.40836	0.002000	0.10522	0.871000	0.50021	3.060000	0.49955	-0.043000	0.13513	0.397000	0.26171	ATT	.	T|1.000;C|0.000		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
TMC6	11322	hgsc.bcm.edu	37	17	76113656	76113656	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr17:76113656C>A	ENST00000590602.1	-	17	2250	c.2091G>T	c.(2089-2091)tgG>tgT	p.W697C	TMC6_ENST00000306591.7_Intron|TMC6_ENST00000322933.4_Missense_Mutation_p.W276C|TMC6_ENST00000322914.3_Missense_Mutation_p.W697C|TMC6_ENST00000392467.3_Missense_Mutation_p.W697C|TMC6_ENST00000591436.1_Missense_Mutation_p.W276C|TMC6_ENST00000592076.1_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	697					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GGTGGCGCACCCACACCCTGC	0.667																																					p.W697C		Atlas-SNP	.											.	TMC6	42	.	0			c.G2091T						.						12.0	13.0	13.0					17																	76113656		2186	4266	6452	SO:0001583	missense	11322	exon17			GCGCACCCACACC	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.2091G>T	chr17.hg19:g.76113656C>A	ENSP00000465261:p.Trp697Cys	86.0	0.0		67.0	20.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476388	0.44044	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933	T;T;T	0.71934	-0.3;-0.3;-0.61	3.69	3.69	0.42338	.	0.204709	0.45606	D	0.000343	T	0.82042	0.4951	M	0.79693	2.465	0.80722	D	1	P;D	0.76494	0.801;0.999	P;D	0.69654	0.447;0.965	D	0.84070	0.0379	10	0.66056	D	0.02	-12.8777	11.0062	0.47635	0.1865:0.8135:0.0:0.0	.	697;276	Q7Z403;Q7Z403-3	TMC6_HUMAN;.	C	697;697;276	ENSP00000313408:W697C;ENSP00000376260:W697C;ENSP00000313479:W276C	ENSP00000313408:W697C	W	-	3	0	TMC6	73625251	1.000000	0.71417	1.000000	0.80357	0.178000	0.23041	5.227000	0.65305	1.894000	0.54839	0.555000	0.69702	TGG	.	.		0.667	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1		
NDC80	10403	hgsc.bcm.edu	37	18	2610833	2610833	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:2610833G>A	ENST00000261597.4	+	16	1946	c.1764G>A	c.(1762-1764)atG>atA	p.M588I		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	588	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						TGTTAGAGATGGTTGCTACAC	0.373																																					p.M588I		Atlas-SNP	.											.	NDC80	62	.	0			c.G1764A						.						169.0	149.0	156.0					18																	2610833		2203	4300	6503	SO:0001583	missense	10403	exon16			AGAGATGGTTGCT	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1764G>A	chr18.hg19:g.2610833G>A	ENSP00000261597:p.Met588Ile	213.0	0.0		174.0	22.0	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	hg19	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.425834	0.25726	.	.	ENSG00000080986	ENST00000261597	T	0.46451	0.87	5.43	4.5	0.54988	.	0.264830	0.45606	D	0.000348	T	0.31702	0.0805	L	0.44542	1.39	0.30725	N	0.74784	B	0.20164	0.042	B	0.13407	0.009	T	0.15752	-1.0426	10	0.32370	T	0.25	-6.95	8.2722	0.31851	0.0842:0.1595:0.7563:0.0	.	588	O14777	NDC80_HUMAN	I	588	ENSP00000261597:M588I	ENSP00000261597:M588I	M	+	3	0	NDC80	2600833	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	1.917000	0.39996	2.547000	0.85894	0.650000	0.86243	ATG	.	.		0.373	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
LAMA1	284217	hgsc.bcm.edu	37	18	7023225	7023225	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:7023225G>T	ENST00000389658.3	-	19	2732	c.2639C>A	c.(2638-2640)gCc>gAc	p.A880D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	880	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTCACAGTGGGCGCCATCTGT	0.602																																					p.A880D		Atlas-SNP	.											.	LAMA1	458	.	0			c.C2639A						.						94.0	70.0	78.0					18																	7023225		2203	4300	6503	SO:0001583	missense	284217	exon19			CAGTGGGCGCCAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2639C>A	chr18.hg19:g.7023225G>T	ENSP00000374309:p.Ala880Asp	122.0	0.0		119.0	10.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	5.205	0.223300	0.09863	.	.	ENSG00000101680	ENST00000389658	T	0.61158	0.13	5.47	4.56	0.56223	EGF-like, laminin (4);	0.881961	0.09731	N	0.763140	T	0.39545	0.1082	N	0.04260	-0.245	0.09310	N	1	P	0.40970	0.734	P	0.46049	0.502	T	0.12041	-1.0563	10	0.32370	T	0.25	.	5.852	0.18697	0.0736:0.3403:0.4635:0.1226	.	880	P25391	LAMA1_HUMAN	D	880	ENSP00000374309:A880D	ENSP00000374309:A880D	A	-	2	0	LAMA1	7013225	0.000000	0.05858	0.952000	0.39060	0.605000	0.37080	0.226000	0.17776	2.578000	0.87016	0.643000	0.83706	GCC	.	.		0.602	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
CEP192	55125	hgsc.bcm.edu	37	18	13049219	13049219	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:13049219A>T	ENST00000325971.8	+	14	2234	c.641A>T	c.(640-642)gAt>gTt	p.D214V	CEP192_ENST00000506447.1_Missense_Mutation_p.D810V|CEP192_ENST00000430049.2_Missense_Mutation_p.D335V			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	214					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GATACTTGGGATTTATCTTTG	0.383																																					p.D810V		Atlas-SNP	.											.	CEP192	340	.	0			c.A2429T						.						103.0	101.0	102.0					18																	13049219		2203	4300	6503	SO:0001583	missense	55125	exon16			CTTGGGATTTATC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.641A>T	chr18.hg19:g.13049219A>T	ENSP00000317156:p.Asp214Val	72.0	0.0		80.0	11.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	A	19.16	3.774142	0.69992	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.07908	3.15;3.17;3.17	5.27	5.27	0.74061	.	0.000000	0.49305	D	0.000160	T	0.25419	0.0618	M	0.62723	1.935	0.52501	D	0.999957	D;D;D	0.76494	0.99;0.996;0.999	P;D;D	0.71656	0.901;0.931;0.974	T	0.00485	-1.1711	10	0.41790	T	0.15	-12.6436	15.4964	0.75653	1.0:0.0:0.0:0.0	.	335;810;214	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	V	810;214;214;335	ENSP00000427550:D810V;ENSP00000317156:D214V;ENSP00000389190:D335V	ENSP00000317156:D214V	D	+	2	0	CEP192	13039219	0.999000	0.42202	1.000000	0.80357	0.900000	0.52787	3.468000	0.53086	2.131000	0.65755	0.528000	0.53228	GAT	.	.		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
ABHD3	171586	hgsc.bcm.edu	37	18	19263896	19263896	+	Silent	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:19263896C>T	ENST00000289119.2	-	4	679	c.540G>A	c.(538-540)gcG>gcA	p.A180A	ABHD3_ENST00000578270.1_5'UTR|RP11-13N13.6_ENST00000578583.1_RNA|MIR320C1_ENST00000408566.1_RNA|ABHD3_ENST00000579875.1_Intron|ABHD3_ENST00000580981.1_Intron	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	180						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						GATTCTCCCCCGCCACTCCTC	0.279																																					p.A180A		Atlas-SNP	.											.	ABHD3	32	.	0			c.G540A						.						67.0	75.0	72.0					18																	19263896		2203	4294	6497	SO:0001819	synonymous_variant	171586	exon4			CTCCCCCGCCACT	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"""Abhydrolase domain containing"""	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.540G>A	chr18.hg19:g.19263896C>T		189.0	0.0		193.0	46.0	NM_138340	B0YIV0|B7Z5C2|O43411	Silent	SNP	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.279	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1		
