#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
ATP13A2	23400	hgsc.bcm.edu	37	1	17331929	17331929	+	Silent	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:17331929C>A	ENST00000326735.8	-	3	261	c.228G>T	c.(226-228)cgG>cgT	p.R76R	ATP13A2_ENST00000452699.1_Silent_p.R76R|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.R76R			Q9NQ11	AT132_HUMAN	ATPase type 13A2	76					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGGGCCGGAGCCGCAGCCGCA	0.607																																					p.R76R		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G228T						.						21.0	27.0	25.0					1																	17331929		2202	4299	6501	SO:0001819	synonymous_variant	23400	exon3			CCGGAGCCGCAGC	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.228G>T	chr1.hg19:g.17331929C>A		236.0	0.0		199.0	35.0	NM_001141973	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	hg19	CCDS175.1	.	.	.	.	.	.	.	.	.	.	c	10.56	1.384756	0.25031	.	.	ENSG00000159363	ENST00000510069;ENST00000509619	.	.	.	4.36	2.14	0.27477	.	.	.	.	.	T	0.67107	0.2858	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.66040	-0.6022	4	.	.	.	-29.9618	13.4176	0.60979	0.0:0.5158:0.4842:0.0	.	.	.	.	S	52;69	.	.	A	-	1	0	ATP13A2	17204516	0.787000	0.28750	0.990000	0.47175	0.987000	0.75469	-0.035000	0.12205	0.913000	0.36797	0.486000	0.48141	GCT	.	.		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
LAPTM5	7805	hgsc.bcm.edu	37	1	31208055	31208055	+	Missense_Mutation	SNP	C	C	A	rs370275111		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:31208055C>A	ENST00000294507.3	-	7	738	c.664G>T	c.(664-666)Gtg>Ttg	p.V222L		NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	222					transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		TTCTCCTCCACCGAGTTCATG	0.537																																					p.V222L		Atlas-SNP	.											.	LAPTM5	30	.	0			c.G664T						.						318.0	276.0	290.0					1																	31208055		2203	4300	6503	SO:0001583	missense	7805	exon7			CCTCCACCGAGTT	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"""lysosomal multispanning membrane protein 5"""			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.664G>T	chr1.hg19:g.31208055C>A	ENSP00000294507:p.Val222Leu	94.0	0.0		91.0	12.0	NM_006762	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	hg19	CCDS337.1	.	.	.	.	.	.	.	.	.	.	C	5.819	0.335391	0.11013	.	.	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.45668	0.89	5.7	2.82	0.32997	.	0.565140	0.17768	N	0.162685	T	0.21387	0.0515	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.19745	-1.0296	10	0.22706	T	0.39	-6.5039	9.7721	0.40595	0.0:0.7581:0.0:0.2419	.	222	Q13571	LAPM5_HUMAN	L	222	ENSP00000294507:V222L	ENSP00000294507:V222L	V	-	1	0	LAPTM5	30980642	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	0.677000	0.25262	0.357000	0.24183	-0.797000	0.03246	GTG	.	.		0.537	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762	
LCK	3932	hgsc.bcm.edu	37	1	32741654	32741655	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:32741654_32741655CC>AA	ENST00000336890.5	+	7	759_760	c.621_622CC>AA	c.(619-624)cgCCat>cgAAat	p.H208N	LCK_ENST00000333070.4_Missense_Mutation_p.H208N|LCK_ENST00000373564.3_Missense_Mutation_p.H266N	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	208	Interaction with PTPRH.|SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.			VRHYTN -> ASAITPI (in Ref. 1; CAA28691). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	AACTGGTCCGCCATTACACCAG	0.569			T	TRB@	T-ALL																																p.R207R|p.H208N		Atlas-SNP	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	LCK	124	.	0			c.C621A|c.C622A						.																																			SO:0001583	missense	3932	exon7			GGTCCGCCATTAC|GTCCGCCATTACA	M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"""SH2 domain containing"""	6524	protein-coding gene	gene with protein product		153390	"""lymphocyte-specific protein tyrosine kinase"""			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	Exception_encountered	chr1.hg19:g.32741654_32741655delinsAA	ENSP00000337825:p.His208Asn	126.0|124.0	0.0		158.0	116.0	NM_005356	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Silent|Missense_Mutation	SNP	ENST00000336890.5	hg19	CCDS359.1																																																																																			.	.		0.569	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356	
HECTD3	79654	hgsc.bcm.edu	37	1	45469577	45469577	+	Silent	SNP	C	C	T	rs373641285		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:45469577C>T	ENST00000372172.4	-	19	2450	c.2379G>A	c.(2377-2379)acG>acA	p.T793T	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Silent_p.T403T	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	793	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GACTGCGGCCCGTGACAAAGC	0.617																																					p.T793T		Atlas-SNP	.											.	HECTD3	158	.	0			c.G2379A						.	C		0,4124		0,0,2062	41.0	49.0	46.0		2379	-11.9	0.0	1		46	1,8345		0,1,4172	no	coding-synonymous	HECTD3	NM_024602.5		0,1,6234	TT,TC,CC		0.012,0.0,0.0080		793/862	45469577	1,12469	2062	4173	6235	SO:0001819	synonymous_variant	79654	exon19			GCGGCCCGTGACA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2379G>A	chr1.hg19:g.45469577C>T		170.0	0.0		182.0	53.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	hg19	CCDS41318.1																																																																																			.	.		0.617	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
COL11A1	1301	hgsc.bcm.edu	37	1	103478004	103478004	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:103478004C>G	ENST00000370096.3	-	14	1906	c.1594G>C	c.(1594-1596)Ggc>Cgc	p.G532R	COL11A1_ENST00000512756.1_Missense_Mutation_p.G416R|COL11A1_ENST00000353414.4_Missense_Mutation_p.G493R|COL11A1_ENST00000358392.2_Missense_Mutation_p.G544R	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	532	Collagen-like 2.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCCATTGGGCCAGGTGGGCCT	0.388																																					p.G544R		Atlas-SNP	.											COL11A1_ENST00000370096,bladder,carcinoma,0,2	COL11A1	972	.	0			c.G1630C						.						40.0	42.0	41.0					1																	103478004		2203	4300	6503	SO:0001583	missense	1301	exon14			TTGGGCCAGGTGG	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1594G>C	chr1.hg19:g.103478004C>G	ENSP00000359114:p.Gly532Arg	139.0	0.0		204.0	148.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364436	0.82463	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239	D;D;D;D;D	0.99353	-5.77;-5.77;-5.77;-5.77;-3.98	5.94	5.94	0.96194	.	0.054058	0.85682	D	0.000000	D	0.99813	0.9918	H	0.99391	4.545	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96880	0.9645	10	0.87932	D	0	.	19.9503	0.97197	0.0:1.0:0.0:0.0	.	416;493;544;532	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	R	532;544;493;416;544	ENSP00000359114:G532R;ENSP00000351163:G544R;ENSP00000302551:G493R;ENSP00000426533:G416R;ENSP00000408640:G544R	ENSP00000302551:G493R	G	-	1	0	COL11A1	103250592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.192000	0.77771	2.812000	0.96745	0.557000	0.71058	GGC	.	.		0.388	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
TCHH	7062	hgsc.bcm.edu	37	1	152080252	152080253	+	Missense_Mutation	DNP	GG	GG	CT			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:152080252_152080253GG>CT	ENST00000368804.1	-	2	5439_5440	c.5440_5441CC>AG	c.(5440-5442)CCc>AGc	p.P1814S		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1814	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGCTGTTGGGGGCGCAGCTGC	0.609																																					p.P1814R|p.P1814T		Atlas-SNP	.											.	TCHH	275	.	0			c.C5441G|c.C5440A						.																																			SO:0001583	missense	7062	exon3			TGTTGGGGGCGCA|GTTGGGGGCGCAG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5440_5441delinsCT	chr1.hg19:g.152080252_152080253delinsCT	ENSP00000357794:p.Pro1814Ser	89.0|88.0	0.0		86.0|85.0	10.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.609	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TCHH	7062	hgsc.bcm.edu	37	1	152080269	152080269	+	Silent	SNP	T	T	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:152080269T>C	ENST00000368804.1	-	2	5423	c.5424A>G	c.(5422-5424)gaA>gaG	p.E1808E		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1808	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGCTGTTCTTCCCTCTCCT	0.597																																					p.E1808E		Atlas-SNP	.											TCHH,bladder,carcinoma,0,3	TCHH	275	.	0			c.A5424G						.						78.0	79.0	78.0					1																	152080269		2010	4183	6193	SO:0001819	synonymous_variant	7062	exon3			CTGTTCTTCCCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5424A>G	chr1.hg19:g.152080269T>C		96.0	0.0		80.0	8.0	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.597	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TCHH	7062	hgsc.bcm.edu	37	1	152080284	152080284	+	Silent	SNP	T	T	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:152080284T>G	ENST00000368804.1	-	2	5408	c.5409A>C	c.(5407-5409)ctA>ctC	p.L1803L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1803	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTCCTGGCGTAGCTGTTCCT	0.577																																					p.L1803L		Atlas-SNP	.											TCHH,bladder,carcinoma,0,1	TCHH	275	.	0			c.A5409C						.						80.0	80.0	80.0					1																	152080284		1984	4176	6160	SO:0001819	synonymous_variant	7062	exon3			CTGGCGTAGCTGT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.5409A>C	chr1.hg19:g.152080284T>G		93.0	0.0		79.0	6.0	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.577	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
SEC16B	89866	hgsc.bcm.edu	37	1	177934193	177934193	+	Silent	SNP	C	C	T	rs564535526	byFrequency	TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:177934193C>T	ENST00000308284.6	-	4	611	c.522G>A	c.(520-522)gaG>gaA	p.E174E	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000464631.2_Silent_p.E174E	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	174	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GGAAGTGGGTCTCACTATTTG	0.443																																					p.E174E		Atlas-SNP	.											.	SEC16B	92	.	0			c.G522A						.						111.0	107.0	109.0					1																	177934193		1938	4141	6079	SO:0001819	synonymous_variant	89866	exon4			GTGGGTCTCACTA	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.522G>A	chr1.hg19:g.177934193C>T		109.0	0.0		114.0	85.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.443	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
RYR2	6262	hgsc.bcm.edu	37	1	237850763	237850763	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:237850763G>T	ENST00000366574.2	+	63	9343	c.9026G>T	c.(9025-9027)tGc>tTc	p.C3009F	RYR2_ENST00000609119.1_Intron|RYR2_ENST00000360064.6_Missense_Mutation_p.C3007F|RYR2_ENST00000542537.1_Missense_Mutation_p.C2993F	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3009					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGCCTATTCTGCAAACTTGGA	0.368																																					p.C3009F		Atlas-SNP	.											.	RYR2	1273	.	0			c.G9026T						.						49.0	45.0	46.0					1																	237850763		1822	4083	5905	SO:0001583	missense	6262	exon63			TATTCTGCAAACT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.9026G>T	chr1.hg19:g.237850763G>T	ENSP00000355533:p.Cys3009Phe	111.0	0.0		93.0	12.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112579	0.77210	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000540213	T;D;T	0.97279	-0.2;-4.32;-0.2	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000002	D	0.98454	0.9485	M	0.82823	2.61	0.80722	D	1	D	0.71674	0.998	D	0.65987	0.94	D	0.99282	1.0896	10	0.87932	D	0	-14.3809	19.6091	0.95594	0.0:0.0:1.0:0.0	.	3009	Q92736	RYR2_HUMAN	F	3009;3007;2993;4	ENSP00000355533:C3009F;ENSP00000353174:C3007F;ENSP00000443798:C2993F	ENSP00000353174:C3007F	C	+	2	0	RYR2	235917386	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.420000	0.97426	2.650000	0.89964	0.655000	0.94253	TGC	.	.		0.368	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
SDCCAG8	10806	hgsc.bcm.edu	37	1	243437866	243437866	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:243437866A>G	ENST00000366541.3	+	4	446	c.328A>G	c.(328-330)Acc>Gcc	p.T110A	SDCCAG8_ENST00000391846.1_Missense_Mutation_p.T110A|SDCCAG8_ENST00000343783.6_Intron|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.T110A	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	110					establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		ACATGAGGAAACCAATATGCC	0.294																																					p.T110A		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.A328G						.						86.0	84.0	84.0					1																	243437866		2203	4297	6500	SO:0001583	missense	10806	exon4			GAGGAAACCAATA	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.328A>G	chr1.hg19:g.243437866A>G	ENSP00000355499:p.Thr110Ala	160.0	0.0		146.0	22.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	A	2.670	-0.277739	0.05679	.	.	ENSG00000054282	ENST00000355875;ENST00000391846;ENST00000366541	T;T	0.41065	1.01;1.01	4.94	2.07	0.26955	.	1.369320	0.04167	N	0.324135	T	0.27489	0.0675	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16364	-1.0405	10	0.14252	T	0.57	1.8244	4.641	0.12548	0.4711:0.1692:0.3597:0.0	.	110	Q86SQ7	SDCG8_HUMAN	A	110	ENSP00000348137:T110A;ENSP00000355499:T110A	ENSP00000348137:T110A	T	+	1	0	SDCCAG8	241504489	0.005000	0.15991	0.036000	0.18154	0.015000	0.08874	0.387000	0.20718	0.170000	0.19704	0.460000	0.39030	ACC	.	.		0.294	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
OR2T27	403239	hgsc.bcm.edu	37	1	248813752	248813752	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr1:248813752A>G	ENST00000344889.3	-	1	433	c.434T>C	c.(433-435)gTg>gCg	p.V145A		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGCTGCCGCCACAATCAACCA	0.552																																					p.V145A		Atlas-SNP	.											.	OR2T27	52	.	0			c.T434C						.						56.0	42.0	47.0					1																	248813752		2196	4246	6442	SO:0001583	missense	403239	exon1			GCCGCCACAATCA		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.434T>C	chr1.hg19:g.248813752A>G	ENSP00000342008:p.Val145Ala	427.0	0.0		268.0	101.0	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	hg19	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	1.572	-0.533764	0.04082	.	.	ENSG00000187701	ENST00000344889	T	0.39056	1.1	3.3	2.18	0.27775	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35838	N	0.002957	T	0.22166	0.0534	L	0.28192	0.835	0.09310	N	1	B	0.19200	0.034	B	0.18871	0.023	T	0.22661	-1.0210	10	0.05833	T	0.94	.	7.8352	0.29365	0.8862:0.0:0.1138:0.0	.	145	Q8NH04	O2T27_HUMAN	A	145	ENSP00000342008:V145A	ENSP00000342008:V145A	V	-	2	0	OR2T27	246880375	0.000000	0.05858	0.089000	0.20774	0.057000	0.15508	0.541000	0.23207	1.511000	0.48818	0.163000	0.16589	GTG	.	.		0.552	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
GCKR	2646	hgsc.bcm.edu	37	2	27741789	27741789	+	Silent	SNP	G	G	T	rs367961156		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:27741789G>T	ENST00000264717.2	+	17	1620	c.1557G>T	c.(1555-1557)gcG>gcT	p.A519A	GCKR_ENST00000424318.2_Silent_p.A329A	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	519					carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					TCTGGCGGGCGCTGGCCATGC	0.522																																					p.A519A		Atlas-SNP	.											.	GCKR	73	.	0			c.G1557T						.						76.0	81.0	79.0					2																	27741789		2203	4300	6503	SO:0001819	synonymous_variant	2646	exon17			GCGGGCGCTGGCC	Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1557G>T	chr2.hg19:g.27741789G>T		85.0	0.0		62.0	21.0	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Silent	SNP	ENST00000264717.2	hg19	CCDS1757.1																																																																																			.	.		0.522	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486	
LTBP1	4052	hgsc.bcm.edu	37	2	33585803	33585803	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:33585803G>T	ENST00000404816.2	+	27	4493	c.4140G>T	c.(4138-4140)tgG>tgT	p.W1380C	LTBP1_ENST00000418533.2_Missense_Mutation_p.W1012C|LTBP1_ENST00000272273.5_Missense_Mutation_p.W278C|LTBP1_ENST00000402934.1_Missense_Mutation_p.W999C|LTBP1_ENST00000390003.4_Missense_Mutation_p.W1055C|LTBP1_ENST00000404525.1_Missense_Mutation_p.W1001C|LTBP1_ENST00000354476.3_Missense_Mutation_p.W1381C|LTBP1_ENST00000407925.1_Missense_Mutation_p.W1054C			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1380	TB 3.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCGTGGGATGGGGAGATAACT	0.493																																					p.W1380C		Atlas-SNP	.											.	LTBP1	317	.	0			c.G4140T						.						112.0	102.0	105.0					2																	33585803		2203	4300	6503	SO:0001583	missense	4052	exon27			GGGATGGGGAGAT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.4140G>T	chr2.hg19:g.33585803G>T	ENSP00000386043:p.Trp1380Cys	134.0	0.0		136.0	43.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308822	0.60305	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669	D;D;D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.07	5.07	0.68467	Matrix fibril-associated (3);TGF-beta binding (1);	.	.	.	.	D	0.99223	0.9730	M	0.92555	3.32	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;1.0;0.999;1.0;0.999;0.999;1.0	D	0.99198	1.0872	9	0.87932	D	0	.	18.8234	0.92106	0.0:0.0:1.0:0.0	.	278;1380;1012;1001;1054;1055;1381	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.;LTBP1_HUMAN;.;.;.;.;.	C	1380;1381;1055;1012;999;1001;1054;278;216	ENSP00000386043:W1380C;ENSP00000346467:W1381C;ENSP00000374653:W1055C;ENSP00000393057:W1012C;ENSP00000384373:W999C;ENSP00000385359:W1001C;ENSP00000384091:W1054C;ENSP00000272273:W278C;ENSP00000395211:W216C	ENSP00000272273:W278C	W	+	3	0	LTBP1	33439307	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	9.743000	0.98849	2.497000	0.84241	0.563000	0.77884	TGG	.	.		0.493	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
SOS1	6654	hgsc.bcm.edu	37	2	39222434	39222434	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:39222434T>C	ENST00000426016.1	-	21	3262	c.3176A>G	c.(3175-3177)gAg>gGg	p.E1059G	SOS1_ENST00000402219.2_Missense_Mutation_p.E1059G|SOS1-IT1_ENST00000594472.1_RNA|SOS1_ENST00000395038.2_Missense_Mutation_p.E1059G			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	1059					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TTTCCTTGGCTCCTGCTGCAG	0.463									Noonan syndrome																												p.E1059G		Atlas-SNP	.											.	SOS1	134	.	0			c.A3176G						.						137.0	130.0	132.0					2																	39222434		2203	4300	6503	SO:0001583	missense	6654	exon20	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CTTGGCTCCTGCT	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.3176A>G	chr2.hg19:g.39222434T>C	ENSP00000387784:p.Glu1059Gly	144.0	0.0		138.0	70.0	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.021765	0.93462	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.78816	-1.07;-1.07;-1.21	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.85969	0.5821	M	0.62723	1.935	0.80722	D	1	D	0.64830	0.994	D	0.64687	0.928	D	0.86854	0.2025	10	0.66056	D	0.02	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	1059	Q07889	SOS1_HUMAN	G	1059;1059;791;1059;1059	ENSP00000387784:E1059G;ENSP00000384675:E1059G;ENSP00000378479:E1059G	ENSP00000263879:E1059G	E	-	2	0	SOS1	39075938	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.331000	0.79192	2.333000	0.79357	0.533000	0.62120	GAG	.	.		0.463	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
NRXN1	9378	hgsc.bcm.edu	37	2	50463974	50463974	+	Silent	SNP	G	G	T	rs199546979		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:50463974G>T	ENST00000406316.2	-	18	4975	c.3499C>A	c.(3499-3501)Cga>Aga	p.R1167R	NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Silent_p.R1159R|NRXN1_ENST00000342183.5_Silent_p.R132R|NRXN1_ENST00000404971.1_Silent_p.R1207R|NRXN1_ENST00000406859.3_Silent_p.R1167R|NRXN1_ENST00000402717.3_Silent_p.R1159R|NRXN1_ENST00000401669.2_Silent_p.R1167R|NRXN1_ENST00000401710.1_Silent_p.R185R	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1167	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.R1207*(1)|p.R1208*(1)|p.R132*(1)|p.R1167*(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTGTCCACTCGCACCAATACG	0.423																																					p.R1207R		Atlas-SNP	.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	.	4	Substitution - Nonsense(4)	endometrium(4)	c.C3619A						.						120.0	107.0	111.0					2																	50463974		2203	4300	6503	SO:0001819	synonymous_variant	9378	exon19			CCACTCGCACCAA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3499C>A	chr2.hg19:g.50463974G>T		147.0	0.0		153.0	66.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.		0.423	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
EFEMP1	2202	hgsc.bcm.edu	37	2	56144961	56144961	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:56144961A>G	ENST00000394555.2	-	4	791	c.356T>C	c.(355-357)gTg>gCg	p.V119A	EFEMP1_ENST00000424836.2_Missense_Mutation_p.V61A|EFEMP1_ENST00000355426.3_Missense_Mutation_p.V119A|EFEMP1_ENST00000394554.1_Missense_Mutation_p.V119A	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	119					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGCACTGGCCACAAAACCACC	0.597																																					p.V119A	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.T356C						.						56.0	55.0	55.0					2																	56144961		2203	4300	6503	SO:0001583	missense	2202	exon4			CTGGCCACAAAAC	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.356T>C	chr2.hg19:g.56144961A>G	ENSP00000378058:p.Val119Ala	75.0	0.0		76.0	35.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912922	0.52439	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000424836;ENST00000355426;ENST00000438672;ENST00000439193	D;D;T;D;T;T	0.83591	-1.74;-1.74;-1.26;-1.74;-1.21;-1.32	4.58	4.58	0.56647	.	0.490245	0.17300	N	0.179299	T	0.64583	0.2611	N	0.08118	0	0.18873	N	0.999982	B;B	0.22541	0.005;0.071	B;B	0.18263	0.015;0.021	T	0.44143	-0.9347	10	0.08837	T	0.75	.	12.5594	0.56273	1.0:0.0:0.0:0.0	.	61;119	B4DW75;Q12805	.;FBLN3_HUMAN	A	119;119;61;119;119;119	ENSP00000378058:V119A;ENSP00000378057:V119A;ENSP00000399145:V61A;ENSP00000347596:V119A;ENSP00000392055:V119A;ENSP00000408195:V119A	ENSP00000347596:V119A	V	-	2	0	EFEMP1	55998465	0.429000	0.25530	0.929000	0.37066	0.995000	0.86356	2.748000	0.47483	2.285000	0.76669	0.528000	0.53228	GTG	.	.		0.597	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
ASTL	431705	hgsc.bcm.edu	37	2	96798324	96798324	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:96798324C>A	ENST00000342380.2	-	6	591	c.592G>T	c.(592-594)Gac>Tac	p.D198Y		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						CGGTCCCGGTCGGCCCGCGTG	0.657																																					p.D198Y		Atlas-SNP	.											.	ASTL	59	.	0			c.G592T						.						67.0	64.0	65.0					2																	96798324		2203	4300	6503	SO:0001583	missense	431705	exon6			CCCGGTCGGCCCG	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.592G>T	chr2.hg19:g.96798324C>A	ENSP00000343674:p.Asp198Tyr	267.0	0.0		211.0	101.0	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	hg19	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598821	0.66332	.	.	ENSG00000188886	ENST00000342380	T	0.76186	-1.0	4.41	4.41	0.53225	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (2);Metallopeptidase, catalytic domain (1);	0.000000	0.48286	D	0.000185	D	0.92113	0.7500	H	0.99555	4.625	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.95296	0.8399	10	0.87932	D	0	-18.085	14.5671	0.68185	0.0:1.0:0.0:0.0	.	198	Q6HA08	ASTL_HUMAN	Y	198	ENSP00000343674:D198Y	ENSP00000343674:D198Y	D	-	1	0	ASTL	96162051	1.000000	0.71417	0.870000	0.34147	0.434000	0.31775	7.050000	0.76620	2.008000	0.58898	0.551000	0.68910	GAC	.	.		0.657	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1		
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105886085	105886085	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:105886085G>A	ENST00000393359.2	-	11	2476	c.2050C>T	c.(2050-2052)Cat>Tat	p.H684Y	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.H684Y			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	684					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						ACCAGGATATGCAGCGCCTTC	0.642																																					p.H684Y	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C2050T						.						27.0	27.0	27.0					2																	105886085		2203	4300	6503	SO:0001583	missense	9392	exon11			GGATATGCAGCGC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2050C>T	chr2.hg19:g.105886085G>A	ENSP00000377027:p.His684Tyr	98.0	0.0		84.0	31.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.892431	0.52121	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.19394	2.15;2.15	5.54	4.64	0.57946	.	0.388763	0.31031	N	0.008390	T	0.34542	0.0901	M	0.74881	2.28	0.44843	D	0.997859	D;B	0.58620	0.983;0.178	P;B	0.51229	0.663;0.393	T	0.19321	-1.0309	10	0.66056	D	0.02	-8.0679	11.254	0.49043	0.0:0.138:0.7185:0.1435	.	139;684	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	Y	684;684;139	ENSP00000377027:H684Y;ENSP00000258449:H684Y	ENSP00000258449:H684Y	H	-	1	0	TGFBRAP1	105252517	1.000000	0.71417	0.948000	0.38648	0.616000	0.37450	3.594000	0.54008	1.308000	0.44962	0.462000	0.41574	CAT	.	.		0.642	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
POTEF	728378	hgsc.bcm.edu	37	2	130832599	130832599	+	Missense_Mutation	SNP	G	G	A	rs532998196		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:130832599G>A	ENST00000409914.2	-	17	2845	c.2446C>T	c.(2446-2448)Cgc>Tgc	p.R816C	POTEF_ENST00000357462.5_Missense_Mutation_p.R816C	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	816	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						ATCTTCTCGCGGTTGGCCTTA	0.597													.|||	1	0.000199681	0.0	0.0	5008	,	,		20953	0.001		0.0	False		,,,				2504	0.0				p.R816C		Atlas-SNP	.											POTEF,trunk,malignant_melanoma,+1,1	POTEF	140	.	0			c.C2446T						.						120.0	131.0	127.0					2																	130832599		2203	4300	6503	SO:0001583	missense	728378	exon17			TCTCGCGGTTGGC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2446C>T	chr2.hg19:g.130832599G>A	ENSP00000386786:p.Arg816Cys	526.0	2.0		446.0	225.0	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	hg19	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	13.07	2.126044	0.37533	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97114	-4.25;-4.25	.	.	.	Actin/actin-like conserved site (1);	.	.	.	.	D	0.98988	0.9655	H	0.99958	5.055	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95089	0.8220	8	0.87932	D	0	.	2.8768	0.05634	3.0E-4:2.0E-4:0.5045:0.4949	.	816	A5A3E0	POTEF_HUMAN	C	816	ENSP00000350052:R816C;ENSP00000386786:R816C	ENSP00000350052:R816C	R	-	1	0	POTEF	130549069	1.000000	0.71417	0.235000	0.24058	0.237000	0.25408	2.711000	0.47177	0.119000	0.18210	0.121000	0.15741	CGC	.	.		0.597	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
LCT	3938	hgsc.bcm.edu	37	2	136579639	136579639	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:136579639C>T	ENST00000264162.2	-	5	947	c.937G>A	c.(937-939)Ggg>Agg	p.G313R	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	313	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	ATATCAAACCCAATGGTGAGC	0.333																																					p.G313R		Atlas-SNP	.											.	LCT	309	.	0			c.G937A						.						130.0	134.0	132.0					2																	136579639		2203	4300	6503	SO:0001583	missense	3938	exon5			CAAACCCAATGGT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.937G>A	chr2.hg19:g.136579639C>T	ENSP00000264162:p.Gly313Arg	77.0	0.0		76.0	16.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.630371	0.87660	.	.	ENSG00000115850	ENST00000264162	T	0.35236	1.32	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.59514	0.2199	M	0.63843	1.955	0.54753	D	0.99998	D	0.89917	1.0	D	0.83275	0.996	T	0.60188	-0.7312	10	0.87932	D	0	-32.4761	17.9984	0.89191	0.0:1.0:0.0:0.0	.	313	P09848	LPH_HUMAN	R	313	ENSP00000264162:G313R	ENSP00000264162:G313R	G	-	1	0	LCT	136296109	1.000000	0.71417	0.916000	0.36221	0.996000	0.88848	4.791000	0.62460	2.832000	0.97577	0.655000	0.94253	GGG	.	.		0.333	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
TTN	7273	hgsc.bcm.edu	37	2	179463972	179463972	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:179463972G>A	ENST00000591111.1	-	240	51849	c.51625C>T	c.(51625-51627)Cta>Tta	p.L17209L	TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.L9785L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.L9977L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Silent_p.L18850L|TTN_ENST00000342992.6_Silent_p.L16282L|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Silent_p.L9910L			Q8WZ42	TITIN_HUMAN	titin	17209	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGCCTTCTAGCAATTTGGGA	0.423																																					p.L18850L		Atlas-SNP	.											.	TTN	18412	.	0			c.C56548T						.						195.0	185.0	188.0					2																	179463972		1899	4114	6013	SO:0001819	synonymous_variant	7273	exon290			CTTCTAGCAATTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51625C>T	chr2.hg19:g.179463972G>A		123.0	0.0		112.0	51.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179665290	179665290	+	Silent	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:179665290G>T	ENST00000591111.1	-	4	639	c.415C>A	c.(415-417)Cgg>Agg	p.R139R	TTN_ENST00000360870.5_Silent_p.R139R|TTN_ENST00000460472.2_Silent_p.R139R|TTN_ENST00000342175.6_Silent_p.R139R|TTN_ENST00000589042.1_Silent_p.R139R|TTN_ENST00000342992.6_Silent_p.R139R|TTN_ENST00000359218.5_Silent_p.R139R			Q8WZ42	TITIN_HUMAN	titin	32757	Ig-like 2.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTCCATCCCGGTAGAACTTC	0.507																																					p.R139R		Atlas-SNP	.											TTN_ENST00000360870,NS,lymphoid_neoplasm,0,18	TTN	18412	.	0			c.C415A						.						141.0	125.0	130.0					2																	179665290		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon4			CATCCCGGTAGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.415C>A	chr2.hg19:g.179665290G>T		108.0	0.0		132.0	51.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.507	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MYO1B	4430	hgsc.bcm.edu	37	2	192273885	192273885	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:192273885G>C	ENST00000392318.3	+	26	2994	c.2747G>C	c.(2746-2748)aGg>aCg	p.R916T	MYO1B_ENST00000304164.4_Missense_Mutation_p.R916T|MYO1B_ENST00000339514.4_Missense_Mutation_p.R858T|MYO1B_ENST00000439065.2_Missense_Mutation_p.R161T|MYO1B_ENST00000392316.1_Missense_Mutation_p.R887T	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	916					actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GAGCTAAAAAGGATTTTCCAC	0.323																																					p.R916T		Atlas-SNP	.											.	MYO1B	160	.	0			c.G2747C						.						82.0	87.0	86.0					2																	192273885		2203	4300	6503	SO:0001583	missense	4430	exon26			TAAAAAGGATTTT	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2747G>C	chr2.hg19:g.192273885G>C	ENSP00000376132:p.Arg916Thr	85.0	0.0		100.0	49.0	NM_001161819	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	hg19	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137546	0.37728	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316;ENST00000439065	D;D;D;D;T	0.87334	-2.23;-2.24;-2.24;-2.24;0.26	5.79	5.79	0.91817	.	0.236043	0.50627	D	0.000106	T	0.81612	0.4859	L	0.37630	1.12	0.54753	D	0.999982	P;B;B	0.38922	0.651;0.136;0.12	B;B;B	0.32677	0.15;0.071;0.076	T	0.81433	-0.0935	10	0.39692	T	0.17	.	18.201	0.89838	0.0:0.0:1.0:0.0	.	161;916;858	E7EPB4;O43795;O43795-2	.;MYO1B_HUMAN;.	T	858;916;916;887;161	ENSP00000341903:R858T;ENSP00000376132:R916T;ENSP00000306382:R916T;ENSP00000376130:R887T;ENSP00000391442:R161T	ENSP00000306382:R916T	R	+	2	0	MYO1B	191982130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.511000	0.67024	2.740000	0.93945	0.561000	0.74099	AGG	.	.		0.323	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
CTLA4	1493	hgsc.bcm.edu	37	2	204732726	204732726	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:204732726C>A	ENST00000302823.3	+	1	218	c.61C>A	c.(61-63)Ccc>Acc	p.P21T	CTLA4_ENST00000427473.2_5'Flank|CTLA4_ENST00000487393.1_3'UTR|CTLA4_ENST00000472206.1_Missense_Mutation_p.P21T|CTLA4_ENST00000295854.6_Missense_Mutation_p.P21T	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	21					B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	CAGGACCTGGCCCTGCACTCT	0.522																																					p.P21T		Atlas-SNP	.											.	CTLA4	24	.	0			c.C61A						.						157.0	136.0	143.0					2																	204732726		2203	4300	6503	SO:0001583	missense	1493	exon1			ACCTGGCCCTGCA		CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	2505	protein-coding gene	gene with protein product		123890	"""celiac disease 3"", ""insulin-dependent diabetes mellitus 12"""	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.61C>A	chr2.hg19:g.204732726C>A	ENSP00000303939:p.Pro21Thr	113.0	0.0		91.0	38.0	NM_005214	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Missense_Mutation	SNP	ENST00000302823.3	hg19	CCDS2362.1	.	.	.	.	.	.	.	.	.	.	C	7.253	0.603599	0.14002	.	.	ENSG00000163599	ENST00000302823;ENST00000541886;ENST00000295854;ENST00000472206	T;T;T	0.38560	1.13;1.13;1.13	6.02	-0.369	0.12534	.	0.517115	0.19439	N	0.114222	T	0.41627	0.1167	L	0.50333	1.59	0.80722	D	1	P;D;B	0.53312	0.775;0.959;0.44	B;P;B	0.50192	0.344;0.634;0.146	T	0.31806	-0.9930	10	0.56958	D	0.05	-4.4291	9.1707	0.37078	0.0:0.4989:0.0:0.5011	.	21;21;21	P16410-4;Q8TDA6;P16410	.;.;CTLA4_HUMAN	T	21	ENSP00000303939:P21T;ENSP00000295854:P21T;ENSP00000417779:P21T	ENSP00000295854:P21T	P	+	1	0	CTLA4	204440971	0.614000	0.27017	0.157000	0.22605	0.005000	0.04900	-0.103000	0.10940	-0.126000	0.11682	-0.345000	0.07892	CCC	.	.		0.522	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214	
PARD3B	117583	hgsc.bcm.edu	37	2	205829899	205829899	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:205829899G>A	ENST00000406610.2	+	3	454	c.247G>A	c.(247-249)Gaa>Aaa	p.E83K	PARD3B_ENST00000349953.3_Missense_Mutation_p.E83K|PARD3B_ENST00000351153.1_Missense_Mutation_p.E83K|PARD3B_ENST00000358768.2_Missense_Mutation_p.E83K|PARD3B_ENST00000462231.1_Missense_Mutation_p.E83K	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	83					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TGAAGAACAAGAACCACTCCA	0.473																																					p.E83K		Atlas-SNP	.											.	PARD3B	314	.	0			c.G247A						.						115.0	110.0	111.0					2																	205829899		1907	4118	6025	SO:0001583	missense	117583	exon3			GAACAAGAACCAC	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.247G>A	chr2.hg19:g.205829899G>A	ENSP00000385848:p.Glu83Lys	67.0	0.0		72.0	16.0	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Missense_Mutation	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.344670	0.95807	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.66479	0.2793	M	0.64997	1.995	0.45502	D	0.998462	D;D;P;D;D	0.65815	0.995;0.977;0.931;0.99;0.995	D;P;P;P;D	0.63877	0.917;0.856;0.647;0.816;0.919	T	0.66586	-0.5886	10	0.56958	D	0.05	.	19.6505	0.95798	0.0:0.0:1.0:0.0	.	83;83;83;83;83	Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5	.;PAR3L_HUMAN;.;.;.	K	83	ENSP00000385848:E83K;ENSP00000351618:E83K;ENSP00000317261:E83K;ENSP00000340280:E83K	ENSP00000340280:E83K	E	+	1	0	PARD3B	205538144	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.957000	0.63652	2.635000	0.89317	0.563000	0.77884	GAA	.	.		0.473	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209141531	209141531	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:209141531G>C	ENST00000264380.4	+	4	576	c.418G>C	c.(418-420)Gaa>Caa	p.E140Q	PIKFYVE_ENST00000392202.3_Intron|PIKFYVE_ENST00000308862.6_Intron|PIKFYVE_ENST00000407449.1_Missense_Mutation_p.E140Q	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	140					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ACGCCTCAAGGAAATCATGGA	0.453																																					p.E140Q		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.G418C						.						62.0	62.0	62.0					2																	209141531		2203	4300	6503	SO:0001583	missense	200576	exon4			CTCAAGGAAATCA	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.418G>C	chr2.hg19:g.209141531G>C	ENSP00000264380:p.Glu140Gln	109.0	0.0		125.0	65.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	hg19	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	G	31	5.088991	0.94100	.	.	ENSG00000115020	ENST00000264380;ENST00000407449;ENST00000422495;ENST00000452564	T;T;T;T	0.66099	1.55;-0.19;-0.15;1.7	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	N	0.19112	0.55	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.993	D;D;D	0.80764	0.986;0.994;0.968	T	0.63681	-0.6582	10	0.23891	T	0.37	-25.0021	20.1047	0.97888	0.0:0.0:1.0:0.0	.	140;140;140	Q9Y2I7;E9PDH4;Q08AR7	FYV1_HUMAN;.;.	Q	140;140;152;140	ENSP00000264380:E140Q;ENSP00000384356:E140Q;ENSP00000414477:E152Q;ENSP00000405736:E140Q	ENSP00000264380:E140Q	E	+	1	0	PIKFYVE	208849776	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.553000	0.98118	2.762000	0.94881	0.655000	0.94253	GAA	.	.		0.453	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
PECR	55825	hgsc.bcm.edu	37	2	216946462	216946462	+	Start_Codon_SNP	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:216946462C>A	ENST00000265322.7	-	1	77	c.3G>T	c.(1-3)atG>atT	p.M1I	TMEM169_ENST00000406027.2_5'Flank|TMEM169_ENST00000437356.2_5'Flank|TMEM169_ENST00000454545.1_5'Flank|PECR_ENST00000497889.1_5'UTR|TMEM169_ENST00000295658.4_5'Flank	NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	1					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CCCAGGAGGCCATCCCTGCAG	0.697																																					p.M1I		Atlas-SNP	.											.	PECR	22	.	0			c.G3T						.						24.0	25.0	25.0					2																	216946462		2203	4299	6502	SO:0001582	initiator_codon_variant	55825	exon1			GGAGGCCATCCCT	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18281	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 29C, member 1"""	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.3G>T	chr2.hg19:g.216946462C>A	ENSP00000265322:p.Met1Ile	111.0	0.0		81.0	45.0	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Missense_Mutation	SNP	ENST00000265322.7	hg19	CCDS33375.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789310	0.70337	.	.	ENSG00000115425	ENST00000265322	D	0.82433	-1.61	3.48	3.48	0.39840	.	0.373325	0.30630	N	0.009219	D	0.89118	0.6624	.	.	.	0.80722	D	1	D;D	0.57899	0.981;0.981	D;D	0.67900	0.932;0.954	D	0.89808	0.3980	9	0.87932	D	0	.	10.7737	0.46338	0.0:1.0:0.0:0.0	.	1;1	B4DJS2;Q9BY49	.;PECR_HUMAN	I	1	ENSP00000265322:M1I	ENSP00000265322:M1I	M	-	3	0	PECR	216654707	0.019000	0.18553	0.047000	0.18901	0.005000	0.04900	2.050000	0.41297	2.248000	0.74166	0.563000	0.77884	ATG	.	.		0.697	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441	Missense_Mutation
SLC4A3	6508	hgsc.bcm.edu	37	2	220500114	220500114	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:220500114G>T	ENST00000358055.3	+	13	2380	c.1868G>T	c.(1867-1869)cGc>cTc	p.R623L	SLC4A3_ENST00000273063.6_Missense_Mutation_p.R650L|SLC4A3_ENST00000373762.3_Missense_Mutation_p.R650L|SLC4A3_ENST00000373760.2_Missense_Mutation_p.R623L|SLC4A3_ENST00000317151.3_Missense_Mutation_p.R623L			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	623					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GACCTGCTGCGCTCCGTGGCT	0.632																																					p.R650L		Atlas-SNP	.											.	SLC4A3	144	.	0			c.G1949T						.						73.0	67.0	69.0					2																	220500114		2203	4300	6503	SO:0001583	missense	6508	exon13			TGCTGCGCTCCGT		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1868G>T	chr2.hg19:g.220500114G>T	ENSP00000350756:p.Arg623Leu	345.0	0.0		239.0	114.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629752	0.46944	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29	4.91	4.91	0.64330	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.128381	0.48286	D	0.000199	T	0.72236	0.3435	L	0.45137	1.4	0.53688	D	0.999978	B;B;B	0.20261	0.002;0.009;0.043	B;B;B	0.21708	0.006;0.004;0.036	T	0.67534	-0.5646	10	0.33141	T	0.24	.	9.5122	0.39085	0.1323:0.0:0.8677:0.0	.	327;623;650	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	L	623;623;650;650;623	ENSP00000350756:R623L;ENSP00000362865:R623L;ENSP00000273063:R650L;ENSP00000362867:R650L;ENSP00000314006:R623L	ENSP00000273063:R650L	R	+	2	0	SLC4A3	220208358	0.949000	0.32298	1.000000	0.80357	0.986000	0.74619	2.191000	0.42640	2.260000	0.74910	0.637000	0.83480	CGC	.	.		0.632	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
PRSS50	29122	hgsc.bcm.edu	37	3	46784019	46784019	+	Intron	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:46784019C>T	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Missense_Mutation_p.G170R			Q9UI38	TSP50_HUMAN	protease, serine, 50						proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						GACAACACCCCAGCCAGAATC	0.537																																					p.G170R	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.G508A						.						130.0	150.0	143.0					3																	46784019		1969	4162	6131	SO:0001627	intron_variant	377047	exon4			ACACCCCAGCCAG	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	17910	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.541+6095G>A	chr3.hg19:g.46784019C>T		159.0	0.0		137.0	59.0	NM_199183		Missense_Mutation	SNP	ENST00000460241.1	hg19	CCDS2745.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872096	0.91587	.	.	ENSG00000188086	ENST00000331814;ENST00000442359	D	0.99545	-6.13	5.65	5.65	0.86999	.	0.000000	0.56097	D	0.000021	D	0.99585	0.9850	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98018	1.0369	9	0.87932	D	0	.	15.093	0.72211	0.0:1.0:0.0:0.0	.	170	Q7RTY3-2	.	R	202;170	ENSP00000401932:G170R	ENSP00000330940:G202R	G	-	1	0	PRSS45	46759023	1.000000	0.71417	0.986000	0.45419	0.966000	0.64601	6.208000	0.72165	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.537	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
ERC2	26059	hgsc.bcm.edu	37	3	55717878	55717878	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:55717878C>G	ENST00000288221.6	-	17	3112	c.2857G>C	c.(2857-2859)Gag>Cag	p.E953Q		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	953						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CATATGCCCTCCTCGTCATCC	0.483																																					p.E951Q		Atlas-SNP	.											.	ERC2	221	.	0			c.G2851C						.						48.0	53.0	51.0					3																	55717878		1864	4109	5973	SO:0001583	missense	26059	exon16			TGCCCTCCTCGTC	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2857G>C	chr3.hg19:g.55717878C>G	ENSP00000288221:p.Glu953Gln	153.0	0.0		87.0	27.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070877	0.76301	.	.	ENSG00000187672	ENST00000288221	T	0.35605	1.3	5.22	5.22	0.72569	.	0.123643	0.53938	D	0.000053	T	0.32556	0.0833	N	0.19112	0.55	0.38483	D	0.947761	P	0.39094	0.659	B	0.42959	0.403	T	0.33445	-0.9868	10	0.72032	D	0.01	-0.1583	17.3208	0.87235	0.0:1.0:0.0:0.0	.	953	O15083	ERC2_HUMAN	Q	953	ENSP00000288221:E953Q	ENSP00000288221:E953Q	E	-	1	0	ERC2	55692918	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.287000	0.65645	2.611000	0.88343	0.561000	0.74099	GAG	.	.		0.483	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