KIAA1328	57536	hgsc.bcm.edu	37	18	34646878	34646878	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:34646878A>G	ENST00000280020.5	+	7	624	c.602A>G	c.(601-603)cAg>cGg	p.Q201R	KIAA1328_ENST00000591619.1_Missense_Mutation_p.Q197R|KIAA1328_ENST00000435985.2_5'UTR|KIAA1328_ENST00000586501.1_5'UTR|KIAA1328_ENST00000543923.1_Missense_Mutation_p.Q93R|KIAA1328_ENST00000586135.1_5'UTR	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	201										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AGCACTCTCCAGTGTTCATCT	0.413																																					p.Q201R		Atlas-SNP	.											.	KIAA1328	39	.	0			c.A602G						.						65.0	61.0	62.0					18																	34646878		1873	4103	5976	SO:0001583	missense	57536	exon7			CTCTCCAGTGTTC	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.602A>G	chr18.hg19:g.34646878A>G	ENSP00000280020:p.Gln201Arg	166.0	0.0		142.0	33.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	hg19	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	A	8.462	0.855430	0.17106	.	.	ENSG00000150477	ENST00000543923;ENST00000280020;ENST00000383055	T;T	0.41065	1.01;2.32	6.17	-12.3	0.00002	.	0.832930	0.10897	N	0.622016	T	0.21145	0.0509	N	0.20986	0.625	0.09310	N	0.999991	B;B	0.14438	0.01;0.002	B;B	0.11329	0.006;0.004	T	0.36625	-0.9740	10	0.09590	T	0.72	.	16.9504	0.86244	0.7855:0.1442:0.0702:0.0	.	201;201	A8K8C3;Q86T90	.;K1328_HUMAN	R	93;201;201	ENSP00000441359:Q93R;ENSP00000280020:Q201R	ENSP00000280020:Q201R	Q	+	2	0	KIAA1328	32900876	0.000000	0.05858	0.000000	0.03702	0.792000	0.44763	-0.845000	0.04340	-2.876000	0.00321	-0.408000	0.06270	CAG	.	.		0.413	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
DCC	1630	hgsc.bcm.edu	37	18	51025767	51025767	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr18:51025767C>T	ENST00000442544.2	+	27	4614	c.3998C>T	c.(3997-3999)aCa>aTa	p.T1333I	DCC_ENST00000581580.1_Missense_Mutation_p.T966I|RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1333					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		ACCATCCCCACAGCTTGTGTT	0.532																																					p.T1333I		Atlas-SNP	.											.	DCC	360	.	0			c.C3998T						.						238.0	181.0	200.0					18																	51025767		2203	4300	6503	SO:0001583	missense	1630	exon27			TCCCCACAGCTTG	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3998C>T	chr18.hg19:g.51025767C>T	ENSP00000389140:p.Thr1333Ile	171.0	0.0		84.0	9.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599054	0.46318	.	.	ENSG00000187323	ENST00000442544	T	0.49432	0.78	6.17	6.17	0.99709	Neogenin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68897	0.3051	M	0.65498	2.005	0.53005	D	0.999961	D	0.67145	0.996	D	0.70227	0.968	T	0.68198	-0.5472	10	0.72032	D	0.01	-6.4138	19.6509	0.95805	0.0:1.0:0.0:0.0	.	1333	P43146	DCC_HUMAN	I	1333	ENSP00000389140:T1333I	ENSP00000389140:T1333I	T	+	2	0	DCC	49279765	1.000000	0.71417	0.969000	0.41365	0.971000	0.66376	6.259000	0.72494	2.941000	0.99782	0.655000	0.94253	ACA	.	.		0.532	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
C2CD4C	126567	hgsc.bcm.edu	37	19	407975	407975	+	Silent	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:407975G>A	ENST00000332235.6	-	2	560	c.387C>T	c.(385-387)gaC>gaT	p.D129D		NM_001136263.1	NP_001129735.1	Q8TF44	C2C4C_HUMAN	C2 calcium-dependent domain containing 4C	129										large_intestine(1)|pancreas(1)	2						GGGCCTGGGGGTCGGCGTCAG	0.687																																					p.D129D		Atlas-SNP	.											.	C2CD4C	13	.	0			c.C387T						.						8.0	12.0	11.0					19																	407975		685	1576	2261	SO:0001819	synonymous_variant	126567	exon2			CTGGGGGTCGGCG	AB075837	CCDS45890.1	19p13.3	2009-09-28	2009-09-28	2009-09-28		ENSG00000183186			29417	protein-coding gene	gene with protein product	"""nuclear localized factor 3"""	610336	"""KIAA1957"", ""family with sequence similarity 148, member C"""	KIAA1957, FAM148C		11853319	Standard	NM_001136263		Approved	NLF3	uc002loo.3	Q8TF44		ENST00000332235.6:c.387C>T	chr19.hg19:g.407975G>A		121.0	0.0		125.0	27.0	NM_001136263	Q8N3H7	Silent	SNP	ENST00000332235.6	hg19	CCDS45890.1																																																																																			.	.		0.687	C2CD4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451789.2	XM_065166	
SEMA6B	10501	hgsc.bcm.edu	37	19	4550257	4550257	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:4550257C>T	ENST00000586582.1	-	12	1459	c.1149G>A	c.(1147-1149)atG>atA	p.M383I	SEMA6B_ENST00000301293.3_Missense_Mutation_p.M383I|SEMA6B_ENST00000586965.1_Missense_Mutation_p.M383I	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	383	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CATTGTACTGCATCCCGGGGG	0.622																																					p.M383I		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G1149A						.						61.0	53.0	56.0					19																	4550257		2203	4300	6503	SO:0001583	missense	10501	exon12			GTACTGCATCCCG	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.1149G>A	chr19.hg19:g.4550257C>T	ENSP00000467290:p.Met383Ile	138.0	0.0		107.0	26.0	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	hg19	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	.	6.001	0.368594	0.11352	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10382	2.88	2.6	1.5	0.22942	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.264529	0.37095	U	0.002241	T	0.08403	0.0209	L	0.39147	1.195	0.22446	N	0.9991	B;B	0.19445	0.036;0.008	B;B	0.29524	0.103;0.065	T	0.34825	-0.9813	10	0.20519	T	0.43	.	6.3431	0.21335	0.209:0.5869:0.2041:0.0	.	383;383	B4DT36;Q9H3T3	.;SEM6B_HUMAN	I	383	ENSP00000301293:M383I	ENSP00000301292:M383I	M	-	3	0	SEMA6B	4501257	0.000000	0.05858	0.925000	0.36789	0.541000	0.35023	-0.102000	0.10956	0.640000	0.30582	0.478000	0.44815	ATG	.	.		0.622	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