LMOD3	56203	hgsc.bcm.edu	37	3	69167886	69167886	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:69167886G>T	ENST00000420581.2	-	2	1799	c.1620C>A	c.(1618-1620)aaC>aaA	p.N540K	LMOD3_ENST00000489031.1_Missense_Mutation_p.N540K|LMOD3_ENST00000475434.1_Missense_Mutation_p.N540K	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	540	WH2.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		GACGAATGTCGTTTAGCAGCT	0.473																																					p.N540K		Atlas-SNP	.											.	LMOD3	92	.	0			c.C1620A						.						98.0	98.0	98.0					3																	69167886		1974	4175	6149	SO:0001583	missense	56203	exon2			AATGTCGTTTAGC	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.1620C>A	chr3.hg19:g.69167886G>T	ENSP00000414670:p.Asn540Lys	197.0	0.0		137.0	46.0	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	hg19	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318800	0.41096	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.12147	2.71;2.71;2.71	5.84	-5.3	0.02738	.	0.198063	0.56097	D	0.000039	T	0.09862	0.0242	L	0.53249	1.67	0.44485	D	0.997428	P	0.44690	0.841	B	0.37780	0.258	T	0.12863	-1.0531	10	0.25751	T	0.34	-36.7382	11.8227	0.52247	0.7624:0.0:0.1554:0.0822	.	540	Q0VAK6	LMOD3_HUMAN	K	540	ENSP00000414670:N540K;ENSP00000417210:N540K;ENSP00000418645:N540K	ENSP00000414670:N540K	N	-	3	2	LMOD3	69250576	0.176000	0.23096	0.948000	0.38648	0.934000	0.57294	-0.239000	0.08965	-0.929000	0.03757	-0.216000	0.12614	AAC	.	.		0.473	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	
ACAD11	84129	hgsc.bcm.edu	37	3	132378583	132378583	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:132378583C>A	ENST00000264990.6	-	1	984	c.13G>T	c.(13-15)Gct>Tct	p.A5S	ACAD11_ENST00000355458.3_Missense_Mutation_p.A5S|UBA5_ENST00000493720.2_5'Flank|UBA5_ENST00000494238.2_5'Flank|UBA5_ENST00000473651.1_5'Flank|ACAD11_ENST00000489991.1_5'UTR|UBA5_ENST00000356232.4_5'UTR|UBA5_ENST00000264991.4_Intron|ACAD11_ENST00000481970.2_Missense_Mutation_p.A5S|ACAD11_ENST00000545291.1_5'UTR	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	5					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.A5S(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						TCGCCAGTAGCACCTGGCTTC	0.607											OREG0015804	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A5S		Atlas-SNP	.											ACAD11,NS,carcinoma,0,1	ACAD11	78	.	1	Substitution - Missense(1)	ovary(1)	c.G13T						.						67.0	69.0	69.0					3																	132378583		2203	4300	6503	SO:0001583	missense	84129	exon1			CAGTAGCACCTGG	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"""acyl-Coenzyme A dehydrogenase family, member 11"""				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.13G>T	chr3.hg19:g.132378583C>A	ENSP00000264990:p.Ala5Ser	125.0	0.0	1594	72.0	34.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	hg19	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.503451	0.44558	.	.	ENSG00000240303	ENST00000355458;ENST00000264990;ENST00000481970	D;D;T	0.96619	-4.03;-4.07;1.91	5.86	2.12	0.27331	.	.	.	.	.	D	0.93324	0.7872	L	0.60455	1.87	0.09310	N	0.999994	B;B	0.28713	0.22;0.043	B;B	0.25140	0.058;0.027	D	0.84386	0.0552	8	.	.	.	.	7.8768	0.29599	0.0:0.6718:0.0:0.3282	.	5;5	D6RDI8;Q709F0	.;ACD11_HUMAN	S	5	ENSP00000347636:A5S;ENSP00000264990:A5S;ENSP00000420907:A5S	.	A	-	1	0	ACAD11	133861273	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.390000	0.20768	0.112000	0.17975	-0.157000	0.13467	GCT	.	.		0.607	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169	
GPR149	344758	hgsc.bcm.edu	37	3	154146874	154146874	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:154146874G>A	ENST00000389740.2	-	1	630	c.531C>T	c.(529-531)cgC>cgT	p.R177R		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	177					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CCCAGGGCGTGCGCACGAAGG	0.667																																					p.R177R		Atlas-SNP	.											.	GPR149	134	.	0			c.C531T						.						24.0	30.0	28.0					3																	154146874		2053	4183	6236	SO:0001819	synonymous_variant	344758	exon1			GGGCGTGCGCACG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.531C>T	chr3.hg19:g.154146874G>A		54.0	0.0		33.0	19.0	NM_001038705		Silent	SNP	ENST00000389740.2	hg19	CCDS43162.1																																																																																			.	.		0.667	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
LRCH3	84859	hgsc.bcm.edu	37	3	197562626	197562626	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr3:197562626G>A	ENST00000425562.2	+	9	1184	c.1184G>A	c.(1183-1185)gGa>gAa	p.G395E	LRCH3_ENST00000414675.2_Intron|LRCH3_ENST00000441090.2_Intron|LRCH3_ENST00000438796.2_Missense_Mutation_p.G395E|LRCH3_ENST00000536618.1_5'UTR|LRCH3_ENST00000334859.4_Missense_Mutation_p.G395E			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	395						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		CAGCCCAAGGGACCAGACCCA	0.488																																					p.G395E		Atlas-SNP	.											.	LRCH3	96	.	0			c.G1184A						.						173.0	155.0	161.0					3																	197562626		2203	4300	6503	SO:0001583	missense	84859	exon9			CCAAGGGACCAGA	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1184G>A	chr3.hg19:g.197562626G>A	ENSP00000393579:p.Gly395Glu	119.0	0.0		88.0	33.0	NM_032773	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.60	2.286497	0.40494	.	.	ENSG00000186001	ENST00000438796;ENST00000334859;ENST00000425562	T;T;T	0.19669	2.13;2.38;2.15	5.27	1.05	0.20165	.	0.443402	0.23504	N	0.047478	T	0.12732	0.0309	L	0.29908	0.895	0.58432	D	0.999995	B;P	0.36282	0.196;0.546	B;B	0.33690	0.158;0.168	T	0.13845	-1.0494	10	0.21540	T	0.41	0.1108	10.4819	0.44698	0.0:0.2413:0.5089:0.2498	.	395;395	Q96II8-2;Q96II8-3	.;.	E	395	ENSP00000399751:G395E;ENSP00000334375:G395E;ENSP00000393579:G395E	ENSP00000334375:G395E	G	+	2	0	LRCH3	199047023	1.000000	0.71417	0.055000	0.19348	0.791000	0.44710	1.512000	0.35812	-0.018000	0.14079	0.644000	0.83932	GGA	.	.		0.488	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
TLR1	7096	hgsc.bcm.edu	37	4	38798659	38798659	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:38798659G>A	ENST00000502213.2	-	3	2023	c.1794C>T	c.(1792-1794)acC>acT	p.T598T	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Silent_p.T598T			Q15399	TLR1_HUMAN	toll-like receptor 1	598					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TGCAGAGGGAGGTCACAGTCA	0.537																																					p.T598T	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.C1794T						.						69.0	89.0	82.0					4																	38798659		2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GAGGGAGGTCACA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1794C>T	chr4.hg19:g.38798659G>A		205.0	1.0		128.0	75.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.537	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
MGARP	84709	hgsc.bcm.edu	37	4	140187811	140187811	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:140187811C>A	ENST00000398955.1	-	4	844	c.665G>T	c.(664-666)gGa>gTa	p.G222V		NM_032623.3	NP_116012.2	Q8TDB4	HUMMR_HUMAN	mitochondria-localized glutamic acid-rich protein	222					anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to hypoxia (GO:0071456)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of mitochondrion organization (GO:0010822)|protein targeting to mitochondrion (GO:0006626)|retrograde axon cargo transport (GO:0008090)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)											TAAATCATCTCCAGCAGAGGA	0.453																																					p.G222V		Atlas-SNP	.											.	.	.	.	0			c.G665T						.						72.0	67.0	69.0					4																	140187811		1920	4137	6057	SO:0001583	missense	84709	exon4			TCATCTCCAGCAG	AF484960	CCDS43269.1	4q31.1	2014-02-19	2014-02-19	2012-04-17	ENSG00000137463	ENSG00000137463			29969	protein-coding gene	gene with protein product	"""ovary-specific acidic protein"", ""corneal endothelium-specific protein 1"", ""hypoxia up-regulated mitochondrial movement regulator"""		"""chromosome 4 open reading frame 49"""	C4orf49			Standard	NM_032623		Approved	OSAP, CESP-1, HUMMR	uc003ihr.1	Q8TDB4	OTTHUMG00000161325	ENST00000398955.1:c.665G>T	chr4.hg19:g.140187811C>A	ENSP00000381928:p.Gly222Val	25.0	0.0		26.0	18.0	NM_032623	Q9BZC3	Missense_Mutation	SNP	ENST00000398955.1	hg19	CCDS43269.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.757452	0.49468	.	.	ENSG00000137463	ENST00000398955	T	0.49139	0.79	5.59	-0.419	0.12340	.	0.596958	0.16975	N	0.191951	T	0.47002	0.1422	L	0.29908	0.895	0.20638	N	0.99987	D	0.61080	0.989	P	0.59487	0.858	T	0.41052	-0.9530	10	0.66056	D	0.02	-24.2898	9.1165	0.36762	0.0:0.4509:0.0:0.5491	.	222	Q8TDB4	CD049_HUMAN	V	222	ENSP00000381928:G222V	ENSP00000381928:G222V	G	-	2	0	C4orf49	140407261	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.489000	0.06490	-0.045000	0.13468	-0.218000	0.12543	GGA	.	.		0.453	MGARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364536.1	NM_032623	
FGA	2243	hgsc.bcm.edu	37	4	155505651	155505651	+	Missense_Mutation	SNP	G	G	C	rs376434823		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:155505651G>C	ENST00000302053.3	-	6	2304	c.2226C>G	c.(2224-2226)ttC>ttG	p.F742L		NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	742	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	AGCCTACCCGGAAGTGATATT	0.522																																					p.F742L	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.C2226G						.						134.0	132.0	133.0					4																	155505651		2203	4300	6503	SO:0001583	missense	2243	exon6			TACCCGGAAGTGA		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.2226C>G	chr4.hg19:g.155505651G>C	ENSP00000306361:p.Phe742Leu	162.0	0.0		112.0	82.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	0.172	-1.070654	0.01918	.	.	ENSG00000171560	ENST00000302053	D	0.99454	-5.92	5.7	-1.7	0.08159	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.841848	0.11129	N	0.596578	D	0.98232	0.9415	M	0.79011	2.435	0.09310	N	0.99999	P	0.41080	0.737	B	0.41135	0.348	D	0.96069	0.9044	10	0.40728	T	0.16	.	3.5098	0.07704	0.2379:0.4336:0.2006:0.1279	.	742	P02671	FIBA_HUMAN	L	742	ENSP00000306361:F742L	ENSP00000306361:F742L	F	-	3	2	FGA	155725101	0.000000	0.05858	0.000000	0.03702	0.387000	0.30353	-1.885000	0.01620	-0.821000	0.04312	-0.145000	0.13849	TTC	.	.		0.522	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
DDX60L	91351	hgsc.bcm.edu	37	4	169305825	169305825	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:169305825G>C	ENST00000511577.1	-	30	4301	c.4054C>G	c.(4054-4056)Ctg>Gtg	p.L1352V	DDX60L_ENST00000260184.7_Missense_Mutation_p.L1352V			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1352	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CGCAGGACCAGGGTTATGCTG	0.502																																					p.L1352V		Atlas-SNP	.											.	DDX60L	116	.	0			c.C4054G						.						75.0	74.0	74.0					4																	169305825		2203	4300	6503	SO:0001583	missense	91351	exon30			GGACCAGGGTTAT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4054C>G	chr4.hg19:g.169305825G>C	ENSP00000422423:p.Leu1352Val	328.0	0.0		354.0	173.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.687	0.495373	0.12762	.	.	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.22743	1.94;1.94	3.55	1.78	0.24846	Helicase, C-terminal (1);	.	.	.	.	T	0.24198	0.0586	M	0.63428	1.95	0.09310	N	1	D	0.60160	0.987	P	0.46110	0.504	T	0.11792	-1.0573	9	0.59425	D	0.04	.	6.8818	0.24177	0.4152:0.0:0.5848:0.0	.	1352	Q5H9U9	DDX6L_HUMAN	V	1352	ENSP00000260184:L1352V;ENSP00000422423:L1352V	ENSP00000260184:L1352V	L	-	1	2	DDX60L	169542400	0.420000	0.25457	0.004000	0.12327	0.087000	0.18053	0.732000	0.26072	0.047000	0.15862	0.563000	0.77884	CTG	.	.		0.502	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
SEMA5A	9037	hgsc.bcm.edu	37	5	9066573	9066573	+	Silent	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:9066573C>T	ENST00000382496.5	-	17	2924	c.2259G>A	c.(2257-2259)cgG>cgA	p.R753R		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	753	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						TAGAACAGTACCGCATTTCGA	0.537																																					p.R753R		Atlas-SNP	.											.	SEMA5A	236	.	0			c.G2259A						.						179.0	171.0	174.0					5																	9066573		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon17			ACAGTACCGCATT	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2259G>A	chr5.hg19:g.9066573C>T		181.0	0.0		157.0	50.0	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1																																																																																			.	.		0.537	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
FAM105A	54491	hgsc.bcm.edu	37	5	14601219	14601219	+	Silent	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:14601219G>T	ENST00000274217.3	+	2	330	c.210G>T	c.(208-210)ggG>ggT	p.G70G		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	70										large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TATATTCAGGGCACAAGCTGA	0.388																																					p.G70G		Atlas-SNP	.											.	FAM105A	32	.	0			c.G210T						.						180.0	170.0	174.0					5																	14601219		2203	4300	6503	SO:0001819	synonymous_variant	54491	exon2			TTCAGGGCACAAG		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"""OTU domain containing"""	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.210G>T	chr5.hg19:g.14601219G>T		63.0	0.0		56.0	24.0	NM_019018	Q53H50|Q9H037	Silent	SNP	ENST00000274217.3	hg19	CCDS3884.1																																																																																			.	.		0.388	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018	
EGFLAM	133584	hgsc.bcm.edu	37	5	38412649	38412649	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:38412649A>T	ENST00000354891.3	+	11	1739	c.1393A>T	c.(1393-1395)Aaa>Taa	p.K465*	EGFLAM_ENST00000397202.2_5'UTR|EGFLAM_ENST00000322350.5_Nonsense_Mutation_p.K465*|EGFLAM_ENST00000336740.6_Nonsense_Mutation_p.K231*	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	465	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AAGTGAGACCAAAATCAAACT	0.493																																					p.K465X	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.A1393T						.						107.0	104.0	105.0					5																	38412649		2203	4300	6503	SO:0001587	stop_gained	133584	exon11			GAGACCAAAATCA	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1393A>T	chr5.hg19:g.38412649A>T	ENSP00000346964:p.Lys465*	85.0	0.0		55.0	4.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Nonsense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	A	41	8.922489	0.99004	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	.	.	.	6.07	4.88	0.63580	.	0.533583	0.22745	N	0.056154	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.4788	13.4556	0.61197	0.8693:0.1307:0.0:0.0	.	.	.	.	X	465;465;231;231	.	ENSP00000313084:K465X	K	+	1	0	EGFLAM	38448406	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.801000	0.47908	1.081000	0.41110	0.528000	0.53228	AAA	.	.		0.493	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
PCDH12	51294	hgsc.bcm.edu	37	5	141337154	141337154	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:141337154G>C	ENST00000231484.3	-	1	1473	c.263C>G	c.(262-264)aCa>aGa	p.T88R	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCCTGCCTGTGCTGAGCAA	0.622																																					p.T88R		Atlas-SNP	.											.	PCDH12	133	.	0			c.C263G						.						53.0	55.0	54.0					5																	141337154		2203	4300	6503	SO:0001583	missense	51294	exon1			CTGCCTGTGCTGA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.263C>G	chr5.hg19:g.141337154G>C	ENSP00000231484:p.Thr88Arg	236.0	0.0		194.0	102.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.248274	0.59103	.	.	ENSG00000113555	ENST00000231484	T	0.28666	1.6	4.81	4.81	0.61882	Cadherin, N-terminal (1);Cadherin (4);	0.000000	0.85682	D	0.000000	T	0.58963	0.2159	M	0.90369	3.11	0.50313	D	0.999867	D	0.89917	1.0	D	0.91635	0.999	T	0.65121	-0.6245	10	0.72032	D	0.01	.	8.8967	0.35470	0.0987:0.0:0.9013:0.0	.	88	Q9NPG4	PCD12_HUMAN	R	88	ENSP00000231484:T88R	ENSP00000231484:T88R	T	-	2	0	PCDH12	141317338	1.000000	0.71417	0.945000	0.38365	0.348000	0.29142	7.796000	0.85898	2.504000	0.84457	0.563000	0.77884	ACA	.	.		0.622	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
HNRNPH1	3187	hgsc.bcm.edu	37	5	179043937	179043937	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr5:179043937G>T	ENST00000356731.5	-	10	2675	c.1140C>A	c.(1138-1140)ttC>ttA	p.F380L	HNRNPH1_ENST00000442819.2_Missense_Mutation_p.F380L|HNRNPH1_ENST00000511300.2_Intron|HNRNPH1_ENST00000510411.1_Intron|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000329433.6_Missense_Mutation_p.F380L|HNRNPH1_ENST00000393432.4_Missense_Mutation_p.F380L			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	380	2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						TAGAATTCAAGAAGAGTTCTA	0.383																																					p.F380L		Atlas-SNP	.											.	HNRNPH1	62	.	0			c.C1140A						.						102.0	100.0	100.0					5																	179043937		2203	4300	6503	SO:0001583	missense	3187	exon11			ATTCAAGAAGAGT	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"""RNA binding motif (RRM) containing"""	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.1140C>A	chr5.hg19:g.179043937G>T	ENSP00000349168:p.Phe380Leu	269.0	0.0		173.0	64.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Missense_Mutation	SNP	ENST00000356731.5	hg19	CCDS4446.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	24.5|24.5|24.5	4.537888|4.537888|4.537888	0.85917|0.85917|0.85917	.|.|.	.|.|.	ENSG00000169045|ENSG00000169045|ENSG00000169045	ENST00000393432;ENST00000442819;ENST00000356731;ENST00000329433;ENST00000523921|ENST00000523449|ENST00000521173	T;T;T;T;T|.|.	0.11604|.|.	2.76;2.76;2.76;2.76;2.76|.|.	5.81|5.81|5.81	5.81|5.81|5.81	0.92471|0.92471|0.92471	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000016|.|.	T|T|T	0.66587|0.66587|0.66587	0.2804|0.2804|0.2804	L|L|L	0.61036|0.61036|0.61036	1.89|1.89|1.89	0.80722|0.80722|0.80722	D|D|D	1|1|1	D|.|.	0.54964|.|.	0.969|.|.	P|.|.	0.54856|.|.	0.762|.|.	T|T|T	0.64089|0.64089|0.64089	-0.6489|-0.6489|-0.6489	10|5|5	0.05351|.|.	T|.|.	0.99|.|.	-3.7755|-3.7755|-3.7755	13.294|13.294|13.294	0.60286|0.60286|0.60286	0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0	.|.|.	380|.|.	P31943|.|.	HNRH1_HUMAN|.|.	L|I|Y	380;380;380;380;174|48|255	ENSP00000377082:F380L;ENSP00000397797:F380L;ENSP00000349168:F380L;ENSP00000327539:F380L;ENSP00000429270:F174L|.|.	ENSP00000327539:F380L|.|.	F|L|S	-|-|-	3|1|2	2|0|0	HNRNPH1|HNRNPH1|HNRNPH1	178976543|178976543|178976543	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	3.427000|3.427000|3.427000	0.52785|0.52785|0.52785	2.734000|2.734000|2.734000	0.93682|0.93682|0.93682	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	TTC|CTT|TCT	.	.		0.383	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520	
ATXN1	6310	hgsc.bcm.edu	37	6	16327490	16327490	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr6:16327490G>A	ENST00000244769.4	-	8	1988	c.1052C>T	c.(1051-1053)tCg>tTg	p.S351L	ATXN1_ENST00000436367.1_Missense_Mutation_p.S351L	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	351					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GTGAGGAACCGACTTGCCGCC	0.667																																					p.S351L		Atlas-SNP	.											.	ATXN1	117	.	0			c.C1052T						.						58.0	66.0	63.0					6																	16327490		2203	4300	6503	SO:0001583	missense	6310	exon7			GGAACCGACTTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1052C>T	chr6.hg19:g.16327490G>A	ENSP00000244769:p.Ser351Leu	97.0	0.0		92.0	8.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902268	0.33628	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.78364	-1.17;-1.17	4.86	3.99	0.46301	.	0.948079	0.08837	N	0.886373	T	0.47377	0.1442	N	0.22421	0.69	0.20196	N	0.999923	B	0.28880	0.226	B	0.17098	0.017	T	0.42464	-0.9450	10	0.38643	T	0.18	-5.3967	13.0006	0.58672	0.0788:0.0:0.9212:0.0	.	351	P54253	ATX1_HUMAN	L	351	ENSP00000244769:S351L;ENSP00000416360:S351L	ENSP00000244769:S351L	S	-	2	0	ATXN1	16435469	1.000000	0.71417	0.513000	0.27749	0.526000	0.34562	6.107000	0.71517	1.031000	0.39867	0.561000	0.74099	TCG	.	.		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
ZDHHC4	55146	hgsc.bcm.edu	37	7	6620253	6620253	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:6620253A>G	ENST00000396706.2	+	3	504	c.61A>G	c.(61-63)Atc>Gtc	p.I21V	ZDHHC4_ENST00000396707.2_Missense_Mutation_p.I21V|ZDHHC4_ENST00000335965.6_Missense_Mutation_p.I21V|ZDHHC4_ENST00000396709.1_Missense_Mutation_p.I21V|ZDHHC4_ENST00000396713.2_Missense_Mutation_p.I21V|ZDHHC4_ENST00000496017.1_3'UTR|AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000405731.3_Missense_Mutation_p.I21V			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	21						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TCTTGTTCTTATCTGCGTCTG	0.493																																					p.I21V		Atlas-SNP	.											.	ZDHHC4	36	.	0			c.A61G						.						359.0	313.0	328.0					7																	6620253		2203	4300	6503	SO:0001583	missense	55146	exon3			GTTCTTATCTGCG	AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"""Zinc fingers, DHHC-type"""	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.61A>G	chr7.hg19:g.6620253A>G	ENSP00000379934:p.Ile21Val	237.0	1.0		168.0	88.0	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Missense_Mutation	SNP	ENST00000396706.2	hg19	CCDS5352.1	.	.	.	.	.	.	.	.	.	.	a	1.652	-0.513707	0.04200	.	.	ENSG00000136247	ENST00000405731;ENST00000396713;ENST00000396707;ENST00000335965;ENST00000396709;ENST00000483589;ENST00000396706	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.64;1.49	4.9	-3.41	0.04839	.	0.947078	0.08924	N	0.873990	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	0.999994	B;B	0.13145	0.0;0.007	B;B	0.14578	0.001;0.011	T	0.33701	-0.9858	10	0.07482	T	0.82	-16.4868	0.4997	0.00578	0.2144:0.2867:0.2499:0.2489	.	21;21	Q9NPG8;C9J5I9	ZDHC4_HUMAN;.	V	21	ENSP00000385027:I21V;ENSP00000379941:I21V;ENSP00000379935:I21V;ENSP00000337475:I21V;ENSP00000379937:I21V;ENSP00000418496:I21V;ENSP00000379934:I21V	ENSP00000337475:I21V	I	+	1	0	ZDHHC4	6586778	0.015000	0.18098	0.011000	0.14972	0.168000	0.22595	0.072000	0.14617	-0.467000	0.06932	0.533000	0.62120	ATC	.	.		0.493	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106	
CRHR2	1395	hgsc.bcm.edu	37	7	30721587	30721587	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:30721587G>T	ENST00000471646.1	-	2	590	c.173C>A	c.(172-174)gCc>gAc	p.A58D	CRHR2_ENST00000348438.4_Missense_Mutation_p.A85D|CRHR2_ENST00000506074.2_Missense_Mutation_p.A58D|CRHR2_ENST00000341843.4_Missense_Mutation_p.A44D	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	58					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CTCCACGAGGGCTCCGGCAGC	0.672																																					p.A85D		Atlas-SNP	.											.	CRHR2	104	.	0			c.C254A						.						30.0	28.0	29.0					7																	30721587		2202	4298	6500	SO:0001583	missense	1395	exon3			ACGAGGGCTCCGG		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.173C>A	chr7.hg19:g.30721587G>T	ENSP00000418722:p.Ala58Asp	102.0	0.0		56.0	10.0	NM_001202475	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	hg19	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177198	0.38413	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	4.27	3.39	0.38822	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	0.472371	0.21192	N	0.078631	T	0.46927	0.1418	L	0.41573	1.285	0.30685	N	0.751898	B;B;P;B;B	0.36048	0.173;0.185;0.534;0.257;0.173	B;B;B;B;B	0.35550	0.046;0.066;0.205;0.149;0.046	T	0.46034	-0.9220	10	0.24483	T	0.36	.	6.294	0.21075	0.1011:0.1865:0.7124:0.0	.	58;58;85;44;58	B3SXT0;B3SXS6;Q13324-2;Q13324-3;Q13324	.;.;.;.;CRFR2_HUMAN	D	58;85;44;58	ENSP00000418722:A58D;ENSP00000340943:A85D;ENSP00000344304:A44D;ENSP00000426498:A58D	ENSP00000344304:A44D	A	-	2	0	CRHR2	30688112	0.858000	0.29795	0.998000	0.56505	0.991000	0.79684	2.020000	0.41010	1.151000	0.42436	0.655000	0.94253	GCC	.	.		0.672	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		
NEUROD6	63974	hgsc.bcm.edu	37	7	31378831	31378831	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:31378831A>T	ENST00000297142.3	-	2	374	c.52T>A	c.(52-54)Tgc>Agc	p.C18S		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	18					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						AACTTTCTGCACATCTGGGAT	0.388																																					p.C18S		Atlas-SNP	.											.	NEUROD6	84	.	0			c.T52A						.						132.0	147.0	142.0					7																	31378831		2203	4300	6503	SO:0001583	missense	63974	exon2			TTCTGCACATCTG	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.52T>A	chr7.hg19:g.31378831A>T	ENSP00000297142:p.Cys18Ser	26.0	0.0		28.0	18.0	NM_022728	Q548T9|Q9H3H6	Missense_Mutation	SNP	ENST00000297142.3	hg19	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397903	0.25205	.	.	ENSG00000164600	ENST00000297142	D	0.94723	-3.5	5.28	5.28	0.74379	.	0.050512	0.85682	D	0.000000	D	0.90065	0.6897	L	0.36672	1.1	0.52099	D	0.999943	B	0.30326	0.276	B	0.25759	0.063	D	0.87798	0.2623	10	0.20046	T	0.44	-21.8478	15.2475	0.73517	1.0:0.0:0.0:0.0	.	18	Q96NK8	NDF6_HUMAN	S	18	ENSP00000297142:C18S	ENSP00000297142:C18S	C	-	1	0	NEUROD6	31345356	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.522000	0.73783	2.012000	0.59069	0.528000	0.53228	TGC	.	.		0.388	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728	
C7orf25	79020	hgsc.bcm.edu	37	7	42949411	42949411	+	Silent	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:42949411C>T	ENST00000350427.4	-	2	1364	c.1089G>A	c.(1087-1089)ggG>ggA	p.G363G	PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000431882.2_Silent_p.G421G|C7orf25_ENST00000438029.1_Silent_p.G363G|C7orf25_ENST00000447342.1_Silent_p.G363G			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	363										endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TGTCTCCCGTCCCAAAAATTG	0.423																																					p.G421G		Atlas-SNP	.											.	C7orf25	36	.	0			c.G1263A						.						83.0	80.0	81.0					7																	42949411		2203	4300	6503	SO:0001819	synonymous_variant	79020	exon2			TCCCGTCCCAAAA	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.1089G>A	chr7.hg19:g.42949411C>T		126.0	0.0		134.0	81.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Silent	SNP	ENST00000350427.4	hg19	CCDS5466.1																																																																																			.	.		0.423	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054	
LRCH4	4034	hgsc.bcm.edu	37	7	100174773	100174773	+	Silent	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:100174773A>G	ENST00000310300.6	-	12	1352	c.1300T>C	c.(1300-1302)Ttg>Ctg	p.L434L	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	434					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCTGGCTTCAAGAGGCTGGAA	0.642																																					p.L434L		Atlas-SNP	.											.	LRCH4	53	.	0			c.T1300C						.						51.0	56.0	55.0					7																	100174773		2203	4300	6503	SO:0001819	synonymous_variant	4034	exon12			GCTTCAAGAGGCT	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1300T>C	chr7.hg19:g.100174773A>G		133.0	0.0		67.0	21.0	NM_002319	A4D2D5|Q8WV85|Q96ID0	Silent	SNP	ENST00000310300.6	hg19	CCDS34706.1																																																																																			.	.		0.642	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
CTTNBP2	83992	hgsc.bcm.edu	37	7	117351762	117351762	+	Silent	SNP	T	T	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:117351762T>A	ENST00000160373.3	-	23	4912	c.4821A>T	c.(4819-4821)tcA>tcT	p.S1607S	CFTR_ENST00000608965.1_Intron	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1607					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)		ATTTAACTCTTGAAACACCCA	0.423																																					p.S1607S		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A4821T						.						135.0	119.0	125.0					7																	117351762		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon23			AACTCTTGAAACA		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.4821A>T	chr7.hg19:g.117351762T>A		40.0	0.0		42.0	23.0	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	8.629	0.893191	0.17613	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.87	-2.48	0.06423	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.9221	1.527	0.02527	0.1147:0.2524:0.2381:0.3948	.	.	.	.	X	1095	.	.	K	-	1	0	CTTNBP2	117138998	0.998000	0.40836	0.990000	0.47175	0.996000	0.88848	0.244000	0.18124	-0.406000	0.07588	0.528000	0.53228	AAG	.	.		0.423	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
CADPS2	93664	hgsc.bcm.edu	37	7	122303420	122303420	+	Silent	SNP	T	T	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:122303420T>C	ENST00000449022.2	-	3	676	c.657A>G	c.(655-657)aaA>aaG	p.K219K	CADPS2_ENST00000412584.2_Silent_p.K219K|CADPS2_ENST00000313070.7_Silent_p.K219K|CADPS2_ENST00000334010.7_Silent_p.K219K	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	219					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						TATTTGGCTGTTTGCACAAGT	0.418																																					p.K219K		Atlas-SNP	.											.	CADPS2	116	.	0			c.A657G						.						156.0	145.0	149.0					7																	122303420		1915	4144	6059	SO:0001819	synonymous_variant	93664	exon3			TGGCTGTTTGCAC		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"""Pleckstrin homology (PH) domain containing"""	16018	protein-coding gene	gene with protein product		609978	"""Ca++-dependent activator protein for secretion 2"""				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.657A>G	chr7.hg19:g.122303420T>C		90.0	0.0		98.0	61.0	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	hg19	CCDS55158.1																																																																																			.	.		0.418	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954	
SND1	27044	hgsc.bcm.edu	37	7	127721412	127721412	+	Splice_Site	SNP	G	G	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:127721412G>C	ENST00000354725.3	+	18	2163	c.1969G>C	c.(1969-1971)Gtc>Ctc	p.V657L	MIR593_ENST00000384856.1_RNA	NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	657	TNase-like 4. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						GAACATGCAGGTCTGGGCCCA	0.572																																					p.V657L		Atlas-SNP	.											.	SND1	104	.	0			c.G1969C						.						104.0	79.0	87.0					7																	127721412		2203	4300	6503	SO:0001630	splice_region_variant	27044	exon18			ATGCAGGTCTGGG		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.1969-1G>C	chr7.hg19:g.127721412G>C		125.0	0.0		92.0	53.0	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	hg19	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.726980	0.30593	.	.	ENSG00000197157	ENST00000354725;ENST00000438400;ENST00000486037	T;T	0.38077	1.85;1.16	4.85	3.8	0.43715	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.543995	0.20281	N	0.095459	T	0.20414	0.0491	N	0.17594	0.5	0.51233	D	0.999915	B	0.02656	0.0	B	0.09377	0.004	T	0.04991	-1.0913	9	.	.	.	-16.5034	9.1195	0.36778	0.139:0.0:0.861:0.0	.	657	Q7KZF4	SND1_HUMAN	L	657;647;143	ENSP00000346762:V657L;ENSP00000419327:V143L	.	V	+	1	0	SND1	127508648	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.398000	0.34554	0.923000	0.37045	0.561000	0.74099	GTC	.	.		0.572	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	Missense_Mutation
METTL2B	55798	hgsc.bcm.edu	37	7	128133954	128133954	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:128133954A>G	ENST00000262432.8	+	6	803	c.766A>G	c.(766-768)Att>Gtt	p.I256V	METTL2B_ENST00000480046.1_Missense_Mutation_p.I191V|RP11-212P7.3_ENST00000462662.1_RNA	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	256					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CAGTCTTGATATTATCATTCT	0.433																																					p.I256V		Atlas-SNP	.											.	METTL2B	34	.	0			c.A766G						.						123.0	115.0	118.0					7																	128133954		2202	4283	6485	SO:0001583	missense	55798	exon6			CTTGATATTATCA	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.766A>G	chr7.hg19:g.128133954A>G	ENSP00000262432:p.Ile256Val	174.0	0.0		160.0	103.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	A	0.184	-1.059334	0.01950	.	.	ENSG00000165055	ENST00000262432;ENST00000480046;ENST00000481392	T;T;T	0.11277	2.79;2.79;2.79	3.16	-1.29	0.09288	Methyltransferase type 12 (1);	0.330183	0.33217	N	0.005152	T	0.03220	0.0094	N	0.03294	-0.36	0.33538	D	0.594458	B;B	0.06786	0.0;0.001	B;B	0.13407	0.007;0.009	T	0.49312	-0.8953	10	0.02654	T	1	-4.4082	9.8744	0.41194	0.2271:0.0:0.7729:0.0	.	191;256	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	V	256;191;20	ENSP00000262432:I256V;ENSP00000418402:I191V;ENSP00000418989:I20V	ENSP00000262432:I256V	I	+	1	0	METTL2B	127921190	0.879000	0.30193	0.944000	0.38274	0.780000	0.44128	0.187000	0.16998	-0.171000	0.10797	0.164000	0.16699	ATT	.	.		0.433	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
HIPK2	28996	hgsc.bcm.edu	37	7	139285298	139285298	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:139285298T>A	ENST00000406875.3	-	11	2394	c.2300A>T	c.(2299-2301)cAg>cTg	p.Q767L	HIPK2_ENST00000342645.6_Missense_Mutation_p.Q767L|HIPK2_ENST00000428878.2_Missense_Mutation_p.Q740L	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	767	Interaction with POU4F1. {ECO:0000250}.|Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					TAGTGCAGGCTGCTGCATGAT	0.542																																					p.Q767L		Atlas-SNP	.											.	HIPK2	192	.	0			c.A2300T						.						110.0	115.0	113.0					7																	139285298		2125	4239	6364	SO:0001583	missense	28996	exon11			GCAGGCTGCTGCA	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.2300A>T	chr7.hg19:g.139285298T>A	ENSP00000385571:p.Gln767Leu	213.0	0.0		166.0	86.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	T	27.0	4.787393	0.90367	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.28454	1.61;1.61;1.61	4.57	4.57	0.56435	.	.	.	.	.	T	0.53626	0.1808	.	.	.	0.58432	D	0.999994	P;P	0.50528	0.936;0.908	P;D	0.64144	0.885;0.922	T	0.59429	-0.7456	8	0.87932	D	0	.	14.4024	0.67056	0.0:0.0:0.0:1.0	.	767;740	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	L	767;740;767	ENSP00000385571:Q767L;ENSP00000413724:Q740L;ENSP00000343108:Q767L	ENSP00000343108:Q767L	Q	-	2	0	HIPK2	138935838	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.482000	0.81143	2.044000	0.60594	0.528000	0.53228	CAG	.	.		0.542	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
TBXAS1	6916	hgsc.bcm.edu	37	7	139655333	139655333	+	Silent	SNP	T	T	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr7:139655333T>A	ENST00000336425.5	+	11	1004	c.615T>A	c.(613-615)ccT>ccA	p.P205P	TBXAS1_ENST00000411653.1_Silent_p.P205P|TBXAS1_ENST00000425687.1_Silent_p.P138P|TBXAS1_ENST00000448866.1_Silent_p.P205P|TBXAS1_ENST00000436047.2_Silent_p.P206P|TBXAS1_ENST00000414508.2_Silent_p.P206P|TBXAS1_ENST00000458722.1_Silent_p.P251P|TBXAS1_ENST00000263552.6_Silent_p.P206P|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000416849.2_Silent_p.P252P			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	205					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	GGCAGGCCCCTGAGGATCCCT	0.572																																					p.P252P		Atlas-SNP	.											.	TBXAS1	121	.	0			c.T756A						.						78.0	82.0	81.0					7																	139655333		2203	4300	6503	SO:0001819	synonymous_variant	6916	exon8			GGCCCCTGAGGAT	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.615T>A	chr7.hg19:g.139655333T>A		61.0	0.0		45.0	9.0	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Silent	SNP	ENST00000336425.5	hg19																																																																																				.	.		0.572	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
TUSC3	7991	hgsc.bcm.edu	37	8	15397946	15397946	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr8:15397946G>T	ENST00000503731.1	+	1	155	c.7G>T	c.(7-9)Gcc>Tcc	p.A3S	TUSC3_ENST00000382020.4_Missense_Mutation_p.A3S|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000506802.1_Missense_Mutation_p.A3S|TUSC3_ENST00000509380.1_Missense_Mutation_p.A3S	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	3					cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		CGCGATGGGGGCCCGGGGCGC	0.741																																					p.A3S		Atlas-SNP	.											.	TUSC3	98	.	0			c.G7T						.						10.0	11.0	10.0					8																	15397946		2131	4236	6367	SO:0001583	missense	7991	exon1			ATGGGGGCCCGGG	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog A (S. cerevisiae)"""	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.7G>T	chr8.hg19:g.15397946G>T	ENSP00000424544:p.Ala3Ser	40.0	0.0		17.0	8.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534879	0.64972	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.48201	0.84;0.82;0.83;0.84	4.3	3.42	0.39159	.	0.157787	0.30051	N	0.010532	T	0.25644	0.0624	N	0.08118	0	0.23351	N	0.997859	B;B;B;B;B;B	0.15930	0.015;0.006;0.01;0.006;0.006;0.001	B;B;B;B;B;B	0.10450	0.002;0.002;0.005;0.001;0.002;0.003	T	0.16660	-1.0395	10	0.54805	T	0.06	0.0533	8.073	0.30699	0.1079:0.0:0.8921:0.0	.	3;3;3;3;3;3	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	S	3	ENSP00000371450:A3S;ENSP00000425777:A3S;ENSP00000423426:A3S;ENSP00000424544:A3S	ENSP00000221167:A3S	A	+	1	0	TUSC3	15442317	1.000000	0.71417	0.988000	0.46212	0.762000	0.43233	0.923000	0.28757	1.412000	0.46977	0.563000	0.77884	GCC	.	.		0.741	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765	
AZIN1	51582	hgsc.bcm.edu	37	8	103842142	103842142	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr8:103842142T>A	ENST00000337198.5	-	10	2090	c.927A>T	c.(925-927)gaA>gaT	p.E309D	AZIN1_ENST00000347770.4_Missense_Mutation_p.E309D	NM_148174.2	NP_680479.1	O14977	AZIN1_HUMAN	antizyme inhibitor 1	309					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of protein catabolic process (GO:0042177)|polyamine biosynthetic process (GO:0006596)|positive regulation of polyamine transmembrane transport (GO:1902269)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|enzyme inhibitor activity (GO:0004857)|ornithine decarboxylase activator activity (GO:0042978)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	9	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			TGAAGGCTGGTTCATCACTTC	0.328																																					p.E309D		Atlas-SNP	.											.	AZIN1	26	.	0			c.A927T						.						96.0	99.0	98.0					8																	103842142		2203	4300	6503	SO:0001583	missense	51582	exon11			GGCTGGTTCATCA	AAC25391	CCDS6295.1	8p22-q21.3	2005-03-21	2005-03-21	2005-03-21		ENSG00000155096			16432	protein-coding gene	gene with protein product	"""ornithine decarboxylase 1-like"""	607909	"""ornithine decarboxylase antizyme inhibitor"""	OAZIN		9349715, 9110174	Standard	XM_005250969		Approved	OAZI, ODC1L	uc003yky.3	O14977		ENST00000337198.5:c.927A>T	chr8.hg19:g.103842142T>A	ENSP00000337180:p.Glu309Asp	94.0	0.0		129.0	88.0	NM_015878	A6NCD5|Q6IBQ7|Q96D20	Missense_Mutation	SNP	ENST00000337198.5	hg19	CCDS6295.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.981586	0.34942	.	.	ENSG00000155096	ENST00000337198;ENST00000347770	T;T	0.40476	1.03;1.03	6.03	2.45	0.29901	Orn/DAP/Arg decarboxylase 2, C-terminal (1);Alanine racemase/group IV decarboxylase, C-terminal (2);	0.133093	0.64402	N	0.000002	T	0.28101	0.0693	L	0.39326	1.205	0.40459	D	0.980222	B	0.02656	0.0	B	0.04013	0.001	T	0.07731	-1.0757	10	0.21540	T	0.41	-16.894	6.002	0.19525	0.0:0.1974:0.1276:0.675	.	309	O14977	AZIN1_HUMAN	D	309	ENSP00000337180:E309D;ENSP00000321507:E309D	ENSP00000337180:E309D	E	-	3	2	AZIN1	103911318	0.946000	0.32159	1.000000	0.80357	0.998000	0.95712	-0.052000	0.11865	0.196000	0.20367	0.455000	0.32223	GAA	.	.		0.328	AZIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380133.1		
TRPM3	80036	hgsc.bcm.edu	37	9	73736204	73736204	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:73736204A>T	ENST00000377111.2	-	1	310	c.67T>A	c.(67-69)Tgg>Agg	p.W23R	TRPM3_ENST00000423814.3_Intron|TRPM3_ENST00000377110.3_Missense_Mutation_p.W23R|TRPM3_ENST00000357533.2_Intron	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	23					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						AAATTCCACCAGGAAAACAAG	0.507																																					p.W23R		Atlas-SNP	.											.	TRPM3	700	.	0			c.T67A						.						82.0	83.0	83.0					9																	73736204		1911	4119	6030	SO:0001583	missense	80036	exon1			TCCACCAGGAAAA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.67T>A	chr9.hg19:g.73736204A>T	ENSP00000366315:p.Trp23Arg	88.0	0.0		68.0	36.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.026	-1.374688	0.01214	.	.	ENSG00000083067	ENST00000377111;ENST00000377110	T;T	0.57595	0.39;0.56	5.68	-0.796	0.10912	.	.	.	.	.	T	0.26048	0.0635	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.15838	-1.0423	9	0.09590	T	0.72	.	10.7478	0.46191	0.5318:0.0:0.4682:0.0	.	23;23;23	Q9HCF6;Q9HCF6-2;Q9HCF6-10	TRPM3_HUMAN;.;.	R	23	ENSP00000366315:W23R;ENSP00000366314:W23R	ENSP00000366314:W23R	W	-	1	0	TRPM3	72926024	0.769000	0.28531	0.651000	0.29564	0.763000	0.43281	-0.053000	0.11846	-0.051000	0.13334	-0.479000	0.04858	TGG	.	.		0.507	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	
ZFP37	7539	hgsc.bcm.edu	37	9	115812084	115812084	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:115812084G>T	ENST00000374227.3	-	2	228	c.201C>A	c.(199-201)aaC>aaA	p.N67K	ZFP37_ENST00000555206.1_Missense_Mutation_p.N68K|ZFP37_ENST00000553380.1_Missense_Mutation_p.N82K	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						TTGAGGCTTGGTTGCAGTAGT	0.423																																					p.N67K		Atlas-SNP	.											.	ZFP37	93	.	0			c.C201A						.						214.0	174.0	188.0					9																	115812084		2203	4300	6503	SO:0001583	missense	7539	exon2			GGCTTGGTTGCAG	AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"""Zinc fingers, C2H2-type"", ""-"""	12863	protein-coding gene	gene with protein product		602951	"""zinc finger protein homologous to Zfp37 in mouse"", ""zinc finger protein 37 homolog (mouse)"""				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.201C>A	chr9.hg19:g.115812084G>T	ENSP00000363344:p.Asn67Lys	156.0	0.0		121.0	70.0	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Missense_Mutation	SNP	ENST00000374227.3	hg19	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.163398	0.38217	.	.	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	T;T;T	0.02579	4.24;4.24;4.24	4.18	-0.204	0.13200	Krueppel-associated box (4);	0.149871	0.30969	N	0.008504	T	0.10680	0.0261	H	0.97214	3.96	0.09310	N	1	B;B;B	0.27882	0.16;0.16;0.192	B;B;B	0.35413	0.128;0.128;0.202	T	0.11108	-1.0601	10	0.87932	D	0	-7.4885	7.7301	0.28781	0.4509:0.0:0.5491:0.0	.	68;82;67	G3V3L7;Q9Y6Q3-2;Q9Y6Q3	.;.;ZFP37_HUMAN	K	67;68;82	ENSP00000363344:N67K;ENSP00000451310:N68K;ENSP00000452552:N82K	ENSP00000363344:N67K	N	-	3	2	ZFP37	114851905	0.000000	0.05858	0.057000	0.19452	0.754000	0.42855	-0.077000	0.11394	-0.037000	0.13646	0.555000	0.69702	AAC	.	.		0.423	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408	