MUC16	94025	hgsc.bcm.edu	37	19	9011461	9011461	+	Silent	SNP	A	A	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:9011461A>G	ENST00000397910.4	-	36	38975	c.38772T>C	c.(38770-38772)gaT>gaC	p.D12924D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12926	SEA 6. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCAGATGGCATCCATTCCAG	0.542																																					p.D12924D		Atlas-SNP	.											.	MUC16	4315	.	0			c.T38772C						.						149.0	133.0	138.0					19																	9011461		1933	4133	6066	SO:0001819	synonymous_variant	94025	exon36			GATGGCATCCATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38772T>C	chr19.hg19:g.9011461A>G		241.0	0.0		154.0	12.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF878	729747	hgsc.bcm.edu	37	19	12155914	12155914	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:12155914G>A	ENST00000547628.1	-	4	439	c.302C>T	c.(301-303)tCa>tTa	p.S101L	CTD-2006C1.2_ENST00000591838.1_RNA|ZNF878_ENST00000602107.1_Missense_Mutation_p.S148L|CTD-2006C1.10_ENST00000547473.1_Intron|CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						GCTTTCATATGATTGTACTCC	0.433																																					p.S101L		Atlas-SNP	.											.	ZNF878	172	.	0			c.C302T						.						66.0	62.0	63.0					19																	12155914		2018	4219	6237	SO:0001583	missense	729747	exon4			TCATATGATTGTA		CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"""Zinc fingers, C2H2-type"", ""-"""	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.302C>T	chr19.hg19:g.12155914G>A	ENSP00000447931:p.Ser101Leu	142.0	0.0		124.0	31.0	NM_001080404		Missense_Mutation	SNP	ENST00000547628.1	hg19	CCDS45984.2	.	.	.	.	.	.	.	.	.	.	G	6.743	0.505917	0.12883	.	.	ENSG00000257446;ENSG00000232371	ENST00000547628;ENST00000440730	T	0.06687	3.27	1.3	1.3	0.21679	.	.	.	.	.	T	0.11922	0.0290	L	0.40543	1.245	0.09310	N	1	D	0.60575	0.988	P	0.53313	0.723	T	0.20140	-1.0284	9	0.44086	T	0.13	.	8.094	0.30818	0.0:0.0:1.0:0.0	.	101	C9JN71	ZN878_HUMAN	L	101;148	ENSP00000447931:S101L	ENSP00000447931:S101L	S	-	2	0	AC022415.4;ZNF878	12016914	0.000000	0.05858	0.003000	0.11579	0.025000	0.11179	0.400000	0.20932	0.675000	0.31264	0.313000	0.20887	TCA	.	.		0.433	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404	
ZNF709	163051	hgsc.bcm.edu	37	19	12575313	12575313	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:12575313G>A	ENST00000397732.3	-	4	1594	c.1423C>T	c.(1423-1425)Ccc>Tcc	p.P475S	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Missense_Mutation_p.P475S	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						CATTCATAGGGTTTCTCTCCA	0.403																																					p.P475S	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.C1423T						.						90.0	96.0	94.0					19																	12575313		2203	4300	6503	SO:0001583	missense	163051	exon4			CATAGGGTTTCTC	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"""Zinc fingers, C2H2-type"", ""-"""	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.1423C>T	chr19.hg19:g.12575313G>A	ENSP00000380840:p.Pro475Ser	51.0	0.0		42.0	8.0	NM_152601	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449384	0.84101	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.16743	2.32;2.32	3.05	3.05	0.35203	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33772	N	0.004580	T	0.32645	0.0836	L	0.53780	1.695	0.31497	N	0.665273	D	0.89917	1.0	D	0.80764	0.994	T	0.19516	-1.0303	10	0.66056	D	0.02	.	10.1848	0.42991	0.0:0.2053:0.7947:0.0	.	475	Q8N972	ZN709_HUMAN	S	475	ENSP00000380840:P475S;ENSP00000404127:P475S	ENSP00000404127:P475S	P	-	1	0	ZNF709;CTD-2192J16.17	12436313	0.554000	0.26522	0.121000	0.21740	0.998000	0.95712	2.607000	0.46300	2.032000	0.59987	0.591000	0.81541	CCC	.	.		0.403	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601	
U2AF1L4	199746	hgsc.bcm.edu	37	19	36236067	36236067	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:36236067C>T	ENST00000412391.2	-	2	104	c.91G>A	c.(91-93)Gac>Aac	p.D31N	PSENEN_ENST00000587708.2_5'UTR|AC002398.9_ENST00000591613.2_5'Flank|IGFLR1_ENST00000344990.3_5'Flank|U2AF1L4_ENST00000292879.5_Missense_Mutation_p.D31N|IGFLR1_ENST00000246532.1_5'Flank|IGFLR1_ENST00000588992.1_5'Flank|AC002398.11_ENST00000591091.1_RNA|AC002398.11_ENST00000585365.1_RNA|U2AF1L4_ENST00000588100.1_5'UTR|PSENEN_ENST00000222266.2_5'Flank|U2AF1L4_ENST00000378975.3_Missense_Mutation_p.D31N|AD000671.6_ENST00000589807.1_Missense_Mutation_p.D31N|IGFLR1_ENST00000592537.1_5'Flank|PSENEN_ENST00000591949.1_5'Flank			Q8WU68	U2AF4_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 4	31					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGCACCGGTCCCCGTGCCGG	0.622																																					p.D31N		Atlas-SNP	.											.	U2AF1L4	34	.	0			c.G91A						.						37.0	44.0	42.0					19																	36236067		2203	4300	6503	SO:0001583	missense	199746	exon2			ACCGGTCCCCGTG	BC021186, AY569437	CCDS12473.1, CCDS42551.1	19q13.13	2013-02-12	2006-04-12	2006-04-12		ENSG00000161265		"""RNA binding motif (RRM) containing"""	23020	protein-coding gene	gene with protein product		601080	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 3"", ""U2 small nuclear RNA auxiliary factor 1-like 3"""	U2AF1L3		8586425, 11739736	Standard	NM_001040425		Approved	MGC33901, U2af26	uc002obf.3	Q8WU68		ENST00000412391.2:c.91G>A	chr19.hg19:g.36236067C>T	ENSP00000397645:p.Asp31Asn	78.0	0.0		56.0	19.0	NM_144987	A6NKI8|Q56UU3	Missense_Mutation	SNP	ENST00000412391.2	hg19		.	.	.	.	.	.	.	.	.	.	C	18.77	3.695790	0.68386	.	.	ENSG00000161265	ENST00000292879;ENST00000378975;ENST00000412391	T;T;T	0.48201	0.82;0.82;0.82	5.19	3.09	0.35607	.	0.673695	0.14230	N	0.332819	T	0.57814	0.2079	.	.	.	0.80722	D	1	P;P	0.49862	0.929;0.918	P;P	0.55303	0.729;0.773	T	0.56195	-0.8019	9	0.56958	D	0.05	-2.2858	9.2691	0.37659	0.0:0.8267:0.0:0.1733	.	31;31	Q8WU68-2;Q8WU68-3	.;.	N	31	ENSP00000292879:D31N;ENSP00000368258:D31N;ENSP00000397645:D31N	ENSP00000292879:D31N	D	-	1	0	U2AF1L4	40927907	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	3.562000	0.53777	0.780000	0.33566	0.643000	0.83706	GAC	.	.		0.622	U2AF1L4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144987	
PSMC4	5704	hgsc.bcm.edu	37	19	40485836	40485836	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:40485836C>G	ENST00000157812.2	+	7	984	c.786C>G	c.(784-786)atC>atG	p.I262M	PSMC4_ENST00000455878.2_Missense_Mutation_p.I231M	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	262					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTGCCATCATCTTCATAGACG	0.572																																					p.I262M	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.C786G						.						71.0	69.0	69.0					19																	40485836		2203	4300	6503	SO:0001583	missense	5704	exon7			CATCATCTTCATA	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9551	protein-coding gene	gene with protein product	"""protease 26S subunit 6"", ""Tat-binding protein 7"", ""MB67 interacting protein"""	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.786C>G	chr19.hg19:g.40485836C>G	ENSP00000157812:p.Ile262Met	188.0	0.0		161.0	34.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Missense_Mutation	SNP	ENST00000157812.2	hg19	CCDS12547.1	.	.	.	.	.	.	.	.	.	.	c	11.95	1.792327	0.31685	.	.	ENSG00000013275	ENST00000157812;ENST00000455878	D;D	0.95949	-3.86;-3.86	6.06	2.25	0.28309	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.046718	0.85682	D	0.000000	D	0.97068	0.9042	M	0.88241	2.94	0.54753	D	0.999985	P;D	0.63046	0.596;0.992	P;D	0.80764	0.498;0.994	D	0.95386	0.8477	10	0.66056	D	0.02	-9.3148	4.3152	0.10990	0.2766:0.5069:0.1348:0.0817	.	231;262	P43686-2;P43686	.;PRS6B_HUMAN	M	262;231	ENSP00000157812:I262M;ENSP00000413869:I231M	ENSP00000157812:I262M	I	+	3	3	PSMC4	45177676	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	3.832000	0.55783	0.849000	0.35215	-0.176000	0.13171	ATC	.	.		0.572	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	