OR1B1	347169	hgsc.bcm.edu	37	9	125391806	125391806	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:125391806G>A	ENST00000304833.3	-	1	46	c.9C>T	c.(7-9)agC>agT	p.S3S	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						TAGGGGCAAAGCTCATCATGA	0.428																																					p.S3S		Atlas-SNP	.											.	OR1B1	48	.	0			c.C9T						.						72.0	74.0	73.0					9																	125391806		2195	4279	6474	SO:0001819	synonymous_variant	347169	exon1			GGCAAAGCTCATC	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.9C>T	chr9.hg19:g.125391806G>A		94.0	0.0		94.0	40.0	NM_001004450	Q6IFN3	Silent	SNP	ENST00000304833.3	hg19	CCDS35126.1																																																																																			.	.		0.428	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
NTNG2	84628	hgsc.bcm.edu	37	9	135117276	135117276	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:135117276C>A	ENST00000393229.3	+	8	2147	c.1371C>A	c.(1369-1371)gaC>gaA	p.D457E	NTNG2_ENST00000393228.4_Missense_Mutation_p.D449E|NTNG2_ENST00000490694.1_3'UTR|NTNG2_ENST00000360670.3_Missense_Mutation_p.D463E	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	457					axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		ACGTGTGCGACGACGACCAGC	0.731																																					p.D457E		Atlas-SNP	.											.	NTNG2	66	.	0			c.C1371A						.						7.0	8.0	7.0					9																	135117276		2047	4050	6097	SO:0001583	missense	84628	exon8			GTGCGACGACGAC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.1371C>A	chr9.hg19:g.135117276C>A	ENSP00000376921:p.Asp457Glu	36.0	0.0		14.0	5.0	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Missense_Mutation	SNP	ENST00000393229.3	hg19	CCDS6946.1	.	.	.	.	.	.	.	.	.	.	c	11.49	1.653576	0.29425	.	.	ENSG00000196358	ENST00000393229;ENST00000393228;ENST00000360670	D;D;D	0.91631	-2.88;-2.88;-2.88	3.39	1.22	0.21188	EGF, extracellular (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.071801	0.52532	U	0.000075	D	0.94558	0.8247	M	0.78637	2.42	0.31534	N	0.660762	D	0.76494	0.999	D	0.85130	0.997	D	0.91931	0.5555	10	0.54805	T	0.06	.	8.3416	0.32247	0.0:0.6839:0.0:0.3161	.	457	Q96CW9	NTNG2_HUMAN	E	457;449;463	ENSP00000376921:D457E;ENSP00000376920:D449E;ENSP00000353888:D463E	ENSP00000353888:D463E	D	+	3	2	NTNG2	134107097	0.961000	0.32948	0.998000	0.56505	0.025000	0.11179	0.182000	0.16900	0.162000	0.19483	-1.676000	0.00740	GAC	.	.		0.731	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
TPRN	286262	hgsc.bcm.edu	37	9	140093451	140093451	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:140093451G>A	ENST00000409012.4	-	1	1799	c.1713C>T	c.(1711-1713)tcC>tcT	p.S571S	TPRN_ENST00000321773.2_Silent_p.S510S|TPRN_ENST00000541945.1_Intron	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	571					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						TCTTTCTTGAGGAGCCAGCCT	0.627																																					p.S571S		Atlas-SNP	.											.	TPRN	28	.	0			c.C1713T						.						60.0	57.0	58.0					9																	140093451		2203	4299	6502	SO:0001819	synonymous_variant	286262	exon1			TCTTGAGGAGCCA	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"""chromosome 9 open reading frame 75"", ""deafness, autosomal recessive 79"""	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1713C>T	chr9.hg19:g.140093451G>A		115.0	0.0		56.0	12.0	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Silent	SNP	ENST00000409012.4	hg19	CCDS56594.1																																																																																			.	.		0.627	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691	
SYT15	83849	hgsc.bcm.edu	37	10	46965864	46965864	+	Missense_Mutation	SNP	G	G	T	rs202146218	byFrequency	TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:46965864G>T	ENST00000374321.4	-	5	739	c.673C>A	c.(673-675)Cag>Aag	p.Q225K	RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.Q278K|SYT15_ENST00000503753.1_Missense_Mutation_p.Q225K|SYT15_ENST00000374325.3_Missense_Mutation_p.Q225K	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	225	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						AGCACCCTCTGGGTGATGGTC	0.592																																					p.Q225K	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											.	SYT15	165	.	0			c.C673A						.						39.0	42.0	41.0					10																	46965864		2117	4239	6356	SO:0001583	missense	83849	exon5			CCCTCTGGGTGAT	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.673C>A	chr10.hg19:g.46965864G>T	ENSP00000363441:p.Gln225Lys	142.0	0.0		90.0	31.0	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	hg19	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	14.75	2.629328	0.46944	.	.	ENSG00000204176	ENST00000416127;ENST00000374328;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321;ENST00000512997	D;T;T;T;T;T	0.95377	-3.69;3.21;3.21;3.21;3.21;3.21	5.13	5.13	0.70059	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.349077	0.31031	N	0.008394	D	0.92665	0.7669	N	0.26042	0.785	0.54753	D	0.999982	B;B	0.25206	0.056;0.12	B;B	0.36186	0.076;0.219	D	0.89516	0.3775	10	0.27082	T	0.32	.	16.4476	0.83942	0.0:0.0:1.0:0.0	.	225;225	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	K	225;15;225;225;64;278;225;109	ENSP00000363448:Q15K;ENSP00000363445:Q225K;ENSP00000427607:Q225K;ENSP00000363443:Q278K;ENSP00000363441:Q225K;ENSP00000424803:Q109K	ENSP00000363441:Q225K	Q	-	1	0	SYT15	46385870	1.000000	0.71417	0.955000	0.39395	0.401000	0.30781	5.731000	0.68554	2.550000	0.86006	0.561000	0.74099	CAG	.	.		0.592	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
CHST3	9469	hgsc.bcm.edu	37	10	73765630	73765630	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:73765630C>A	ENST00000373115.4	+	2	467	c.30C>A	c.(28-30)gaC>gaA	p.D10E		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	10					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TGCCCCAGGACTGCCGGGACT	0.522																																					p.D10E		Atlas-SNP	.											.	CHST3	36	.	0			c.C30A						.						147.0	133.0	138.0					10																	73765630		2203	4300	6503	SO:0001583	missense	9469	exon2			CCAGGACTGCCGG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"""Sulfotransferases, membrane-bound"""	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.30C>A	chr10.hg19:g.73765630C>A	ENSP00000362207:p.Asp10Glu	95.0	0.0		62.0	47.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.660319	0.67586	.	.	ENSG00000122863	ENST00000373115	D	0.96802	-4.13	5.82	-0.827	0.10802	.	0.188213	0.37053	N	0.002280	D	0.91509	0.7319	L	0.44542	1.39	0.28254	N	0.925154	B	0.06786	0.001	B	0.06405	0.002	D	0.84614	0.0680	10	0.87932	D	0	-28.5081	5.5251	0.16953	0.0:0.2793:0.4232:0.2976	.	10	Q7LGC8	CHST3_HUMAN	E	10	ENSP00000362207:D10E	ENSP00000362207:D10E	D	+	3	2	CHST3	73435636	0.014000	0.17966	0.993000	0.49108	0.686000	0.39977	-0.010000	0.12743	0.035000	0.15519	0.655000	0.94253	GAC	.	.		0.522	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273	
LOXL4	84171	hgsc.bcm.edu	37	10	100021841	100021841	+	Missense_Mutation	SNP	C	C	T	rs377758453		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:100021841C>T	ENST00000260702.3	-	3	557	c.407G>A	c.(406-408)cGc>cAc	p.R136H		NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	136						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GCCACGATGGCGCCGGGGGTG	0.602																																					p.R136H		Atlas-SNP	.											.	LOXL4	60	.	0			c.G407A						.	C	HIS/ARG	0,4406		0,0,2203	47.0	43.0	44.0		407	3.8	1.0	10		44	1,8599	1.2+/-3.3	0,1,4299	no	missense	LOXL4	NM_032211.6	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	136/757	100021841	1,13005	2203	4300	6503	SO:0001583	missense	84171	exon3			CGATGGCGCCGGG	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.407G>A	chr10.hg19:g.100021841C>T	ENSP00000260702:p.Arg136His	75.0	0.0		51.0	11.0	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	hg19	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402475	0.62288	0.0	1.16E-4	ENSG00000138131	ENST00000260702	T	0.49139	0.79	4.69	3.78	0.43462	Speract/scavenger receptor-related (1);	0.103756	0.64402	D	0.000004	T	0.65417	0.2689	M	0.74881	2.28	0.36182	D	0.849478	D	0.89917	1.0	D	0.70935	0.971	T	0.75354	-0.3347	10	0.72032	D	0.01	.	12.1953	0.54294	0.0:0.9173:0.0:0.0827	.	136	Q96JB6	LOXL4_HUMAN	H	136	ENSP00000260702:R136H	ENSP00000260702:R136H	R	-	2	0	LOXL4	100011831	0.875000	0.30112	0.998000	0.56505	0.329000	0.28539	1.151000	0.31651	2.157000	0.67596	0.561000	0.74099	CGC	.	.		0.602	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
NOLC1	9221	hgsc.bcm.edu	37	10	103921354	103921354	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:103921354G>T	ENST00000605788.1	+	11	2018	c.1783G>T	c.(1783-1785)Gca>Tca	p.A595S	NOLC1_ENST00000488254.2_Missense_Mutation_p.A596S|NOLC1_ENST00000603742.1_Missense_Mutation_p.A314S|NOLC1_ENST00000477977.1_3'UTR|NOLC1_ENST00000405356.1_Missense_Mutation_p.A605S	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	595					cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		TGCCAAGGAGGCAGAGACTCC	0.478																																					p.A595S		Atlas-SNP	.											.	NOLC1	61	.	0			c.G1783T						.						45.0	41.0	42.0					10																	103921354		2203	4300	6503	SO:0001583	missense	9221	exon11			AAGGAGGCAGAGA	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.1783G>T	chr10.hg19:g.103921354G>T	ENSP00000474710:p.Ala595Ser	99.0	0.0		45.0	33.0	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	hg19	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217457	0.39201	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.47177	0.85	6.07	0.394	0.16299	.	0.528716	0.18826	N	0.130117	T	0.31231	0.0790	L	0.45581	1.43	0.34553	D	0.711586	B;B;B	0.34372	0.451;0.451;0.272	B;B;B	0.31442	0.13;0.13;0.045	T	0.23726	-1.0180	10	0.25106	T	0.35	0.3724	4.0351	0.09725	0.3199:0.0:0.2444:0.4357	.	596;605;595	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	S	605;595	ENSP00000385410:A605S	ENSP00000359024:A595S	A	+	1	0	NOLC1	103911344	0.006000	0.16342	0.967000	0.41034	0.881000	0.50899	-0.537000	0.06128	0.022000	0.15160	0.650000	0.86243	GCA	.	.		0.478	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
SFXN2	118980	hgsc.bcm.edu	37	10	104489489	104489489	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:104489489C>T	ENST00000369893.5	+	6	684	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S		NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	173				QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 4). {ECO:0000305}.	iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		GAAAGCGCCGCCCTTGGTGGG	0.552											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P173S		Atlas-SNP	.											.	SFXN2	40	.	0			c.C517T						.						74.0	83.0	80.0					10																	104489489		2203	4300	6503	SO:0001583	missense	118980	exon6			GCGCCGCCCTTGG	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.517C>T	chr10.hg19:g.104489489C>T	ENSP00000358909:p.Pro173Ser	33.0	0.0	1382	25.0	21.0	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	hg19	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.612353	0.66672	.	.	ENSG00000156398	ENST00000369893	T	0.33216	1.42	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.46386	0.1390	M	0.69358	2.11	0.80722	D	1	P	0.46656	0.882	P	0.53102	0.718	T	0.21211	-1.0252	10	0.34782	T	0.22	-14.0701	15.4376	0.75157	0.1394:0.8605:0.0:0.0	.	173	Q96NB2	SFXN2_HUMAN	S	173	ENSP00000358909:P173S	ENSP00000358909:P173S	P	+	1	0	SFXN2	104479479	0.998000	0.40836	0.900000	0.35374	0.245000	0.25701	3.938000	0.56583	2.675000	0.91044	0.655000	0.94253	CCC	.	.		0.552	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116061116	116061116	+	Silent	SNP	A	A	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:116061116A>C	ENST00000304129.4	-	13	1568	c.1539T>G	c.(1537-1539)gcT>gcG	p.A513A	AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000369271.3_Silent_p.A513A|AFAP1L2_ENST00000545353.1_Silent_p.A566A			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	513					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		TCCTTACCGCAGCTGTGAGCT	0.587																																					p.A513A		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.T1539G						.						89.0	77.0	81.0					10																	116061116		2203	4300	6503	SO:0001819	synonymous_variant	84632	exon13			TACCGCAGCTGTG	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1539T>G	chr10.hg19:g.116061116A>C		74.0	0.0		34.0	27.0	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	hg19	CCDS31286.1																																																																																			.	.		0.587	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
MMP21	118856	hgsc.bcm.edu	37	10	127455372	127455372	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr10:127455372G>A	ENST00000368808.3	-	7	1568	c.1569C>T	c.(1567-1569)ggC>ggT	p.G523G		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	523					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	AGTATGCATTGCCTTTGAAAA	0.358																																					p.G523G		Atlas-SNP	.											.	MMP21	46	.	0			c.C1569T						.						127.0	127.0	127.0					10																	127455372		2203	4300	6503	SO:0001819	synonymous_variant	118856	exon7			TGCATTGCCTTTG	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"""matrix metalloproteinase 21"""			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1569C>T	chr10.hg19:g.127455372G>A		97.0	0.0		57.0	42.0	NM_147191	Q5VZP9|Q8NG02	Silent	SNP	ENST00000368808.3	hg19	CCDS7647.1																																																																																			.	.		0.358	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1		
TH	7054	hgsc.bcm.edu	37	11	2189846	2189846	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:2189846G>A	ENST00000381178.1	-	4	473	c.455C>T	c.(454-456)cCg>cTg	p.P152L	TH_ENST00000381175.1_Missense_Mutation_p.P148L|TH_ENST00000333684.5_Missense_Mutation_p.P125L|TH_ENST00000352909.3_Missense_Mutation_p.P121L	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	152					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCAGCTCGCGGCCTCTGGGC	0.627																																					p.P152L		Atlas-SNP	.											.	TH	43	.	0			c.C455T						.						11.0	15.0	14.0					11																	2189846		2170	4289	6459	SO:0001583	missense	7054	exon4			GCTCGCGGCCTCT	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.455C>T	chr11.hg19:g.2189846G>A	ENSP00000370571:p.Pro152Leu	33.0	0.0		18.0	12.0	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Missense_Mutation	SNP	ENST00000381178.1	hg19	CCDS7731.1	.	.	.	.	.	.	.	.	.	.	G	0.099	-1.155156	0.01700	.	.	ENSG00000180176	ENST00000381178;ENST00000381175;ENST00000352909;ENST00000333684	D;D;D;D	0.99418	-5.87;-5.87;-5.87;-5.56	3.14	-0.0864	0.13681	.	0.671891	0.14769	N	0.299505	D	0.97046	0.9035	N	0.20986	0.625	0.19575	N	0.999968	B;B;B;B;B;B	0.09022	0.0;0.002;0.002;0.002;0.001;0.001	B;B;B;B;B;B	0.06405	0.001;0.001;0.001;0.001;0.001;0.002	D	0.93140	0.6540	10	0.36615	T	0.2	.	10.848	0.46754	0.1924:0.0:0.8076:0.0	.	125;125;121;121;152;148	B7ZL73;Q0PWM2;Q0PWM3;P07101-3;P07101;P07101-2	.;.;.;.;TY3H_HUMAN;.	L	152;148;121;125	ENSP00000370571:P152L;ENSP00000370567:P148L;ENSP00000325951:P121L;ENSP00000328814:P125L	ENSP00000328814:P125L	P	-	2	0	TH	2146422	0.251000	0.23961	0.000000	0.03702	0.000000	0.00434	1.341000	0.33907	-0.317000	0.08677	-2.087000	0.00375	CCG	.	.		0.627	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
OR2D3	120775	hgsc.bcm.edu	37	11	6943217	6943217	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:6943217A>T	ENST00000317834.3	+	1	1013	c.985A>T	c.(985-987)Agg>Tgg	p.R329W		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	329						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTTCTCTCATAGGCAGTGACC	0.403																																					p.R329W		Atlas-SNP	.											OR2D3,NS,carcinoma,0,1	OR2D3	51	.	0			c.A985T						.						53.0	55.0	54.0					11																	6943217		2200	4294	6494	SO:0001583	missense	120775	exon1			TCTCATAGGCAGT	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.985A>T	chr11.hg19:g.6943217A>T	ENSP00000320560:p.Arg329Trp	54.0	0.0		48.0	20.0	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	hg19	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428322	0.43122	.	.	ENSG00000178358	ENST00000317834	T	0.01584	4.75	4.38	0.74	0.18330	.	1.633600	0.03837	N	0.269968	T	0.02727	0.0082	N	0.14661	0.345	0.09310	N	1	D	0.63880	0.993	P	0.55923	0.787	T	0.37220	-0.9715	10	0.87932	D	0	12.9762	2.8365	0.05516	0.5936:0.0:0.2031:0.2033	.	329	Q8NGH3	OR2D3_HUMAN	W	329	ENSP00000320560:R329W	ENSP00000320560:R329W	R	+	1	2	OR2D3	6899793	0.300000	0.24435	0.000000	0.03702	0.000000	0.00434	1.143000	0.31553	0.106000	0.17784	-0.438000	0.05819	AGG	.	.		0.403	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
RAG1	5896	hgsc.bcm.edu	37	11	36595488	36595488	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:36595488G>T	ENST00000299440.5	+	2	746	c.634G>T	c.(634-636)Gac>Tac	p.D212Y		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	212	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				ACCATCCTGTGACATCTGCAA	0.527									Familial Hemophagocytic Lymphohistiocytosis																												p.D212Y	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.G634T						.						78.0	71.0	74.0					11																	36595488		2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TCCTGTGACATCT	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.634G>T	chr11.hg19:g.36595488G>T	ENSP00000299440:p.Asp212Tyr	81.0	0.0		74.0	17.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.111924	0.56398	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	T;T	0.38401	1.14;1.14	5.9	5.9	0.94986	.	0.357073	0.31199	N	0.008065	T	0.62221	0.2410	M	0.92317	3.295	0.44469	D	0.997404	D	0.55385	0.971	P	0.53102	0.718	T	0.71800	-0.4483	10	0.87932	D	0	.	15.7737	0.78193	0.0:0.1354:0.8646:0.0	.	212	P15918	RAG1_HUMAN	Y	212	ENSP00000434610:D212Y;ENSP00000299440:D212Y	ENSP00000299440:D212Y	D	+	1	0	RAG1	36552064	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.169000	0.31871	2.822000	0.97130	0.650000	0.86243	GAC	.	.		0.527	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
TMEM132A	54972	hgsc.bcm.edu	37	11	60698051	60698051	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:60698051G>T	ENST00000453848.2	+	5	1094	c.936G>T	c.(934-936)aaG>aaT	p.K312N	TMEM132A_ENST00000005286.4_Missense_Mutation_p.K312N			Q24JP5	T132A_HUMAN	transmembrane protein 132A	312						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GGACTGCCAAGCTGGACCGCT	0.622																																					p.K312N		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G936T						.						81.0	86.0	84.0					11																	60698051		2203	4299	6502	SO:0001583	missense	54972	exon5			TGCCAAGCTGGAC	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.936G>T	chr11.hg19:g.60698051G>T	ENSP00000405823:p.Lys312Asn	80.0	0.0		42.0	11.0	NM_178031	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	hg19	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334728	0.41297	.	.	ENSG00000006118	ENST00000544065;ENST00000444690;ENST00000453848;ENST00000005286	T;T;T	0.13778	2.78;2.56;2.56	5.4	3.49	0.39957	.	0.082213	0.49305	D	0.000141	T	0.12817	0.0311	L	0.50333	1.59	0.32122	N	0.587816	B;B;B;B	0.21225	0.053;0.021;0.029;0.029	B;B;B;B	0.18561	0.022;0.022;0.022;0.022	T	0.05666	-1.0871	10	0.87932	D	0	.	7.7328	0.28796	0.1576:0.1383:0.7041:0.0	.	301;62;312;312	Q24JP5-3;Q24JP5-4;Q24JP5;Q24JP5-2	.;.;T132A_HUMAN;.	N	50;62;312;312	ENSP00000442754:K50N;ENSP00000405823:K312N;ENSP00000005286:K312N	ENSP00000005286:K312N	K	+	3	2	TMEM132A	60454627	0.995000	0.38212	0.999000	0.59377	0.914000	0.54420	0.631000	0.24568	1.421000	0.47157	0.655000	0.94253	AAG	.	.		0.622	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
DDB1	1642	hgsc.bcm.edu	37	11	61096943	61096943	+	Silent	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:61096943G>A	ENST00000301764.7	-	4	838	c.441C>T	c.(439-441)cgC>cgT	p.R147R	DDB1_ENST00000450997.2_Intron|DDB1_ENST00000545930.1_5'Flank	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	147	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CTTTATTATCGCGATCTAGTG	0.483								Nucleotide excision repair (NER)																													p.R147R		Atlas-SNP	.											.	DDB1	100	.	0			c.C441T						.						94.0	92.0	93.0					11																	61096943		2203	4299	6502	SO:0001819	synonymous_variant	1642	exon4			ATTATCGCGATCT	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"""damage-specific DNA binding protein 1 (127kD)"""			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.441C>T	chr11.hg19:g.61096943G>A		120.0	0.0		82.0	5.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent	SNP	ENST00000301764.7	hg19	CCDS31576.1																																																																																			.	.		0.483	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923	
FAT3	120114	hgsc.bcm.edu	37	11	92577730	92577730	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:92577730A>G	ENST00000298047.6	+	18	11214	c.11197A>G	c.(11197-11199)Atg>Gtg	p.M3733V	FAT3_ENST00000533797.1_Missense_Mutation_p.M68V|FAT3_ENST00000409404.2_Missense_Mutation_p.M3733V|FAT3_ENST00000525166.1_Missense_Mutation_p.M3583V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3733					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGAGAATATCATGCGCATCTC	0.532										TCGA Ovarian(4;0.039)																											p.M3733V		Atlas-SNP	.											.	FAT3	1822	.	0			c.A11197G						.						89.0	88.0	88.0					11																	92577730		2111	4239	6350	SO:0001583	missense	120114	exon18			AATATCATGCGCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11197A>G	chr11.hg19:g.92577730A>G	ENSP00000298047:p.Met3733Val	234.0	0.0		157.0	71.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	2.265	-0.368362	0.05069	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.97	0.735	0.18300	.	.	.	.	.	T	0.05640	0.0148	N	0.00377	-1.585	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40534	-0.9558	9	0.02654	T	1	.	5.7419	0.18098	0.6342:0.1295:0.2362:0.0	.	3733;3733	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	V	3733;3733;3583;68	ENSP00000298047:M3733V;ENSP00000387040:M3733V;ENSP00000432586:M3583V;ENSP00000436399:M68V	ENSP00000298047:M3733V	M	+	1	0	FAT3	92217378	1.000000	0.71417	0.579000	0.28588	0.699000	0.40488	1.802000	0.38853	0.082000	0.17018	-0.256000	0.11100	ATG	.	.		0.532	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
DDI1	414301	hgsc.bcm.edu	37	11	103908038	103908038	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:103908038G>A	ENST00000302259.3	+	1	731	c.488G>A	c.(487-489)cGc>cAc	p.R163H	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	163							aspartic-type endopeptidase activity (GO:0004190)	p.R163L(2)		central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		CTCAAGGAACGCAACCCTCCC	0.612																																					p.R163H		Atlas-SNP	.											DDI1_ENST00000302259,caecum,carcinoma,0,2	DDI1	222	.	2	Substitution - Missense(2)	lung(2)	c.G488A						.						64.0	62.0	62.0					11																	103908038		2202	4299	6501	SO:0001583	missense	414301	exon1			AGGAACGCAACCC		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.488G>A	chr11.hg19:g.103908038G>A	ENSP00000302805:p.Arg163His	78.0	0.0		47.0	11.0	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	hg19	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.179662	0.78564	.	.	ENSG00000170967	ENST00000302259	T	0.24908	1.83	5.02	4.1	0.47936	.	0.000000	0.85682	D	0.000000	T	0.48187	0.1486	M	0.75615	2.305	0.42064	D	0.991176	D	0.89917	1.0	D	0.91635	0.999	T	0.46816	-0.9164	10	0.37606	T	0.19	-25.855	11.9064	0.52715	0.0857:0.0:0.9143:0.0	.	163	Q8WTU0	DDI1_HUMAN	H	163	ENSP00000302805:R163H	ENSP00000302805:R163H	R	+	2	0	DDI1	103413248	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	7.217000	0.77982	1.480000	0.48289	0.655000	0.94253	CGC	.	.		0.612	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
KMT2A	4297	hgsc.bcm.edu	37	11	118376454	118376454	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:118376454C>T	ENST00000389506.5	+	27	9838	c.9838C>T	c.(9838-9840)Cga>Tga	p.R3280*	KMT2A_ENST00000354520.4_Nonsense_Mutation_p.R3242*|KMT2A_ENST00000534358.1_Nonsense_Mutation_p.R3283*			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3280					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R3283*(1)|p.R3280*(1)									TTCATCTCACCGAACTGTCCC	0.433																																					p.R3283X		Atlas-SNP	.											MLL_ENST00000534358,bladder,carcinoma,0,2	MLL	548	.	2	Substitution - Nonsense(2)	urinary_tract(2)	c.C9847T						.						109.0	109.0	109.0					11																	118376454		2200	4295	6495	SO:0001587	stop_gained	4297	exon27			TCTCACCGAACTG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.9838C>T	chr11.hg19:g.118376454C>T	ENSP00000374157:p.Arg3280*	71.0	0.0		65.0	29.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Nonsense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	50	16.745021	0.99871	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	.	.	.	5.98	4.04	0.47022	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5277	0.39173	0.2425:0.6837:0.0:0.0739	.	.	.	.	X	3283;3280;3242;2190	.	ENSP00000346516:R3242X	R	+	1	2	MLL	117881664	0.995000	0.38212	1.000000	0.80357	0.982000	0.71751	2.957000	0.49137	2.847000	0.97988	0.591000	0.81541	CGA	.	.		0.433	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
ROBO4	54538	hgsc.bcm.edu	37	11	124765401	124765401	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:124765401C>A	ENST00000306534.3	-	6	1473	c.988G>T	c.(988-990)Gct>Tct	p.A330S	ROBO4_ENST00000533054.1_Missense_Mutation_p.A185S|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	330	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGCCTCGAGCCCGGCCAGAG	0.617																																					p.A330S		Atlas-SNP	.											.	ROBO4	130	.	0			c.G988T						.						49.0	57.0	54.0					11																	124765401		2198	4290	6488	SO:0001583	missense	54538	exon6			CTCGAGCCCGGCC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.988G>T	chr11.hg19:g.124765401C>A	ENSP00000304945:p.Ala330Ser	34.0	0.0		43.0	21.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.474876	0.63737	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.52983	0.64;0.64	4.72	3.81	0.43845	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.38959	N	0.001520	T	0.49423	0.1556	L	0.57536	1.79	0.18873	N	0.999981	D;D	0.53619	0.961;0.958	P;P	0.52066	0.689;0.531	T	0.39961	-0.9588	10	0.10902	T	0.67	.	11.065	0.47970	0.0:0.9129:0.0:0.087	.	220;330	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	S	330;220;185	ENSP00000304945:A330S;ENSP00000437129:A185S	ENSP00000304945:A330S	A	-	1	0	ROBO4	124270611	0.518000	0.26234	0.956000	0.39512	0.997000	0.91878	0.572000	0.23684	1.216000	0.43427	0.561000	0.74099	GCT	.	.		0.617	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
LRRK2	120892	hgsc.bcm.edu	37	12	40657644	40657644	+	Missense_Mutation	SNP	G	G	T	rs267603454		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr12:40657644G>T	ENST00000298910.7	+	14	1655	c.1597G>T	c.(1597-1599)Gtt>Ttt	p.V533F	LRRK2_ENST00000343742.2_Missense_Mutation_p.V533F	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	533					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GCTAAATATGGTTAAAAAACA	0.299																																					p.V533F		Atlas-SNP	.											.	LRRK2	763	.	0			c.G1597T						.						83.0	88.0	86.0					12																	40657644		2203	4297	6500	SO:0001583	missense	120892	exon14			AATATGGTTAAAA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1597G>T	chr12.hg19:g.40657644G>T	ENSP00000298910:p.Val533Phe	140.0	0.0		101.0	21.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	8.364	0.833807	0.16820	.	.	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	T;T;T	0.64991	-0.13;1.35;1.35	5.66	-1.91	0.07641	Armadillo-like helical (1);Armadillo-type fold (1);	0.485960	0.21586	N	0.072179	T	0.31796	0.0808	N	0.08118	0	0.09310	N	1	B;B	0.29188	0.002;0.236	B;B	0.29353	0.003;0.101	T	0.16928	-1.0386	10	0.72032	D	0.01	.	1.846	0.03159	0.4417:0.1376:0.2887:0.1319	.	533;533	E9PC85;Q5S007	.;LRRK2_HUMAN	F	281;533;533	ENSP00000398726:V281F;ENSP00000341930:V533F;ENSP00000298910:V533F	ENSP00000298910:V533F	V	+	1	0	LRRK2	38943911	0.982000	0.34865	0.006000	0.13384	0.125000	0.20455	0.056000	0.14256	-0.158000	0.11040	-0.142000	0.14014	GTT	.	.		0.299	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
CCNT1	904	hgsc.bcm.edu	37	12	49089809	49089809	+	Missense_Mutation	SNP	C	C	A	rs35965578	byFrequency	TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr12:49089809C>A	ENST00000261900.3	-	7	901	c.679G>T	c.(679-681)Gcc>Tcc	p.A227S		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	227					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						GTCACAGTGGCGTCAACATAC	0.498																																					p.A227S		Atlas-SNP	.											.	CCNT1	55	.	0			c.G679T						.						105.0	81.0	89.0					12																	49089809		2203	4300	6503	SO:0001583	missense	904	exon7			CAGTGGCGTCAAC	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.679G>T	chr12.hg19:g.49089809C>A	ENSP00000261900:p.Ala227Ser	125.0	0.0		94.0	24.0	NM_001240	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	hg19	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	c	14.13	2.443468	0.43429	.	.	ENSG00000129315	ENST00000261900	T	0.38887	1.11	5.79	5.79	0.91817	.	0.169435	0.53938	D	0.000051	T	0.29126	0.0724	N	0.12182	0.205	0.30771	N	0.743014	B	0.02656	0.0	B	0.10450	0.005	T	0.08764	-1.0706	10	0.24483	T	0.36	-8.8347	18.7919	0.91976	0.0:1.0:0.0:0.0	.	227	O60563	CCNT1_HUMAN	S	227	ENSP00000261900:A227S	ENSP00000261900:A227S	A	-	1	0	CCNT1	47376076	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.645000	0.46621	2.740000	0.93945	0.561000	0.74099	GCC	.	C|0.500;G|0.500		0.498	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
PDX1	3651	hgsc.bcm.edu	37	13	28498513	28498513	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr13:28498513G>T	ENST00000381033.4	+	2	646	c.527G>T	c.(526-528)cGg>cTg	p.R176L	PDX1-AS1_ENST00000499662.2_RNA	NM_000209.3	NP_000200.1	O00330	ODPX_HUMAN	pancreatic and duodenal homeobox 1	0					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)					all_cancers(110;0.175)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		CGGCCGCGCCGGGTGGAGCTG	0.572																																					p.R176L		Atlas-SNP	.											.	PDX1	7	.	0			c.G527T						.						54.0	57.0	56.0					13																	28498513		2203	4300	6503	SO:0001583	missense	3651	exon2			CGCGCCGGGTGGA	AF035260	CCDS9327.1	13q12.1	2012-03-09	2006-12-01	2006-12-01	ENSG00000139515	ENSG00000139515		"""Homeoboxes / ANTP class : HOXL subclass"""	6107	protein-coding gene	gene with protein product	"""somatostatin transcription factor 1"""	600733	"""insulin promoter factor 1, homeodomain transcription factor"""	IPF1		7590740	Standard	NM_000209		Approved	IDX-1, STF-1, PDX-1, MODY4	uc001urt.2	P52945	OTTHUMG00000016638	ENST00000381033.4:c.527G>T	chr13.hg19:g.28498513G>T	ENSP00000370421:p.Arg176Leu	161.0	1.0		45.0	38.0	NM_000209	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000381033.4	hg19	CCDS9327.1	.	.	.	.	.	.	.	.	.	.	G	34	5.293103	0.95546	.	.	ENSG00000139515	ENST00000381033	D	0.97232	-4.3	4.86	4.86	0.63082	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99099	0.9690	H	0.97291	3.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99167	1.0863	10	0.87932	D	0	.	18.338	0.90295	0.0:0.0:1.0:0.0	.	176	P52945	PDX1_HUMAN	L	176	ENSP00000370421:R176L	ENSP00000370421:R176L	R	+	2	0	PDX1	27396513	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.770000	0.98971	2.382000	0.81193	0.555000	0.69702	CGG	.	.		0.572	PDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044310.2	NM_000209	
HNRNPC	3183	hgsc.bcm.edu	37	14	21679444	21679444	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr14:21679444C>A	ENST00000320084.7	-	8	1098	c.859G>T	c.(859-861)Gaa>Taa	p.E287*	HNRNPC_ENST00000449098.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000555309.1_Nonsense_Mutation_p.E286*|HNRNPC_ENST00000554455.1_Nonsense_Mutation_p.E287*|HNRNPC_ENST00000336053.6_3'UTR|HNRNPC_ENST00000556628.1_Nonsense_Mutation_p.E207*|HNRNPC_ENST00000557201.1_Nonsense_Mutation_p.E287*|HNRNPC_ENST00000553753.1_3'UTR|HNRNPC_ENST00000555883.1_Nonsense_Mutation_p.E231*|HNRNPC_ENST00000430246.2_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000556142.1_3'UTR|HNRNPC_ENST00000556897.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000420743.2_Nonsense_Mutation_p.E287*|HNRNPC_ENST00000556513.1_3'UTR|HNRNPC_ENST00000554969.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000553300.1_Nonsense_Mutation_p.E274*|HNRNPC_ENST00000555914.1_Nonsense_Mutation_p.E273*	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	287	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		GCCTCTTTTTCATCATCCTTG	0.478																																					p.E287X	NSCLC(108;607 2244 12726 38757)	Atlas-SNP	.											.	HNRNPC	31	.	0			c.G859T						.						129.0	139.0	136.0					14																	21679444		2153	4265	6418	SO:0001587	stop_gained	3183	exon9			CTTTTTCATCATC		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"""RNA binding motif (RRM) containing"""	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.859G>T	chr14.hg19:g.21679444C>A	ENSP00000319690:p.Glu287*	129.0	0.0		75.0	30.0	NM_031314	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Nonsense_Mutation	SNP	ENST00000320084.7	hg19	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	C	37	6.573695	0.97676	.	.	ENSG00000092199	ENST00000320084;ENST00000449098;ENST00000554969;ENST00000554455;ENST00000430246;ENST00000400042;ENST00000555914;ENST00000555309;ENST00000556628;ENST00000555883;ENST00000557201;ENST00000553300;ENST00000556897;ENST00000420743;ENST00000557157;ENST00000445284;ENST00000554539	.	.	.	5.85	5.85	0.93711	.	0.264293	0.28549	U	0.014958	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.9211	0.92525	0.0:1.0:0.0:0.0	.	.	.	.	X	287;274;274;287;274;83;273;286;207;231;287;274;274;287;195;287;171	.	ENSP00000319690:E287X	E	-	1	0	HNRNPC	20749284	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.962000	0.63687	2.755000	0.94549	0.655000	0.94253	GAA	.	.		0.478	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1		
LTBP2	4053	hgsc.bcm.edu	37	14	75016623	75016623	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr14:75016623C>A	ENST00000261978.4	-	8	2118	c.1732G>T	c.(1732-1734)Ggc>Tgc	p.G578C	LTBP2_ENST00000556690.1_Missense_Mutation_p.G578C|LTBP2_ENST00000557425.1_5'UTR|CTD-2207P18.1_ENST00000554552.1_lincRNA	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	578	TB 1.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CCCACACTGCCACAGCAGTCC	0.622																																					p.G578C		Atlas-SNP	.											.	LTBP2	158	.	0			c.G1732T						.						111.0	96.0	101.0					14																	75016623		2203	4300	6503	SO:0001583	missense	4053	exon8			CACTGCCACAGCA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1732G>T	chr14.hg19:g.75016623C>A	ENSP00000261978:p.Gly578Cys	154.0	0.0		79.0	31.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.340642	0.81911	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	D;D	0.84298	-1.83;-1.83	5.61	4.72	0.59763	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.42964	D	0.000640	D	0.90345	0.6979	M	0.69823	2.125	0.48696	D	0.999692	D	0.76494	0.999	D	0.70016	0.967	D	0.89024	0.3437	10	0.31617	T	0.26	.	12.9331	0.58299	0.0:0.9251:0.0:0.0749	.	578	Q14767	LTBP2_HUMAN	C	578	ENSP00000261978:G578C;ENSP00000451477:G578C	ENSP00000261978:G578C	G	-	1	0	LTBP2	74086376	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	5.559000	0.67326	1.521000	0.48983	0.655000	0.94253	GGC	.	.		0.622	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
MLH3	27030	hgsc.bcm.edu	37	14	75515470	75515470	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr14:75515470G>A	ENST00000556740.1	-	1	924	c.889C>T	c.(889-891)Cgg>Tgg	p.R297W	MLH3_ENST00000355774.2_Missense_Mutation_p.R297W|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000238662.7_Missense_Mutation_p.R297W|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000556257.1_Missense_Mutation_p.R297W			Q9UHC1	MLH3_HUMAN	mutL homolog 3	297					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GGGGTAGACCGGTGCCGAAGA	0.398								Mismatch excision repair (MMR)																													p.R297W		Atlas-SNP	.											.	MLH3	200	.	0			c.C889T						.						105.0	113.0	110.0					14																	75515470		2203	4299	6502	SO:0001583	missense	27030	exon2			TAGACCGGTGCCG	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.889C>T	chr14.hg19:g.75515470G>A	ENSP00000452316:p.Arg297Trp	109.0	0.0		58.0	16.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.953462	0.53293	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85	5.8	2.85	0.33270	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, C-terminal (1);	0.123449	0.53938	D	0.000053	D	0.91710	0.7379	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.92559	0.6056	10	0.87932	D	0	-6.8703	15.1529	0.72717	0.0:0.0:0.6313:0.3687	.	297;297	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	W	297	ENSP00000348020:R297W;ENSP00000238662:R297W;ENSP00000451540:R297W;ENSP00000452316:R297W	ENSP00000238662:R297W	R	-	1	2	MLH3	74585223	0.858000	0.29795	0.952000	0.39060	0.684000	0.39900	1.816000	0.38992	0.774000	0.33427	0.655000	0.94253	CGG	.	.		0.398	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381	
NPAP1	23742	hgsc.bcm.edu	37	15	24921322	24921322	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:24921322G>A	ENST00000329468.2	+	1	782	c.308G>A	c.(307-309)cGg>cAg	p.R103Q		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	103					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CTGCCTGCTCGGAACCCCCCG	0.677																																					p.R103Q		Atlas-SNP	.											C15orf2,colon,carcinoma,0,1	.	.	.	0			c.G308A						.						38.0	31.0	33.0					15																	24921322		2199	4291	6490	SO:0001583	missense	23742	exon1			CTGCTCGGAACCC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.308G>A	chr15.hg19:g.24921322G>A	ENSP00000333735:p.Arg103Gln	39.0	0.0		24.0	11.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	12.22	1.871769	0.33069	.	.	ENSG00000185823	ENST00000329468	T	0.08008	3.14	2.15	-4.3	0.03710	.	.	.	.	.	T	0.13670	0.0331	L	0.38175	1.15	0.09310	N	1	D	0.69078	0.997	D	0.67103	0.949	T	0.05989	-1.0852	9	0.52906	T	0.07	.	7.3249	0.26549	0.2365:0.5849:0.1787:0.0	.	103	Q9NZP6	CO002_HUMAN	Q	103	ENSP00000333735:R103Q	ENSP00000333735:R103Q	R	+	2	0	C15orf2	22472415	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.051000	0.03507	-2.205000	0.00742	-1.483000	0.00984	CGG	.	.		0.677	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
HERC2	8924	hgsc.bcm.edu	37	15	28518063	28518063	+	Silent	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:28518063C>A	ENST00000261609.7	-	8	996	c.888G>T	c.(886-888)ctG>ctT	p.L296L		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCTGCACAGCCAGCTCCAGCA	0.592																																					p.L296L		Atlas-SNP	.											.	HERC2	501	.	0			c.G888T						.						43.0	41.0	42.0					15																	28518063		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon8			CACAGCCAGCTCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.888G>T	chr15.hg19:g.28518063C>A		40.0	0.0		24.0	11.0	NM_004667		Silent	SNP	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
RTF1	23168	hgsc.bcm.edu	37	15	41763423	41763423	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:41763423A>G	ENST00000389629.4	+	8	1091	c.1079A>G	c.(1078-1080)aAt>aGt	p.N360S		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	360	Plus3. {ECO:0000255|PROSITE- ProRule:PRU00693}.				DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		GAAGAATTGAATCGGGTTCGA	0.438																																					p.N360S		Atlas-SNP	.											.	RTF1	76	.	0			c.A1079G						.						151.0	147.0	149.0					15																	41763423		2203	4300	6503	SO:0001583	missense	23168	exon8			AATTGAATCGGGT	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1079A>G	chr15.hg19:g.41763423A>G	ENSP00000374280:p.Asn360Ser	110.0	0.0		72.0	16.0	NM_015138	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	hg19	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504255	0.64410	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.87	5.87	0.94306	Plus-3 domain, subgroup (1);Plus-3 (2);	0.000000	0.85682	D	0.000000	T	0.60753	0.2293	N	0.17082	0.46	0.80722	D	1	P	0.49253	0.921	D	0.68353	0.957	T	0.57476	-0.7805	9	0.19147	T	0.46	-25.3025	16.2806	0.82678	1.0:0.0:0.0:0.0	.	360	Q92541	RTF1_HUMAN	S	360	.	ENSP00000374280:N360S	N	+	2	0	RTF1	39550715	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.248000	0.74166	0.533000	0.62120	AAT	.	.		0.438	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138	
DUOXA1	90527	hgsc.bcm.edu	37	15	45411339	45411339	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:45411339C>T	ENST00000560572.1	-	6	1002	c.997G>A	c.(997-999)Gag>Aag	p.E333K	DUOXA1_ENST00000558422.1_Missense_Mutation_p.E288K|DUOXA1_ENST00000558996.1_Missense_Mutation_p.E288K|DUOXA1_ENST00000559014.1_Intron|DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000267803.4_Intron	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1	333					hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		GGGTGTGCCTCCTTACAGTAT	0.572																																					p.E333K		Atlas-SNP	.											.	DUOXA1	32	.	0			c.G997A						.						96.0	97.0	96.0					15																	45411339		2198	4298	6496	SO:0001583	missense	90527	exon6			GTGCCTCCTTACA	BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.997G>A	chr15.hg19:g.45411339C>T	ENSP00000454084:p.Glu333Lys	101.0	0.0		89.0	23.0	NM_001276266	Q8N6K9|Q96MI4	Missense_Mutation	SNP	ENST00000560572.1	hg19																																																																																				.	.		0.572	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565	
FBN1	2200	hgsc.bcm.edu	37	15	48829964	48829964	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:48829964T>A	ENST00000316623.5	-	7	1035	c.580A>T	c.(580-582)Atg>Ttg	p.M194L		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	194	TB 1.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CCCTGGCACATCTGGTTGCTG	0.498																																					p.M194L		Atlas-SNP	.											.	FBN1	310	.	0			c.A580T						.						76.0	77.0	77.0					15																	48829964		2197	4296	6493	SO:0001583	missense	2200	exon7			GGCACATCTGGTT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.580A>T	chr15.hg19:g.48829964T>A	ENSP00000325527:p.Met194Leu	71.0	0.0		72.0	20.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.358987	0.41801	.	.	ENSG00000166147	ENST00000316623;ENST00000544030;ENST00000537463	D;T	0.92446	-3.04;-0.07	5.44	5.44	0.79542	Matrix fibril-associated (3);TGF-beta binding (1);	0.037975	0.85682	D	0.000000	D	0.85940	0.5814	N	0.22421	0.69	0.80722	D	1	B	0.18166	0.026	B	0.25614	0.062	T	0.81123	-0.1076	10	0.10902	T	0.67	.	15.6649	0.77221	0.0:0.0:0.0:1.0	.	194	P35555	FBN1_HUMAN	L	194	ENSP00000325527:M194L;ENSP00000440294:M194L	ENSP00000325527:M194L	M	-	1	0	FBN1	46617256	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.097000	0.71452	2.281000	0.76405	0.533000	0.62120	ATG	.	.		0.498	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