LYPD3	27076	hgsc.bcm.edu	37	19	43969676	43969676	+	Silent	SNP	T	T	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:43969676T>A	ENST00000244333.3	-	1	136	c.48A>T	c.(46-48)gcA>gcT	p.A16A		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	16					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				GCAGCCAGCCTGCAGTCCAGA	0.692																																					p.A16A		Atlas-SNP	.											.	LYPD3	24	.	0			c.A48T						.						94.0	82.0	86.0					19																	43969676		2203	4300	6503	SO:0001819	synonymous_variant	27076	exon1			CCAGCCTGCAGTC	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.48A>T	chr19.hg19:g.43969676T>A		64.0	0.0		56.0	12.0	NM_014400	Q9UJ74	Silent	SNP	ENST00000244333.3	hg19	CCDS12620.1																																																																																			.	.		0.692	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
KLC3	147700	hgsc.bcm.edu	37	19	45853937	45853937	+	Silent	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:45853937G>A	ENST00000391946.2	+	11	1413	c.1311G>A	c.(1309-1311)gaG>gaA	p.E437E	KLC3_ENST00000470402.1_Silent_p.E451E|ERCC2_ENST00000391945.4_3'UTR|KLC3_ENST00000585434.1_Silent_p.E436E	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	437					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AGATCCGTGAGTCTATCAGGC	0.682																																					p.E437E		Atlas-SNP	.											.	KLC3	37	.	0			c.G1311A						.						21.0	26.0	24.0					19																	45853937		1938	4126	6064	SO:0001819	synonymous_variant	147700	exon11			CCGTGAGTCTATC	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.1311G>A	chr19.hg19:g.45853937G>A		184.0	0.0		159.0	37.0	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	hg19	CCDS12660.2																																																																																			.	.		0.682	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
ERCC1	2067	hgsc.bcm.edu	37	19	45924624	45924624	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:45924624T>C	ENST00000300853.3	-	3	724	c.133A>G	c.(133-135)Agc>Ggc	p.S45G	ERCC1_ENST00000589165.1_Missense_Mutation_p.S45G|ERCC1_ENST00000340192.7_Missense_Mutation_p.S45G|ERCC1_ENST00000591636.1_Missense_Mutation_p.S45G|ERCC1_ENST00000013807.5_Missense_Mutation_p.S45G|ERCC1_ENST00000423698.2_Intron	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	45					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		GTGGGAAGGCTCTGTGTAGAT	0.622								Nucleotide excision repair (NER)																													p.S45G		Atlas-SNP	.											.	ERCC1	46	.	0			c.A133G						.						67.0	64.0	65.0					19																	45924624		2203	4300	6503	SO:0001583	missense	2067	exon3			GAAGGCTCTGTGT		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.133A>G	chr19.hg19:g.45924624T>C	ENSP00000300853:p.Ser45Gly	74.0	0.0		74.0	10.0	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	hg19	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.649248	0.29336	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000013807	T;T;T	0.48522	0.84;0.83;0.81	4.25	3.21	0.36854	.	0.868449	0.10211	N	0.702162	T	0.31420	0.0796	N	0.24115	0.695	0.09310	N	1	B;B;B	0.26318	0.146;0.049;0.02	B;B;B	0.22152	0.038;0.016;0.016	T	0.19712	-1.0297	10	0.34782	T	0.22	-6.0974	6.72	0.23325	0.0:0.1103:0.0:0.8897	.	45;45;45	Q7Z7F5;Q96S40;P07992	.;.;ERCC1_HUMAN	G	45	ENSP00000300853:S45G;ENSP00000345203:S45G;ENSP00000013807:S45G	ENSP00000013807:S45G	S	-	1	0	ERCC1	50616464	0.519000	0.26242	0.009000	0.14445	0.068000	0.16541	1.701000	0.37825	0.753000	0.32945	0.402000	0.26972	AGC	.	.		0.622	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
ZC3H4	23211	hgsc.bcm.edu	37	19	47569634	47569634	+	Silent	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:47569634C>A	ENST00000253048.5	-	15	3928	c.3891G>T	c.(3889-3891)acG>acT	p.T1297T	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1297							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)		AGGGGGAGGCCGTGGGGTCGA	0.627																																					p.T1297T		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G3891T						.						9.0	11.0	10.0					19																	47569634		1904	4069	5973	SO:0001819	synonymous_variant	23211	exon15			GGAGGCCGTGGGG	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.3891G>T	chr19.hg19:g.47569634C>A		73.0	0.0		64.0	12.0	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	hg19	CCDS42582.1																																																																																			.	.		0.627	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
KCNA7	3743	hgsc.bcm.edu	37	19	49574011	49574011	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:49574011C>A	ENST00000221444.1	-	2	1035	c.680G>T	c.(679-681)cGc>cTc	p.R227L		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	227					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GACCAGGAGGCGTACCAGCAG	0.527																																					p.R227L	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.G680T						.						146.0	106.0	119.0					19																	49574011		2203	4300	6503	SO:0001583	missense	3743	exon2			AGGAGGCGTACCA	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.680G>T	chr19.hg19:g.49574011C>A	ENSP00000221444:p.Arg227Leu	83.0	0.0		67.0	20.0	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	hg19	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.349632	0.61183	.	.	ENSG00000104848	ENST00000221444	D	0.98684	-5.07	4.49	4.49	0.54785	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.98818	4.34	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97677	1.0170	10	0.87932	D	0	.	16.3041	0.82841	0.0:1.0:0.0:0.0	.	227	Q96RP8	KCNA7_HUMAN	L	227	ENSP00000221444:R227L	ENSP00000221444:R227L	R	-	2	0	KCNA7	54265823	1.000000	0.71417	0.954000	0.39281	0.149000	0.21700	7.811000	0.86092	2.234000	0.73211	0.313000	0.20887	CGC	.	.		0.527	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