LYSMD4	145748	hgsc.bcm.edu	37	15	100269392	100269392	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr15:100269392A>T	ENST00000409796.1	-	3	889	c.827T>A	c.(826-828)gTt>gAt	p.V276D	LYSMD4_ENST00000604213.1_Intron|LYSMD4_ENST00000545021.1_Missense_Mutation_p.V150D|LYSMD4_ENST00000344791.2_Missense_Mutation_p.V277D|LYSMD4_ENST00000332728.4_Missense_Mutation_p.V276D	NM_001284417.1|NM_001284418.1|NM_001284420.1	NP_001271346.1|NP_001271347.1|NP_001271349.1	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain containing 4	276						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)	10	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			TGGCACTGCAACTGCTAGTCT	0.527																																					p.V277D		Atlas-SNP	.											.	LYSMD4	21	.	0			c.T830A						.						82.0	83.0	83.0					15																	100269392		2203	4300	6503	SO:0001583	missense	145748	exon6			ACTGCAACTGCTA	BC041097	CCDS10381.1, CCDS66876.1, CCDS66877.1, CCDS73788.1	15q26.3	2005-10-24			ENSG00000183060	ENSG00000183060			26571	protein-coding gene	gene with protein product						12477932	Standard	NM_001284418		Approved	FLJ33008	uc002bvl.3	Q5XG99	OTTHUMG00000149853	ENST00000409796.1:c.827T>A	chr15.hg19:g.100269392A>T	ENSP00000386283:p.Val276Asp	181.0	0.0		138.0	56.0	NM_152449	A6NII6|A8K2N1|Q96LY7	Missense_Mutation	SNP	ENST00000409796.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.29	1.894802	0.33442	.	.	ENSG00000183060	ENST00000409796;ENST00000344791;ENST00000332728;ENST00000545021	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.96	0.872	0.19113	.	0.695791	0.13061	N	0.416876	T	0.14485	0.0350	L	0.36672	1.1	0.09310	N	1	P;P	0.35982	0.531;0.531	B;B	0.31686	0.134;0.071	T	0.25641	-1.0126	10	0.87932	D	0	-5.0315	0.7236	0.00944	0.4796:0.1703:0.1858:0.1642	.	277;276	Q5XG99-2;Q5XG99	.;LYSM4_HUMAN	D	276;277;276;150	ENSP00000386283:V276D;ENSP00000342840:V277D;ENSP00000333008:V276D;ENSP00000445357:V150D	ENSP00000333008:V276D	V	-	2	0	LYSMD4	98086915	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.071000	0.11505	0.192000	0.20272	0.528000	0.53228	GTT	.	.		0.527	LYSMD4-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335634.1	NM_152449	
TP53	7157	hgsc.bcm.edu	37	17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	rs28934571		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	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_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank	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	249.0	2.0		89.0	69.0	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	
MYH10	4628	hgsc.bcm.edu	37	17	8390877	8390877	+	Silent	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:8390877C>T	ENST00000269243.4	-	34	4965	c.4827G>A	c.(4825-4827)agG>agA	p.R1609R	MYH10_ENST00000379980.4_Silent_p.R1625R|MYH10_ENST00000396239.1_Silent_p.R1630R|MYH10_ENST00000360416.3_Silent_p.R1640R	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1609					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CCCGCTGTTTCCTCTCATCCT	0.542																																					p.R1640R		Atlas-SNP	.											.	MYH10	148	.	0			c.G4920A						.						211.0	214.0	213.0					17																	8390877		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon36			CTGTTTCCTCTCA	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.4827G>A	chr17.hg19:g.8390877C>T		58.0	0.0		41.0	29.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.		0.542	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
RHBDL3	162494	hgsc.bcm.edu	37	17	30616004	30616004	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:30616004C>T	ENST00000269051.4	+	4	502	c.488C>T	c.(487-489)cCc>cTc	p.P163L	RHBDL3_ENST00000538145.1_Missense_Mutation_p.P155L|RHBDL3_ENST00000536287.1_Missense_Mutation_p.P65L	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	163						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				TGCCCCCCACCCTGGTTCATG	0.612																																					p.P163L		Atlas-SNP	.											.	RHBDL3	49	.	0			c.C488T						.						58.0	55.0	56.0					17																	30616004		2203	4300	6503	SO:0001583	missense	162494	exon4			CCCCACCCTGGTT	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"""EF-hand domain containing"""	16502	protein-coding gene	gene with protein product			"""rhomboid, veinlet-like 4 (Drosophila)"""	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.488C>T	chr17.hg19:g.30616004C>T	ENSP00000269051:p.Pro163Leu	359.0	0.0		194.0	83.0	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	hg19	CCDS32613.1	.	.	.	.	.	.	.	.	.	.	C	32	5.187494	0.94923	.	.	ENSG00000141314	ENST00000431505;ENST00000269051;ENST00000538145;ENST00000536287	T;T;T;T	0.14640	2.49;2.49;2.49;2.49	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.13980	-1.0489	10	0.87932	D	0	-12.0137	20.4239	0.99064	0.0:1.0:0.0:0.0	.	163;155;163	E9PD28;Q495Y5;P58872	.;.;RHBL3_HUMAN	L	163;163;155;65	ENSP00000394849:P163L;ENSP00000269051:P163L;ENSP00000442092:P155L;ENSP00000466508:P65L	ENSP00000269051:P163L	P	+	2	0	RHBDL3	27640117	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.453000	0.80700	2.828000	0.97474	0.655000	0.94253	CCC	.	.		0.612	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328	
NKIRAS2	28511	hgsc.bcm.edu	37	17	40174597	40174597	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:40174597A>G	ENST00000307641.5	+	3	896	c.275A>G	c.(274-276)gAg>gGg	p.E92G	ZNF385C_ENST00000461831.1_5'Flank|NKIRAS2_ENST00000479407.1_Missense_Mutation_p.S60G|NKIRAS2_ENST00000393884.2_Missense_Mutation_p.E90G|NKIRAS2_ENST00000393885.4_Missense_Mutation_p.E92G|NKIRAS2_ENST00000462043.2_Intron|NKIRAS2_ENST00000449471.4_Intron|NKIRAS2_ENST00000316082.4_Missense_Mutation_p.E92G|NKIRAS2_ENST00000393881.3_Missense_Mutation_p.E92G|NKIRAS2_ENST00000393880.1_Missense_Mutation_p.E92G	NM_001001349.2	NP_001001349.1	Q9NYR9	KBRS2_HUMAN	NFKB inhibitor interacting Ras-like 2	92	Small GTPase-like.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	9		all_cancers(22;1.1e-05)|Breast(137;0.000143)|all_epithelial(22;0.000319)				GATAGCAGAGAGTCTTTTCAG	0.547																																					p.E92G		Atlas-SNP	.											.	NKIRAS2	15	.	0			c.A275G						.						81.0	73.0	76.0					17																	40174597		2203	4300	6503	SO:0001583	missense	28511	exon3			GCAGAGAGTCTTT	AF229840	CCDS11415.1, CCDS45679.1, CCDS45680.1	17q21.31	2014-05-09	2004-05-20		ENSG00000168256	ENSG00000168256			17898	protein-coding gene	gene with protein product		604497	"""NFKB inhibitor interacting Ras-like protein 2"""			10657303	Standard	NM_001001349		Approved	KBRAS2, DKFZP434N1526, kappaB-Ras2	uc002hys.3	Q9NYR9	OTTHUMG00000133503	ENST00000307641.5:c.275A>G	chr17.hg19:g.40174597A>G	ENSP00000303580:p.Glu92Gly	91.0	0.0		45.0	23.0	NM_001144927	A6NCZ5|B3KNN0|B4DNM3|Q6PK52|Q96KC7|Q9NSX1	Missense_Mutation	SNP	ENST00000307641.5	hg19	CCDS11415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.280799|4.280799	0.80692|0.80692	.|.	.|.	ENSG00000168256|ENSG00000168256	ENST00000307641;ENST00000393884;ENST00000393880;ENST00000393881;ENST00000393885;ENST00000316082|ENST00000449471	T;T;T;T;T;T|.	0.80994|.	-1.44;-1.44;-1.44;-1.44;-1.44;-0.4|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Small GTP-binding protein domain (1);|.	0.045277|.	0.85682|.	D|.	0.000000|.	T|T	0.53981|0.53981	0.1830|0.1830	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|B	0.53885|0.21381	0.963|0.055	P|B	0.55260|0.29942	0.772|0.109	T|T	0.48980|0.48980	-0.8986|-0.8986	9|6	0.54805|.	T|.	0.06|.	-12.6837|-12.6837	15.7679|15.7679	0.78141|0.78141	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	92|60	Q9NYR9|E9PAZ8	KBRS2_HUMAN|.	G|G	92;90;92;92;92;92|60	ENSP00000303580:E92G;ENSP00000377462:E90G;ENSP00000377458:E92G;ENSP00000377459:E92G;ENSP00000377463:E92G;ENSP00000312773:E92G|.	ENSP00000303580:E92G|.	E|S	+|+	2|1	0|0	NKIRAS2|NKIRAS2	37428123|37428123	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.339000|0.339000	0.28857|0.28857	9.339000|9.339000	0.96797|0.96797	2.194000|2.194000	0.70268|0.70268	0.477000|0.477000	0.44152|0.44152	GAG|AGT	.	.		0.547	NKIRAS2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257457.1	NM_017595	
CRHR1	1394	hgsc.bcm.edu	37	17	43861914	43861914	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:43861914G>T	ENST00000398285.3	+	1	4	c.4G>T	c.(4-6)Gga>Tga	p.G2*	CRHR1_ENST00000339069.5_Intron|CRHR1_ENST00000293493.7_Intron|RP11-105N13.4_ENST00000587305.1_RNA|CRHR1_ENST00000314537.5_Nonsense_Mutation_p.G2*|CRHR1_ENST00000577353.1_Nonsense_Mutation_p.G2*|CRHR1_ENST00000352855.5_Nonsense_Mutation_p.G2*	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	2					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCCGAGGATGGGAGGGCACCC	0.766																																					p.G2X	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.G4T						.						7.0	12.0	10.0					17																	43861914		1850	4016	5866	SO:0001587	stop_gained	1394	exon1			AGGATGGGAGGGC	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.4G>T	chr17.hg19:g.43861914G>T	ENSP00000381333:p.Gly2*	74.0	0.0		31.0	15.0	NM_001145148	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Nonsense_Mutation	SNP	ENST00000398285.3	hg19	CCDS45712.1	.	.	.	.	.	.	.	.	.	.	G	38	7.270165	0.98179	.	.	ENSG00000120088	ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	9.657	0.39932	0.0:0.0:1.0:0.0	.	.	.	.	X	2	.	ENSP00000326060:G2X	G	+	1	0	CRHR1	41217677	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	1.690000	0.37711	1.714000	0.51371	0.442000	0.29010	GGA	.	.		0.766	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
ITGA3	3675	hgsc.bcm.edu	37	17	48149396	48149396	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:48149396G>T	ENST00000320031.8	+	7	1336	c.1006G>T	c.(1006-1008)Gag>Tag	p.E336*	ITGA3_ENST00000007722.7_Nonsense_Mutation_p.E336*|ITGA3_ENST00000544892.1_Nonsense_Mutation_p.E111*	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	336					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						CGAGAGGAAAGAGGAAGTAGG	0.582																																					p.E336X		Atlas-SNP	.											.	ITGA3	128	.	0			c.G1006T						.						79.0	65.0	70.0					17																	48149396		2203	4300	6503	SO:0001587	stop_gained	3675	exon7			AGGAAAGAGGAAG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1006G>T	chr17.hg19:g.48149396G>T	ENSP00000315190:p.Glu336*	213.0	0.0		155.0	68.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Nonsense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	G	39	7.379660	0.98248	.	.	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	.	.	.	5.55	3.57	0.40892	.	0.196127	0.53938	D	0.000055	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	10.7526	0.46217	0.1567:0.0:0.8433:0.0	.	.	.	.	X	111;336;322;336	.	ENSP00000007722:E336X	E	+	1	0	ITGA3	45504395	0.897000	0.30589	0.874000	0.34290	0.389000	0.30415	1.705000	0.37867	1.351000	0.45789	0.563000	0.77884	GAG	.	.		0.582	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
MED13	9969	hgsc.bcm.edu	37	17	60024306	60024306	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:60024306C>G	ENST00000397786.2	-	29	6440	c.6364G>C	c.(6364-6366)Gac>Cac	p.D2122H		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2122					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGATTTGAGTCAAGTGGGTGG	0.398																																					p.D2122H		Atlas-SNP	.											.	MED13	181	.	0			c.G6364C						.						175.0	179.0	178.0					17																	60024306		1968	4164	6132	SO:0001583	missense	9969	exon29			TTGAGTCAAGTGG	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.6364G>C	chr17.hg19:g.60024306C>G	ENSP00000380888:p.Asp2122His	125.0	0.0		168.0	27.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.896684	0.91962	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.83506	-1.73	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.92525	0.7626	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93627	0.6953	10	0.87932	D	0	-9.3552	18.9301	0.92561	0.0:1.0:0.0:0.0	.	2122	Q9UHV7	MED13_HUMAN	H	2122;2121	ENSP00000380888:D2122H	ENSP00000262436:D2121H	D	-	1	0	MED13	57379088	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.429000	0.80309	2.464000	0.83262	0.467000	0.42956	GAC	.	.		0.398	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
USH1G	124590	hgsc.bcm.edu	37	17	72916210	72916210	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:72916210C>A	ENST00000319642.1	-	2	903	c.721G>T	c.(721-723)Gcc>Tcc	p.A241S		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	241					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)		HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					AGCGAGCGGGCGCTCTTGCGC	0.692																																					p.A241S		Atlas-SNP	.											.	USH1G	40	.	0			c.G721T						.						36.0	41.0	39.0					17																	72916210		2201	4279	6480	SO:0001583	missense	124590	exon2			AGCGGGCGCTCTT	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.721G>T	chr17.hg19:g.72916210C>A	ENSP00000320076:p.Ala241Ser	32.0	0.0		39.0	28.0	NM_173477	Q8N251	Missense_Mutation	SNP	ENST00000319642.1	hg19	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.302940	0.23736	.	.	ENSG00000182040	ENST00000319642	T	0.70045	-0.45	3.68	2.7	0.31948	.	0.154968	0.42172	D	0.000741	T	0.42765	0.1217	N	0.08118	0	0.25320	N	0.98913	B	0.09022	0.002	B	0.12156	0.007	T	0.22661	-1.0210	10	0.22109	T	0.4	-23.5737	11.8892	0.52620	0.0:0.9078:0.0:0.0922	.	241	Q495M9	USH1G_HUMAN	S	241	ENSP00000320076:A241S	ENSP00000320076:A241S	A	-	1	0	USH1G	70427805	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	4.718000	0.61930	2.075000	0.62263	0.485000	0.47835	GCC	.	.		0.692	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477	
LRRC45	201255	hgsc.bcm.edu	37	17	79988573	79988573	+	Missense_Mutation	SNP	G	G	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr17:79988573G>C	ENST00000306688.3	+	17	2247	c.1905G>C	c.(1903-1905)gaG>gaC	p.E635D	RAC3_ENST00000306897.4_5'Flank	NM_144999.2	NP_659436.1	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	635						centrosome (GO:0005813)				lung(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GGGAGGCGGAGATCGCCCGCA	0.701																																					p.E635D		Atlas-SNP	.											.	LRRC45	22	.	0			c.G1905C						.						8.0	11.0	10.0					17																	79988573		2130	4212	6342	SO:0001583	missense	201255	exon17			GGCGGAGATCGCC	BC014109	CCDS11797.1	17q25.3	2005-08-09				ENSG00000169683			28302	protein-coding gene	gene with protein product						12477932	Standard	NM_144999		Approved	MGC20806	uc002kde.3	Q96CN5		ENST00000306688.3:c.1905G>C	chr17.hg19:g.79988573G>C	ENSP00000306760:p.Glu635Asp	72.0	0.0		74.0	49.0	NM_144999		Missense_Mutation	SNP	ENST00000306688.3	hg19	CCDS11797.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.092972	0.56075	.	.	ENSG00000169683	ENST00000306688	T	0.45276	0.9	4.5	2.49	0.30216	.	0.070853	0.56097	D	0.000036	T	0.24160	0.0585	N	0.24115	0.695	0.38100	D	0.93724	B	0.17465	0.022	B	0.14578	0.011	T	0.08146	-1.0736	9	.	.	.	-20.4498	7.3647	0.26766	0.1596:0.1385:0.7019:0.0	.	635	Q96CN5	LRC45_HUMAN	D	635	ENSP00000306760:E635D	.	E	+	3	2	LRRC45	77581862	1.000000	0.71417	0.134000	0.22075	0.989000	0.77384	2.128000	0.42045	0.514000	0.28300	0.491000	0.48974	GAG	.	.		0.701	LRRC45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442058.1	NM_144999	
DCC	1630	hgsc.bcm.edu	37	18	50923774	50923774	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr18:50923774A>T	ENST00000442544.2	+	18	3401	c.2785A>T	c.(2785-2787)Agt>Tgt	p.S929C	DCC_ENST00000581580.1_Missense_Mutation_p.S564C|DCC_ENST00000412726.1_Missense_Mutation_p.S757C	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	929	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CAGAAGGTCCAGTACTTGGAG	0.438																																					p.S929C		Atlas-SNP	.											.	DCC	360	.	0			c.A2785T						.						123.0	105.0	111.0					18																	50923774		2203	4300	6503	SO:0001583	missense	1630	exon18			AGGTCCAGTACTT	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.2785A>T	chr18.hg19:g.50923774A>T	ENSP00000389140:p.Ser929Cys	87.0	0.0		73.0	20.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766314	0.49574	.	.	ENSG00000187323	ENST00000442544;ENST00000412726	T;T	0.60672	0.17;0.17	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.80449	0.4625	M	0.89785	3.06	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.84390	0.0554	10	0.66056	D	0.02	.	15.1301	0.72517	1.0:0.0:0.0:0.0	.	757;757;929	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	C	929;757	ENSP00000389140:S929C;ENSP00000397322:S757C	ENSP00000397322:S757C	S	+	1	0	DCC	49177772	1.000000	0.71417	0.958000	0.39756	0.971000	0.66376	9.220000	0.95180	2.213000	0.71641	0.528000	0.53228	AGT	.	.		0.438	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
SMARCA4	6597	hgsc.bcm.edu	37	19	11096863	11096863	+	Splice_Site	SNP	A	A	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:11096863A>T	ENST00000429416.3	+	5	636		c.e5-1		SMARCA4_ENST00000541122.2_Splice_Site|SMARCA4_ENST00000413806.3_Splice_Site|SMARCA4_ENST00000344626.4_Splice_Site|SMARCA4_ENST00000358026.2_Splice_Site|SMARCA4_ENST00000590574.1_Splice_Site|SMARCA4_ENST00000450717.3_Splice_Site|SMARCA4_ENST00000589677.1_Splice_Site|SMARCA4_ENST00000444061.3_Splice_Site	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4						aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTTTCTCTGCAGGTTACCCCT	0.607			"""F, N, Mis"""		NSCLC																																.		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.356-2A>T						.						42.0	42.0	42.0					19																	11096863		2203	4299	6502	SO:0001630	splice_region_variant	6597	exon4			CTCTGCAGGTTAC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.356-1A>T	chr19.hg19:g.11096863A>T		87.0	0.0		34.0	25.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Splice_Site	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	17.06	3.292810	0.60086	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.	.	.	4.43	4.43	0.53597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8185	0.57679	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMARCA4	10957863	1.000000	0.71417	0.992000	0.48379	0.711000	0.40976	4.620000	0.61226	1.868000	0.54150	0.379000	0.24179	.	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	Intron
PLD3	23646	hgsc.bcm.edu	37	19	40872522	40872522	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:40872522G>T	ENST00000409587.1	+	4	430	c.33G>T	c.(31-33)aaG>aaT	p.K11N	PLD3_ENST00000409419.1_Missense_Mutation_p.K11N|PLD3_ENST00000356508.5_Missense_Mutation_p.K11N|PLD3_ENST00000409281.1_Missense_Mutation_p.K11N|PLD3_ENST00000409735.4_Missense_Mutation_p.K11N			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	11					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CCCAGCTGAAGGTGCCTGCAG	0.632																																					p.K11N		Atlas-SNP	.											.	PLD3	71	.	0			c.G33T						.						53.0	60.0	57.0					19																	40872522		2203	4300	6503	SO:0001583	missense	23646	exon4			GCTGAAGGTGCCT	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.33G>T	chr19.hg19:g.40872522G>T	ENSP00000387050:p.Lys11Asn	69.0	0.0		44.0	25.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300667	0.60195	.	.	ENSG00000105223	ENST00000392032;ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281;ENST00000359274	T;T;T;T;T;T;T	0.53206	0.63;0.78;0.78;0.78;0.78;0.78;0.67	4.39	3.36	0.38483	.	0.415050	0.25484	N	0.030344	T	0.49881	0.1583	N	0.22421	0.69	0.44711	D	0.997706	D;D	0.89917	1.0;0.981	D;D	0.83275	0.996;0.95	T	0.48175	-0.9058	10	0.48119	T	0.1	-12.0868	8.3596	0.32351	0.1049:0.0:0.8951:0.0	.	11;11	B4DEL6;Q8IV08	.;PLD3_HUMAN	N	11	ENSP00000375886:K11N;ENSP00000386293:K11N;ENSP00000387050:K11N;ENSP00000348901:K11N;ENSP00000386938:K11N;ENSP00000387022:K11N;ENSP00000352220:K11N	ENSP00000348901:K11N	K	+	3	2	PLD3	45564362	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.007000	0.40883	1.441000	0.47550	0.655000	0.94253	AAG	.	.		0.632	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
SRRM5	100170229	hgsc.bcm.edu	37	19	44116304	44116304	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:44116304A>G	ENST00000607544.1	+	3	353	c.31A>G	c.(31-33)Agt>Ggt	p.S11G	SRRM5_ENST00000417606.1_Missense_Mutation_p.S11G|SRRM5_ENST00000526798.1_Missense_Mutation_p.S26G|ZNF428_ENST00000300811.3_Intron			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	11	Ser-rich.									endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						TTCAAAGCCCAGTATGTCTCT	0.537																																					p.S11G		Atlas-SNP	.											.	SRRM5	38	.	0			c.A31G						.						238.0	214.0	221.0					19																	44116304		692	1591	2283	SO:0001583	missense	100170229	exon1			AAGCCCAGTATGT	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.31A>G	chr19.hg19:g.44116304A>G	ENSP00000476253:p.Ser11Gly	288.0	0.0		189.0	67.0	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	hg19	CCDS46095.1	.	.	.	.	.	.	.	.	.	.	A	9.428	1.084667	0.20309	.	.	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.87	0.33	0.15929	.	.	.	.	.	T	0.29321	0.0730	N	0.19112	0.55	0.80722	D	1	B	0.23058	0.079	B	0.27796	0.083	T	0.06862	-1.0803	8	0.09843	T	0.71	.	4.9412	0.13967	0.5902:0.1516:0.2582:0.0	.	11	B3KS81	SRRM5_HUMAN	G	26;11	.	ENSP00000414512:S11G	S	+	1	0	SRRM5	48808144	0.175000	0.23083	0.680000	0.29994	0.038000	0.13279	-0.191000	0.09601	0.059000	0.16252	-0.250000	0.11733	AGT	.	.		0.537	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