FPR1	2357	hgsc.bcm.edu	37	19	52249985	52249985	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:52249985C>A	ENST00000595042.1	-	3	404	c.263G>T	c.(262-264)gGa>gTa	p.G88V	FPR1_ENST00000304748.4_Missense_Mutation_p.G88V	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	88					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CCAATGTCCTCCCATGGCCTT	0.507																																					p.G88V		Atlas-SNP	.											.	FPR1	64	.	0			c.G263T						.						137.0	105.0	116.0					19																	52249985		2203	4300	6503	SO:0001583	missense	2357	exon3			TGTCCTCCCATGG	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.263G>T	chr19.hg19:g.52249985C>A	ENSP00000471493:p.Gly88Val	204.0	0.0		183.0	35.0	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	hg19	CCDS12839.1	.	.	.	.	.	.	.	.	.	.	.	7.804	0.714234	0.15306	.	.	ENSG00000171051	ENST00000304748	T	0.37058	1.22	3.72	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.745223	0.12330	N	0.478436	T	0.44244	0.1284	L	0.58810	1.83	0.40445	D	0.980084	P	0.37276	0.589	P	0.50896	0.653	T	0.26916	-1.0089	10	0.27785	T	0.31	.	6.5403	0.22377	0.0:0.7644:0.0:0.2356	.	88	P21462	FPR1_HUMAN	V	88	ENSP00000302707:G88V	ENSP00000302707:G88V	G	-	2	0	FPR1	56941797	0.000000	0.05858	0.002000	0.10522	0.031000	0.12232	-0.015000	0.12634	0.844000	0.35094	0.563000	0.77884	GGA	.	.		0.507	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Nonsense_Mutation	SNP	A	A	T	rs398101268|rs34470614		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:52887146A>T	ENST00000422689.2	+	4	328	c.313A>T	c.(313-315)Aaa>Taa	p.K105*	ZNF880_ENST00000424032.2_3'UTR	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	105					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)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAGTCTCTTAAAAATCAACT	0.368																																					p.K105X		Atlas-SNP	.											.	ZNF880	45	.	0			c.A313T						.						61.0	45.0	50.0					19																	52887146		690	1569	2259	SO:0001587	stop_gained	400713	exon4			TCTCTTAAAAATC	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.313A>T	chr19.hg19:g.52887146A>T	ENSP00000406318:p.Lys105*	93.0	0.0		109.0	6.0	NM_001145434	B4DNA6	Nonsense_Mutation	SNP	ENST00000422689.2	hg19	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	8.517	0.867766	0.17250	.	.	ENSG00000221923	ENST00000422689	.	.	.	1.6	-2.54	0.06307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.7816	0.03033	0.4842:0.0:0.2398:0.276	.	.	.	.	X	105	.	ENSP00000406318:K105X	K	+	1	0	ZNF880	57578958	0.000000	0.05858	0.006000	0.13384	0.124000	0.20399	-1.231000	0.02939	-0.761000	0.04670	0.368000	0.22195	AAA	.	.		0.368	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
DNAAF3	352909	hgsc.bcm.edu	37	19	55670500	55670500	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr19:55670500T>C	ENST00000524407.2	-	12	1589	c.1556A>G	c.(1555-1557)gAg>gGg	p.E519G	CTD-2587H24.5_ENST00000591665.1_RNA|TNNI3_ENST00000590463.1_5'Flank|DNAAF3_ENST00000455045.1_Missense_Mutation_p.E465G|DNAAF3_ENST00000587789.2_5'UTR|DNAAF3_ENST00000391720.4_Missense_Mutation_p.E566G|DNAAF3_ENST00000527223.2_Missense_Mutation_p.E586G|CTD-2587H24.4_ENST00000587871.1_Intron|TNNI3_ENST00000588882.1_5'Flank|TNNI3_ENST00000344887.5_5'Flank			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	519					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											AGCCAGAACCTCTGAGAGTGA	0.617																																					p.E586G		Atlas-SNP	.											.	.	.	.	0			c.A1757G						.						25.0	27.0	27.0					19																	55670500		1857	4113	5970	SO:0001583	missense	352909	exon12			AGAACCTCTGAGA	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.1556A>G	chr19.hg19:g.55670500T>C	ENSP00000432046:p.Glu519Gly	168.0	0.0		133.0	31.0	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	hg19	CCDS59422.1	.	.	.	.	.	.	.	.	.	.	t	12.02	1.813756	0.32053	.	.	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.20069	2.13;2.1	3.77	2.71	0.32032	.	0.416306	0.17608	N	0.168190	T	0.16171	0.0389	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.33612	0.419;0.253;0.16;0.16	B;B;B;B	0.36244	0.22;0.128;0.128;0.128	T	0.15235	-1.0444	10	0.72032	D	0.01	-6.6568	8.6882	0.34251	0.0:0.0:0.1928:0.8072	.	586;465;539;519	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	G	586;465;566	ENSP00000394343:E465G;ENSP00000375600:E566G	ENSP00000301249:E586G	E	-	2	0	C19orf51	60362312	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.064000	0.11636	0.776000	0.33473	0.454000	0.30748	GAG	.	.		0.617	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
PHF20	51230	hgsc.bcm.edu	37	20	34515736	34515736	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr20:34515736G>T	ENST00000374012.3	+	14	2168	c.2039G>T	c.(2038-2040)tGc>tTc	p.C680F	PHF20_ENST00000439301.1_3'UTR|RNU6-937P_ENST00000384325.1_RNA			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	680					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CATGGGGTCTGCATGGGATTA	0.438																																					p.C680F		Atlas-SNP	.											.	PHF20	94	.	0			c.G2039T						.						149.0	146.0	147.0					20																	34515736		2203	4300	6503	SO:0001583	missense	51230	exon14			GGGTCTGCATGGG	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.2039G>T	chr20.hg19:g.34515736G>T	ENSP00000363124:p.Cys680Phe	120.0	0.0		139.0	50.0	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	hg19	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875229	0.91664	.	.	ENSG00000025293	ENST00000374012	D	0.99252	-5.63	5.91	5.91	0.95273	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99746	0.9899	H	0.98965	4.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97171	0.9844	10	0.87932	D	0	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	680	Q9BVI0	PHF20_HUMAN	F	680	ENSP00000363124:C680F	ENSP00000363124:C680F	C	+	2	0	PHF20	33979150	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.296000	0.96104	2.793000	0.96121	0.655000	0.94253	TGC	.	.		0.438	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	
MATN4	8785	hgsc.bcm.edu	37	20	43933399	43933399	+	Missense_Mutation	SNP	C	C	T	rs114313957	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr20:43933399C>T	ENST00000372754.1	-	2	120	c.112G>A	c.(112-114)Gtg>Atg	p.V38M	RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000342716.4_Missense_Mutation_p.V38M|MATN4_ENST00000360607.6_Missense_Mutation_p.V38M|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000537548.1_Missense_Mutation_p.V38M|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000372756.1_Missense_Mutation_p.V38M|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000353917.5_Missense_Mutation_p.V38M			O95460	MATN4_HUMAN	matrilin 4	38	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CTGTCAATCACGAACACCAGA	0.642																																					p.V38M		Atlas-SNP	.											.	MATN4	57	.	0			c.G112A						.						25.0	22.0	23.0					20																	43933399		2198	4284	6482	SO:0001583	missense	8785	exon3			CAATCACGAACAC	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.112G>A	chr20.hg19:g.43933399C>T	ENSP00000361840:p.Val38Met	88.0	0.0		116.0	28.0	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.12	2.141067	0.37825	.	.	ENSG00000124159	ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132	D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	4.2	2.1	0.27182	.	0.567187	0.14655	N	0.306376	D	0.82912	0.5140	M	0.67700	2.07	0.80722	D	1	B;B;B	0.28512	0.032;0.097;0.214	B;B;B	0.28139	0.023;0.086;0.086	T	0.79588	-0.1741	10	0.54805	T	0.06	.	4.952	0.14019	0.0:0.6284:0.1751:0.1964	.	38;38;38	A6NNA4;O95460-4;O95460-2	.;.;.	M	38	ENSP00000361840:V38M;ENSP00000361842:V38M;ENSP00000243983:V38M;ENSP00000353819:V38M;ENSP00000343164:V38M;ENSP00000440328:V38M	ENSP00000255132:V38M	V	-	1	0	MATN4	43366813	0.999000	0.42202	0.988000	0.46212	0.975000	0.68041	1.406000	0.34646	0.943000	0.37553	0.462000	0.41574	GTG	.	C|0.987;G|0.013		0.642	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
DSCR3	10311	hgsc.bcm.edu	37	21	38597864	38597864	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr21:38597864A>T	ENST00000309117.6	-	8	1112	c.875T>A	c.(874-876)cTg>cAg	p.L292Q	AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000398998.1_Missense_Mutation_p.L244Q|DSCR3_ENST00000399000.3_5'UTR|DSCR3_ENST00000476950.1_Missense_Mutation_p.L265Q|DSCR3_ENST00000399001.1_Missense_Mutation_p.L167Q|DSCR3_ENST00000539844.1_Missense_Mutation_p.L215Q|DSCR3_ENST00000288304.5_Missense_Mutation_p.L248Q	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	292						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						GCAGAGCTTCAGCGGGAAGTT	0.527																																					p.L292Q		Atlas-SNP	.											.	DSCR3	21	.	0			c.T875A						.						82.0	75.0	78.0					21																	38597864		2203	4300	6503	SO:0001583	missense	10311	exon8			AGCTTCAGCGGGA	D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538			3044	protein-coding gene	gene with protein product		605298				9399594	Standard	NM_006052		Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.875T>A	chr21.hg19:g.38597864A>T	ENSP00000311399:p.Leu292Gln	120.0	0.0		106.0	20.0	NM_006052	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	Missense_Mutation	SNP	ENST00000309117.6	hg19	CCDS33553.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.854712	0.91355	.	.	ENSG00000157538	ENST00000309117;ENST00000288304;ENST00000539844;ENST00000399001;ENST00000476950;ENST00000398998	.	.	.	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000002	T	0.77089	0.4079	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.995;1.0	D;D;D;D	0.69142	0.931;0.962;0.947;0.927	T	0.80469	-0.1369	9	0.87932	D	0	-6.6983	14.973	0.71249	1.0:0.0:0.0:0.0	.	167;215;265;292	A8MY26;B7Z606;B7Z6B1;O14972	.;.;.;DSCR3_HUMAN	Q	292;248;215;167;265;244	.	ENSP00000288304:L248Q	L	-	2	0	DSCR3	37519734	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.338000	0.90038	2.001000	0.58596	0.533000	0.62120	CTG	.	.		0.527	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194807.1		
SSTR3	6753	hgsc.bcm.edu	37	22	37602722	37602722	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr22:37602722A>T	ENST00000328544.3	-	2	1654	c.1121T>A	c.(1120-1122)gTc>gAc	p.V374D	SSTR3_ENST00000402501.1_Missense_Mutation_p.V374D	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	374					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GATCTGGCTGACCCGGCCGTT	0.677																																					p.V374D		Atlas-SNP	.											.	SSTR3	42	.	0			c.T1121A						.						45.0	42.0	43.0					22																	37602722		2203	4300	6503	SO:0001583	missense	6753	exon2			TGGCTGACCCGGC		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1121T>A	chr22.hg19:g.37602722A>T	ENSP00000330138:p.Val374Asp	89.0	0.0		58.0	16.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.648189	0.47258	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.72505	-0.66;-0.66	5.33	5.33	0.75918	.	1.359230	0.05115	N	0.489532	T	0.70684	0.3252	L	0.54323	1.7	0.50813	D	0.99989	P	0.48407	0.91	B	0.43575	0.424	T	0.58515	-0.7623	10	0.24483	T	0.36	.	11.6877	0.51497	1.0:0.0:0.0:0.0	.	374	P32745	SSR3_HUMAN	D	374	ENSP00000330138:V374D;ENSP00000384904:V374D	ENSP00000330138:V374D	V	-	2	0	SSTR3	35932668	1.000000	0.71417	0.795000	0.32087	0.863000	0.49368	3.695000	0.54749	2.008000	0.58898	0.482000	0.46254	GTC	.	.		0.677	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
PCDH19	57526	hgsc.bcm.edu	37	X	99551540	99551540	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:99551540G>T	ENST00000373034.4	-	6	4857	c.3182C>A	c.(3181-3183)gCg>gAg	p.A1061E	PCDH19_ENST00000420881.2_Missense_Mutation_p.A1013E|PCDH19_ENST00000464981.1_5'Flank|PCDH19_ENST00000255531.7_Missense_Mutation_p.A1014E	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1061					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						AGGGCTAATCGCCTCACAGCC	0.607																																					p.A1061E		Atlas-SNP	.											.	PCDH19	269	.	0			c.C3182A						.						53.0	56.0	55.0					X																	99551540		2137	4232	6369	SO:0001583	missense	57526	exon6			CTAATCGCCTCAC	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3182C>A	chrX.hg19:g.99551540G>T	ENSP00000362125:p.Ala1061Glu	65.0	0.0		46.0	22.0	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	hg19	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.007882	0.54361	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.55234	0.53;0.73;0.53	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.66277	0.2773	L	0.51422	1.61	0.80722	D	1	D;B;B	0.76494	0.999;0.388;0.269	D;B;B	0.81914	0.995;0.299;0.157	T	0.58836	-0.7566	10	0.12430	T	0.62	.	18.9069	0.92466	0.0:0.0:1.0:0.0	.	1061;1014;1013	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	E	1013;1061;1014	ENSP00000400327:A1013E;ENSP00000362125:A1061E;ENSP00000255531:A1014E	ENSP00000255531:A1014E	A	-	2	0	PCDH19	99438196	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.087000	0.94110	2.413000	0.81919	0.600000	0.82982	GCG	.	.		0.607	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
MAP7D3	79649	hgsc.bcm.edu	37	X	135314089	135314089	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:135314089C>G	ENST00000316077.9	-	8	1247	c.1027G>C	c.(1027-1029)Gtg>Ctg	p.V343L	MAP7D3_ENST00000370661.1_Missense_Mutation_p.V308L|MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370663.5_Missense_Mutation_p.V325L	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	343					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					GACACGTCCACGCTCACCACA	0.567																																					p.V343L		Atlas-SNP	.											.	MAP7D3	102	.	0			c.G1027C						.						103.0	107.0	106.0					X																	135314089		2186	4252	6438	SO:0001583	missense	79649	exon8			CGTCCACGCTCAC	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1027G>C	chrX.hg19:g.135314089C>G	ENSP00000318086:p.Val343Leu	114.0	0.0		101.0	55.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	hg19	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	C	9.134	1.012172	0.19277	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	4.19	0.94	0.19513	.	.	.	.	.	T	0.04634	0.0126	L	0.27053	0.805	0.09310	N	1	B;B;B;B	0.28439	0.212;0.068;0.212;0.032	B;B;B;B	0.22386	0.039;0.02;0.039;0.034	T	0.42085	-0.9472	9	0.27785	T	0.31	-0.1196	2.2736	0.04096	0.1892:0.3311:0.3653:0.1144	.	325;302;343;308	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	L	308;343;325;302	ENSP00000359695:V308L;ENSP00000318086:V343L;ENSP00000359697:V325L;ENSP00000359694:V302L	ENSP00000318086:V343L	V	-	1	0	MAP7D3	135141755	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-5.194000	0.00142	0.291000	0.22468	-0.229000	0.12294	GTG	.	.		0.567	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
MAGEC2	51438	hgsc.bcm.edu	37	X	141291370	141291370	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:141291370G>A	ENST00000247452.3	-	3	751	c.404C>T	c.(403-405)tCc>tTc	p.S135F		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	135	Interaction with TRIM28.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					TGTGAAAGAGGACTCACTGTC	0.522										HNSCC(46;0.14)																											p.S135F		Atlas-SNP	.											.	MAGEC2	102	.	0			c.C404T						.						103.0	102.0	102.0					X																	141291370		2203	4300	6503	SO:0001583	missense	51438	exon3			AAAGAGGACTCAC	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"""cancer/testis antigen 10"""	300468	"""melanoma antigen, family E, 1, cancer/testis specific"""	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.404C>T	chrX.hg19:g.141291370G>A	ENSP00000354660:p.Ser135Phe	38.0	0.0		35.0	16.0	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	hg19	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	4.658	0.122303	0.08931	.	.	ENSG00000046774	ENST00000247452	T	0.02863	4.13	1.13	1.13	0.20643	.	.	.	.	.	T	0.03564	0.0102	L	0.53617	1.68	0.09310	N	1	B	0.14012	0.009	B	0.15484	0.013	T	0.35748	-0.9776	9	0.54805	T	0.06	.	5.306	0.15803	0.0:0.0:1.0:0.0	.	135	Q9UBF1	MAGC2_HUMAN	F	135	ENSP00000354660:S135F	ENSP00000354660:S135F	S	-	2	0	MAGEC2	141119036	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.273000	0.18662	0.861000	0.35504	0.458000	0.33432	TCC	.	.		0.522	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249	
TMEM185A	84548	hgsc.bcm.edu	37	X	148693147	148693147	+	Splice_Site	SNP	C	C	A	rs376945268		TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrX:148693147C>A	ENST00000316916.8	-	2	343		c.e2-1		TMEM185A_ENST00000507237.1_Splice_Site|TMEM185A_ENST00000536359.1_Intron	NM_032508.2	NP_115897.1	Q8NFB2	T185A_HUMAN	transmembrane protein 185A							dendrite (GO:0030425)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(10)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GAGGAATTTACTAGGAGAAAA	0.423																																					.		Atlas-SNP	.											.	TMEM185A	26	.	0			c.39-1G>T						.	C	,	1,3834		0,1,1631,571	122.0	123.0	123.0		,	5.1	1.0	X		123	0,6727		0,0,2428,1871	no	intron,splice-3	TMEM185A	NM_001174092.1,NM_032508.2	,	0,1,4059,2442	AA,AC,CC,C		0.0,0.0261,0.0095	,	,	148693147	1,10561	2203	4299	6502	SO:0001630	splice_region_variant	84548	exon3			AATTTACTAGGAG	AF353675	CCDS14689.1, CCDS55523.1, CCDS76041.1	Xq28	2014-01-28	2007-02-05	2007-02-05	ENSG00000155984	ENSG00000269556			17125	protein-coding gene	gene with protein product		300031	"""chromosome X open reading frame 13"", ""family with sequence similarity 11, member A"""	CXorf13, FAM11A		12404111	Standard	NM_032508		Approved		uc022cgl.1	Q8NFB2	OTTHUMG00000022625	ENST00000316916.8:c.39-1G>T	chrX.hg19:g.148693147C>A		60.0	0.0		56.0	32.0	NM_032508	B3KTZ3|Q3SYH1|Q96CW3|Q96KE8	Splice_Site	SNP	ENST00000316916.8	hg19	CCDS14689.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.437393	0.62955	2.61E-4	0.0	ENSG00000155984	ENST00000316916;ENST00000507237	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6197	0.84927	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM185A	148500948	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.249000	0.78278	2.126000	0.65437	0.600000	0.82982	.	.	.		0.423	TMEM185A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058710.4	NM_032508	Intron
PCDH11Y	83259	hgsc.bcm.edu	37	Y	4966401	4966401	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chrY:4966401G>C	ENST00000333703.4	+	5	1262	c.749G>C	c.(748-750)aGa>aCa	p.R250T	PCDH11Y_ENST00000215473.6_Missense_Mutation_p.R261T|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.R261T	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	261	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R250K(2)|p.R261K(1)		autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TTTCCTCAAAGATCCAGTACT	0.393																																					p.R261T		Atlas-SNP	.											.	PCDH11Y	163	.	3	Substitution - Missense(3)	large_intestine(3)	c.G782C						.																																			SO:0001583	missense	83259	exon2			CTCAAAGATCCAG	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"""Cadherins / Protocadherins : Non-clustered"""	15813	protein-coding gene	gene with protein product		400022	"""protocadherin 22"""	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.749G>C	chrY.hg19:g.4966401G>C	ENSP00000330552:p.Arg250Thr	284.0	0.0		162.0	21.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.393	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973	
HNRNPD	3184	hgsc.bcm.edu	37	4	83278019	83278020	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:83278019_83278020insC	ENST00000313899.7	-	6	1059_1060	c.782_783insG	c.(781-783)gaafs	p.E261fs	HNRNPD_ENST00000352301.4_Frame_Shift_Ins_p.E242fs|HNRNPD_ENST00000508119.1_5'UTR|HNRNPD_ENST00000541060.1_Frame_Shift_Ins_p.E107fs|HNRNPD_ENST00000543098.1_Frame_Shift_Ins_p.E209fs|HNRNPD_ENST00000353341.4_Frame_Shift_Ins_p.E261fs	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	261	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						GCTGATATTGTTCCTTCGACAT	0.366																																					p.E261fs		Atlas-INDEL	.											.	HNRNPD	23	.	0			c.783_784insG						.																																			SO:0001589	frameshift_variant	3184	exon6			.	AF026126	CCDS3590.1, CCDS3591.1, CCDS3592.1	4q21	2013-02-12	2002-08-29	2008-04-18	ENSG00000138668	ENSG00000138668		"""RNA binding motif (RRM) containing"""	5036	protein-coding gene	gene with protein product		601324	"""heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)"""	AUF1, HNRPD		9615222	Standard	NM_001003810		Approved		uc003hmm.1	Q14103	OTTHUMG00000130290	ENST00000313899.7:c.782_783insG	chr4.hg19:g.83278019_83278020insC	ENSP00000313199:p.Glu261fs	175.0	0.0		132.0	23.0	NM_002138	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Frame_Shift_Ins	INS	ENST00000313899.7	hg19	CCDS3592.1																																																																																			.	.		0.366	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370	
TET2	54790	hgsc.bcm.edu	37	4	106155168	106155169	+	Frame_Shift_Ins	INS	-	-	CA			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:106155168_106155169insCA	ENST00000540549.1	+	3	929_930	c.69_70insCA	c.(70-72)attfs	p.I24fs	TET2_ENST00000380013.4_Frame_Shift_Ins_p.I24fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.I24fs|TET2_ENST00000305737.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000513237.1_Frame_Shift_Ins_p.I45fs|TET2_ENST00000413648.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000545826.1_Frame_Shift_Ins_p.I24fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	24					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CATCACCTCCCATTTGCCAGAC	0.515			"""Mis N, F"""		MDS																																p.P23fs		Atlas-INDEL	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.69_70insCA						.																																			SO:0001589	frameshift_variant	54790	exon3			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	Exception_encountered	chr4.hg19:g.106155168_106155169insCA	ENSP00000442788:p.Ile24fs	92.0	0.0		48.0	11.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	ENST00000540549.1	hg19	CCDS47120.1																																																																																			.	.		0.515	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
TET2	54790	hgsc.bcm.edu	37	4	106155167	106155168	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr4:106155167_106155168insT	ENST00000540549.1	+	3	928_929	c.68_69insT	c.(67-72)cccattfs	p.I24fs	TET2_ENST00000380013.4_Frame_Shift_Ins_p.I24fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.I24fs|TET2_ENST00000305737.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000513237.1_Frame_Shift_Ins_p.I45fs|TET2_ENST00000413648.2_Frame_Shift_Ins_p.I24fs|TET2_ENST00000545826.1_Frame_Shift_Ins_p.I24fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	24					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CCATCACCTCCCATTTGCCAGA	0.52			"""Mis N, F"""		MDS																																p.P23fs		Atlas-INDEL	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.68_69insT						.																																			SO:0001589	frameshift_variant	54790	exon3			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	Exception_encountered	chr4.hg19:g.106155167_106155168insT	ENSP00000442788:p.Ile24fs	89.0	0.0		47.0	11.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	ENST00000540549.1	hg19	CCDS47120.1																																																																																			.	.		0.520	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
CDC45	8318	hgsc.bcm.edu	37	22	19492928	19492929	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr22:19492928_19492929insC	ENST00000407835.1	+	11	1004_1005	c.748_749insC	c.(748-750)tccfs	p.S250fs	CDC45_ENST00000404724.3_Frame_Shift_Ins_p.S204fs|CDC45_ENST00000437685.2_Frame_Shift_Ins_p.S282fs|CDC45_ENST00000263201.1_Frame_Shift_Ins_p.S250fs			O75419	CDC45_HUMAN	cell division cycle 45	250					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						GCGCCACGTTTCCCGCCACAAC	0.55																																					p.S282fs		Atlas-INDEL	.											.	CDC45	48	.	0			c.844_845insC						.																																			SO:0001589	frameshift_variant	8318	exon11			.	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.751dupC	chr22.hg19:g.19492931_19492931dupC	ENSP00000385240:p.Ser250fs	125.0	0.0		130.0	10.0	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Frame_Shift_Ins	INS	ENST00000407835.1	hg19	CCDS13762.1																																																																																			.	.		0.550	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	
TRIM4	89122	hgsc.bcm.edu	37	7	99490170	99490171	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr7:99490170_99490171insT	ENST00000355947.2	-	7	1247_1248	c.1118_1119insA	c.(1117-1119)aacfs	p.N373fs	TRIM4_ENST00000349062.2_Frame_Shift_Ins_p.N347fs	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	373	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				AGGTGAAAACGTTTTTTCCCAG	0.46																																					p.N373fs		Atlas-INDEL	.											.	TRIM4	33	.	0			c.1119_1120insA						.																																			SO:0001589	frameshift_variant	89122	exon7			.	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16275	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM4"", ""tripartite motif protein 4"""		"""tripartite motif-containing 4"""			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.1119dupA	chr7.hg19:g.99490176_99490176dupT	ENSP00000348216:p.Asn373fs	139.0	0.0		139.0	18.0	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Frame_Shift_Ins	INS	ENST00000355947.2	hg19	CCDS5679.1																																																																																			.	.		0.460	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
GPR128	84873	hgsc.bcm.edu	37	3	100354665	100354810	+	Splice_Site	DEL	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	-	rs78754646|rs1520652|rs569801502|rs79409266|rs183117613|rs201699644|rs573702880|rs548009741|rs532138567|rs529836893|rs1718281|rs188782193	byFrequency	TCGA-CC-A3M9-01A-11D-A20W-10	TCGA-CC-A3M9-10A-01D-A20W-10	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a532b617-df73-4bc6-aa5f-40882defe2f0	0249fd94-5666-465e-9f4a-8c1f2bf0bbc6	g.chr3:100354665_100354810delCCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	ENST00000273352.3	+	5	860_865	c.592_597delCCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG	c.(592-597)cctgagdel	p.PE198fs	GPR128_ENST00000475887.1_5'UTR	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	198					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.?(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						AAATGCTTCACCTGAGGTAAAACTCACAGAGCtttaaaaaaaattttttttttatttttaGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTGCATAGCACTC	0.358																																					p.197_199del	Pancreas(87;185 1975 7223 18722)	Pindel	.											.	GPR128	126	.	1	Unknown(1)	kidney(1)	c.591_597del						.																																			SO:0001630	splice_region_variant	84873	exon5			.	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.597+1CCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG>-	chr3.hg19:g.100354665_100354810delCCTGAGGTAAAACTCACAGAGCTTTAAAAAAAATTTTTTTTTTATTTTTAGAGGGGGTGTTGGGAAAGAAAGAGAGATGTCCTGAATACCACTCCTTATTCCACAATATGGTTTGAGCATGGTTTAAGTTGCTTAAAGGCATTTTG		47.0	0.0		42.0	15.0	NM_032787	Q14D94|Q86SQ2	Frame_Shift_Del	DEL	ENST00000273352.3	hg19	CCDS2938.1																																																																																			.	.		0.358	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		Frame_Shift_Del