ZNF223	7766	hgsc.bcm.edu	37	19	44571032	44571032	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:44571032A>G	ENST00000434772.3	+	5	1306	c.1051A>G	c.(1051-1053)Aag>Gag	p.K351E	ZNF223_ENST00000591793.1_Missense_Mutation_p.K461E	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				AGAATGTGGGAAGAGCTTCAG	0.438																																					p.K351E		Atlas-SNP	.											.	ZNF223	61	.	0			c.A1051G						.						101.0	104.0	103.0					19																	44571032		2203	4300	6503	SO:0001583	missense	7766	exon5			TGTGGGAAGAGCT	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.1051A>G	chr19.hg19:g.44571032A>G	ENSP00000401947:p.Lys351Glu	124.0	0.0		96.0	36.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Missense_Mutation	SNP	ENST00000434772.3	hg19	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.945120	0.92593	.	.	ENSG00000178386	ENST00000434772	T	0.27104	1.69	2.46	2.46	0.29980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49474	0.1559	M	0.82517	2.595	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.53107	-0.8485	9	0.66056	D	0.02	.	9.5423	0.39260	1.0:0.0:0.0:0.0	.	351	Q9UK11	ZN223_HUMAN	E	351	ENSP00000401947:K351E	ENSP00000401947:K351E	K	+	1	0	ZNF223	49262872	0.951000	0.32395	0.041000	0.18516	0.972000	0.66771	2.519000	0.45546	1.118000	0.41863	0.260000	0.18958	AAG	.	.		0.438	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
VASP	7408	hgsc.bcm.edu	37	19	46021343	46021343	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:46021343G>T	ENST00000245932.6	+	3	690	c.334G>T	c.(334-336)Gcg>Tcg	p.A112S	VASP_ENST00000586619.1_3'UTR	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	112	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		TGCCCTAGAGGCGTTGGAAGG	0.642																																					p.A112S		Atlas-SNP	.											.	VASP	26	.	0			c.G334T						.						24.0	26.0	25.0					19																	46021343		2203	4299	6502	SO:0001583	missense	7408	exon3			CTAGAGGCGTTGG		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552		ENST00000245932.6:c.334G>T	chr19.hg19:g.46021343G>T	ENSP00000245932:p.Ala112Ser	148.0	0.0		68.0	26.0	NM_003370	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.537725	0.65085	.	.	ENSG00000125753	ENST00000245932	T	0.42513	0.97	4.89	3.84	0.44239	EVH1 (1);Pleckstrin homology-type (1);	0.064889	0.64402	D	0.000011	T	0.21387	0.0515	N	0.08118	0	0.45284	D	0.998281	B	0.10296	0.003	B	0.19946	0.027	T	0.05566	-1.0877	10	0.08179	T	0.78	-12.0642	12.5819	0.56394	0.0:0.0:0.8323:0.1677	.	112	P50552	VASP_HUMAN	S	112	ENSP00000245932:A112S	ENSP00000245932:A112S	A	+	1	0	VASP	50713183	0.985000	0.35326	0.984000	0.44739	0.900000	0.52787	2.737000	0.47393	1.173000	0.42796	-0.181000	0.13052	GCG	.	.		0.642	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1		
PPP2R1A	5518	hgsc.bcm.edu	37	19	52714742	52714742	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:52714742G>A	ENST00000322088.6	+	4	558	c.500G>A	c.(499-501)cGa>cAa	p.R167Q	PPP2R1A_ENST00000462990.1_5'UTR|PPP2R1A_ENST00000444322.2_Missense_Mutation_p.R112Q|PPP2R1A_ENST00000473455.2_3'UTR	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	167	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.|SV40 small T antigen binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GCGGAACTTCGACAGTGAGTC	0.617			Mis		clear cell ovarian carcinoma																																p.R167Q		Atlas-SNP	.		Dom?	yes		19	19q13.41	5518	"""protein phosphatase 2, regulatory subunit A, alpha"""		E	.	PPP2R1A	187	.	0			c.G500A						.						52.0	49.0	50.0					19																	52714742		2203	4300	6503	SO:0001583	missense	5518	exon4			AACTTCGACAGTG		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9302	protein-coding gene	gene with protein product	"""protein phosphatase 2A, regulatory subunit A, alpha isoform"", ""protein phosphatase 2, 65kDa regulatory subunit A"""	605983	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"""				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.500G>A	chr19.hg19:g.52714742G>A	ENSP00000324804:p.Arg167Gln	36.0	0.0		43.0	16.0	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	hg19	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	G	34	5.307079	0.95629	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.06687	3.27;3.27	4.58	4.58	0.56647	Armadillo-like helical (1);Armadillo-type fold (1);	0.123358	0.33553	N	0.004795	T	0.39759	0.1090	H	0.94620	3.56	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.916;0.991;0.991	T	0.55016	-0.8206	10	0.87932	D	0	-1.3519	15.2851	0.73822	0.0:0.0:1.0:0.0	.	112;167;167	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	Q	157;87;167;112	ENSP00000324804:R167Q;ENSP00000415067:R112Q	ENSP00000324804:R167Q	R	+	2	0	PPP2R1A	57406554	1.000000	0.71417	0.979000	0.43373	0.989000	0.77384	8.532000	0.90613	2.547000	0.85894	0.655000	0.94253	CGA	.	.		0.617	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225	
ZNF534	147658	hgsc.bcm.edu	37	19	52941617	52941617	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:52941617G>T	ENST00000332323.6	+	4	1004	c.943G>T	c.(943-945)Gaa>Taa	p.E315*	ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000433050.1_Nonsense_Mutation_p.E302*	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						CAAATGTAGTGAATGTGGCAA	0.398																																					p.E315X		Atlas-SNP	.											.	ZNF534	105	.	0			c.G943T						.						70.0	61.0	64.0					19																	52941617		1568	3582	5150	SO:0001587	stop_gained	147658	exon4			TGTAGTGAATGTG	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"""Zinc fingers, C2H2-type"", ""-"""	26337	protein-coding gene	gene with protein product			"""KRAB domain only 3"""	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.943G>T	chr19.hg19:g.52941617G>T	ENSP00000327538:p.Glu315*	122.0	0.0		87.0	28.0	NM_001143939	Q76KX9	Nonsense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384284	0.42308	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	.	.	.	1.82	0.468	0.16732	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	9.1116	0.36732	0.0:0.2272:0.7728:0.0	.	.	.	.	X	315;302;314	.	ENSP00000327538:E315X	E	+	1	0	ZNF534	57633429	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-0.781000	0.04648	0.983000	0.38602	0.467000	0.42956	GAA	.	.		0.398	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512	
SOGA1	140710	hgsc.bcm.edu	37	20	35437004	35437004	+	Missense_Mutation	SNP	A	A	G			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:35437004A>G	ENST00000357779.3	-	8	2338	c.2012T>C	c.(2011-2013)tTc>tCc	p.F671S	SOGA1_ENST00000456801.2_Missense_Mutation_p.F512S|SOGA1_ENST00000279034.6_Missense_Mutation_p.F671S|SOGA1_ENST00000237536.4_Missense_Mutation_p.F909S			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	671					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GAGCAGCAGGAAGTTGTGCTT	0.572											OREG0025909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F909S		Atlas-SNP	.											.	SOGA1	136	.	0			c.T2726C						.						49.0	54.0	52.0					20																	35437004		2009	4168	6177	SO:0001583	missense	140710	exon8			AGCAGGAAGTTGT	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.2012T>C	chr20.hg19:g.35437004A>G	ENSP00000350424:p.Phe671Ser	69.0	0.0	855	51.0	20.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	A	24.6	4.546492	0.86022	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.28	5.28	0.74379	.	0.054564	0.85682	D	0.000000	T	0.33323	0.0859	L	0.40543	1.245	0.37256	D	0.906773	P	0.44734	0.842	B	0.37650	0.255	T	0.32428	-0.9907	10	0.29301	T	0.29	-34.8934	14.3227	0.66496	1.0:0.0:0.0:0.0	.	671	O94964-4	.	S	909;671;512;671	ENSP00000237536:F909S;ENSP00000279034:F671S;ENSP00000413886:F512S;ENSP00000350424:F671S	ENSP00000237536:F909S	F	-	2	0	KIAA0889	34870418	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.064000	0.64338	2.216000	0.71823	0.533000	0.62120	TTC	.	.		0.572	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	
WFDC3	140686	hgsc.bcm.edu	37	20	44403077	44403077	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:44403077G>A	ENST00000243938.4	-	7	769	c.686C>T	c.(685-687)cCg>cTg	p.P229L	WFDC3_ENST00000372632.2_Missense_Mutation_p.P135L|WFDC3_ENST00000372630.2_Missense_Mutation_p.P92L|WFDC3_ENST00000481847.1_5'UTR	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	229						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P229L(1)		endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				CTAGGGCACCGGGATCTctgc	0.498																																					p.P229L		Atlas-SNP	.											WFDC3,NS,carcinoma,0,1	WFDC3	18	.	1	Substitution - Missense(1)	endometrium(1)	c.C686T						.						118.0	108.0	111.0					20																	44403077		2203	4300	6503	SO:0001583	missense	140686	exon7			GGCACCGGGATCT	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"""WAP four-disulfide core domain containing"""	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.686C>T	chr20.hg19:g.44403077G>A	ENSP00000243938:p.Pro229Leu	70.0	0.0		53.0	12.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Missense_Mutation	SNP	ENST00000243938.4	hg19	CCDS33478.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.45|16.45	3.127840|3.127840	0.56721|0.56721	.|.	.|.	ENSG00000124116|ENSG00000124116	ENST00000243938;ENST00000372630;ENST00000372632|ENST00000337205	T;T;T|.	0.21734|.	1.99;1.99;2.0|.	3.39|3.39	-2.53|-2.53	0.06326|0.06326	.|.	1.482020|.	0.04855|.	N|.	0.443060|.	T|T	0.19644|0.19644	0.0472|0.0472	N|N	0.22421|0.22421	0.69|0.69	0.18873|0.18873	N|N	0.999988|0.999988	B|.	0.12013|.	0.005|.	B|.	0.08055|.	0.003|.	T|T	0.26849|0.26849	-1.0091|-1.0091	10|5	0.59425|.	D|.	0.04|.	0.1205|0.1205	3.6363|3.6363	0.08150|0.08150	0.504:0.0:0.3045:0.1915|0.504:0.0:0.3045:0.1915	.|.	229|.	Q8IUB2|.	WFDC3_HUMAN|.	L|W	229;92;135|223	ENSP00000243938:P229L;ENSP00000361713:P92L;ENSP00000361715:P135L|.	ENSP00000243938:P229L|.	P|R	-|-	2|1	0|2	WFDC3|WFDC3	43836484|43836484	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.767000|0.767000	0.43475|0.43475	-1.356000|-1.356000	0.02609|0.02609	-0.521000|-0.521000	0.06426|0.06426	0.650000|0.650000	0.86243|0.86243	CCG|CGG	.	.		0.498	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1		
PREX1	57580	hgsc.bcm.edu	37	20	47342858	47342858	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:47342858T>A	ENST00000371941.3	-	5	612	c.590A>T	c.(589-591)cAg>cTg	p.Q197L	PREX1_ENST00000396220.1_Missense_Mutation_p.Q197L	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	197	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCAGATCCTCTGGATCGGAGA	0.483																																					p.Q197L		Atlas-SNP	.											.	PREX1	441	.	0			c.A590T						.						95.0	80.0	85.0					20																	47342858		2203	4300	6503	SO:0001583	missense	57580	exon5			ATCCTCTGGATCG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.590A>T	chr20.hg19:g.47342858T>A	ENSP00000361009:p.Gln197Leu	187.0	0.0		128.0	57.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	t	31	5.078331	0.94000	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.77358	-1.09;-1.09	5.51	5.51	0.81932	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.52532	U	0.000077	D	0.91700	0.7376	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94123	0.7381	10	0.87932	D	0	.	14.906	0.70718	0.0:0.0:0.0:1.0	.	197	Q8TCU6	PREX1_HUMAN	L	197	ENSP00000361009:Q197L;ENSP00000379522:Q197L	ENSP00000361009:Q197L	Q	-	2	0	PREX1	46776265	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.292000	0.78731	2.215000	0.71742	0.529000	0.55759	CAG	.	.		0.483	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872915	51872915	+	Missense_Mutation	SNP	G	G	T	rs201353411		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:51872915G>T	ENST00000371497.5	+	2	3805	c.2918G>T	c.(2917-2919)cGg>cTg	p.R973L	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R970L|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R970L	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	973					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			GAGATCTCCCGGGTATCGTCG	0.488																																					p.R973L		Atlas-SNP	.											TSHZ2,NS,carcinoma,0,1	TSHZ2	209	.	0			c.G2918T						.						75.0	69.0	71.0					20																	51872915		2203	4300	6503	SO:0001583	missense	128553	exon2			TCTCCCGGGTATC	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2918G>T	chr20.hg19:g.51872915G>T	ENSP00000360552:p.Arg973Leu	130.0	1.0		126.0	43.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857789	0.71834	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.15718	2.4;2.4	5.7	5.7	0.88788	.	0.098653	0.64402	D	0.000002	T	0.25419	0.0618	N	0.16478	0.41	0.53005	D	0.999962	D	0.63046	0.992	P	0.57846	0.828	T	0.03829	-1.1000	10	0.87932	D	0	0.2578	19.8272	0.96622	0.0:0.0:1.0:0.0	.	973	Q9NRE2	TSH2_HUMAN	L	973;970;499	ENSP00000360552:R973L;ENSP00000333114:R970L	ENSP00000333114:R970L	R	+	2	0	TSHZ2	51306322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.860000	0.55995	2.685000	0.91497	0.643000	0.83706	CGG	.	.		0.488	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
NPEPL1	79716	hgsc.bcm.edu	37	20	57288476	57288476	+	Splice_Site	SNP	G	G	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr20:57288476G>A	ENST00000356091.6	+	9	1290	c.1002G>A	c.(1000-1002)aaG>aaA	p.K334K	RP11-261P9.4_ENST00000530479.1_RNA|NPEPL1_ENST00000525967.1_Splice_Site_p.K306K|NPEPL1_ENST00000525817.1_Splice_Site_p.K286K|STX16-NPEPL1_ENST00000530122.1_3'UTR	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	334						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CATGCCCCAGGACGGTGGAAA	0.607																																					p.K334K		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G1002A						.						34.0	39.0	37.0					20																	57288476		2061	4181	6242	SO:0001630	splice_region_variant	79716	exon9			CCCCAGGACGGTG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1002-1G>A	chr20.hg19:g.57288476G>A		159.0	0.0		125.0	53.0	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.		0.607	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	Silent
ADAMTS1	9510	hgsc.bcm.edu	37	21	28217002	28217002	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr21:28217002G>T	ENST00000284984.3	-	1	726	c.272C>A	c.(271-273)cCc>cAc	p.P91H		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	91					heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		GCTGCTGTCGGGCCGCAGCTC	0.692											OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P91H		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.C272A						.						10.0	12.0	11.0					21																	28217002		2190	4278	6468	SO:0001583	missense	9510	exon1			CTGTCGGGCCGCA	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.272C>A	chr21.hg19:g.28217002G>T	ENSP00000284984:p.Pro91His	82.0	0.0	800	56.0	15.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658283	0.47467	.	.	ENSG00000154734	ENST00000284984	T	0.07800	3.16	4.06	3.18	0.36537	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.11793	0.0287	L	0.56769	1.78	0.58432	D	0.999999	B	0.18166	0.026	B	0.29176	0.099	T	0.04320	-1.0960	9	0.49607	T	0.09	.	11.7641	0.51920	0.0862:0.0:0.9138:0.0	.	91	Q9UHI8	ATS1_HUMAN	H	91	ENSP00000284984:P91H	ENSP00000284984:P91H	P	-	2	0	ADAMTS1	27138873	1.000000	0.71417	0.912000	0.35992	0.236000	0.25371	5.919000	0.70005	0.925000	0.37094	0.555000	0.69702	CCC	.	.		0.692	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
SYNJ1	8867	hgsc.bcm.edu	37	21	34100328	34100328	+	5'Flank	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr21:34100328C>A	ENST00000322229.7	-	0	0				SYNJ1_ENST00000382499.2_Missense_Mutation_p.W8C|PAXBP1-AS1_ENST00000455170.1_RNA|SYNJ1_ENST00000382491.3_5'Flank|SYNJ1_ENST00000433931.2_Missense_Mutation_p.W8C|PAXBP1-AS1_ENST00000458479.1_RNA|SYNJ1_ENST00000357345.3_5'Flank|PAXBP1-AS1_ENST00000440052.1_RNA			O43426	SYNJ1_HUMAN	synaptojanin 1						cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						CACTTCCGCTCCAGCAGGCCC	0.741											OREG0003584|OREG0003585	type=REGULATORY REGION|Gene=AK056384|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=SYNJ1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.W8C		Atlas-SNP	.											.	SYNJ1	253	.	0			c.G24T						.						3.0	6.0	5.0					21																	34100328		616	1499	2115	SO:0001631	upstream_gene_variant	8867	exon1			TCCGCTCCAGCAG	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926		chr21.hg19:g.34100328C>A	Exception_encountered	12.0	0.0	845	11.0	10.0	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332360	0.81801	.	.	ENSG00000159082	ENST00000382499;ENST00000433931	D;D	0.93488	-3.23;-2.39	4.7	3.74	0.42951	.	.	.	.	.	D	0.85022	0.5602	N	0.08118	0	0.80722	D	1	B	0.27732	0.187	B	0.27170	0.077	D	0.83919	0.0300	9	0.56958	D	0.05	.	11.9699	0.53058	0.173:0.827:0.0:0.0	.	8	C9JFZ1	.	C	8	ENSP00000371939:W8C;ENSP00000409667:W8C	ENSP00000371939:W8C	W	-	3	0	SYNJ1	33022199	0.950000	0.32346	0.997000	0.53966	0.886000	0.51366	1.664000	0.37439	2.322000	0.78497	0.650000	0.86243	TGG	.	.		0.741	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
DIP2A	23181	hgsc.bcm.edu	37	21	47952072	47952072	+	Silent	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr21:47952072G>T	ENST00000417564.2	+	10	1248	c.1227G>T	c.(1225-1227)gtG>gtT	p.V409V	DIP2A_ENST00000435722.3_Silent_p.V409V|DIP2A_ENST00000457905.3_Silent_p.V409V|DIP2A_ENST00000400274.1_Silent_p.V405V|DIP2A_ENST00000318711.7_Silent_p.V410V|DIP2A_ENST00000427143.2_Silent_p.V345V|DIP2A_ENST00000466639.1_Silent_p.V366V			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	409					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GTGACCCTGTGATGTTCATGG	0.418																																					p.V409V		Atlas-SNP	.											.	DIP2A	332	.	0			c.G1227T						.						178.0	172.0	174.0					21																	47952072		1954	4146	6100	SO:0001819	synonymous_variant	23181	exon10			CCCTGTGATGTTC	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.1227G>T	chr21.hg19:g.47952072G>T		153.0	0.0		124.0	76.0	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.		0.418	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
NEFH	4744	hgsc.bcm.edu	37	22	29886676	29886676	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr22:29886676C>A	ENST00000310624.6	+	4	3080	c.3047C>A	c.(3046-3048)gCc>gAc	p.A1016D		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	1022	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GAAGACAAGGCCGCCAAGGGG	0.498																																					p.A1016D		Atlas-SNP	.											.	NEFH	178	.	0			c.C3047A						.						26.0	27.0	27.0					22																	29886676		2201	4297	6498	SO:0001583	missense	4744	exon4			ACAAGGCCGCCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.3047C>A	chr22.hg19:g.29886676C>A	ENSP00000311997:p.Ala1016Asp	80.0	0.0		65.0	39.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	hg19	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.327626	0.24080	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.89810	-2.57	5.94	4.91	0.64330	.	0.123818	0.37095	N	0.002242	D	0.87525	0.6199	L	0.57536	1.79	0.36312	D	0.857701	D	0.54397	0.966	P	0.44860	0.462	D	0.90671	0.4598	10	0.87932	D	0	.	11.6908	0.51514	0.1396:0.7262:0.1342:0.0	.	1022	P12036	NFH_HUMAN	D	967;1016	ENSP00000311997:A1016D	ENSP00000311997:A1016D	A	+	2	0	NEFH	28216676	0.098000	0.21812	0.939000	0.37840	0.185000	0.23345	1.202000	0.32271	1.504000	0.48704	0.561000	0.74099	GCC	.	.		0.498	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964608	37964608	+	Missense_Mutation	SNP	G	G	T	rs568152455		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr22:37964608G>T	ENST00000249014.4	+	3	1377	c.957G>T	c.(955-957)agG>agT	p.R319S		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	319					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					CCCTCGGCAGGCACTGGGGAG	0.701																																					p.R319S		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.G957T						.						11.0	13.0	12.0					22																	37964608		2192	4285	6477	SO:0001583	missense	11135	exon3			CGGCAGGCACTGG	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.957G>T	chr22.hg19:g.37964608G>T	ENSP00000249014:p.Arg319Ser	132.0	0.0		71.0	27.0	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	hg19	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151370	0.94645	.	.	ENSG00000128283	ENST00000249014	T	0.34072	1.38	4.81	4.81	0.61882	.	2.233790	0.01933	N	0.041365	T	0.32585	0.0834	L	0.27053	0.805	0.36720	D	0.881119	P	0.38922	0.651	B	0.30943	0.122	T	0.36696	-0.9737	10	0.40728	T	0.16	-25.9918	17.2474	0.87032	0.0:0.0:1.0:0.0	.	319	Q00587	BORG5_HUMAN	S	319	ENSP00000249014:R319S	ENSP00000249014:R319S	R	+	3	2	CDC42EP1	36294554	1.000000	0.71417	0.989000	0.46669	0.335000	0.28730	3.665000	0.54532	2.375000	0.81037	0.561000	0.74099	AGG	.	.		0.701	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
TAF1	6872	hgsc.bcm.edu	37	X	70674056	70674056	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chrX:70674056T>C	ENST00000373790.4	+	33	4838	c.4787T>C	c.(4786-4788)aTt>aCt	p.I1596T	TAF1_ENST00000423759.1_Missense_Mutation_p.I1617T|TAF1_ENST00000449580.1_Missense_Mutation_p.I1596T|TAF1_ENST00000276072.3_Missense_Mutation_p.I1617T|TAF1_ENST00000461764.1_3'UTR	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1596	Interaction with ASF1A and ASF1B.|Protein kinase 2.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GCCCAGGAGATTGTGAACGTC	0.403																																					p.I1617T		Atlas-SNP	.											.	TAF1	439	.	0			c.T4850C						.						85.0	73.0	77.0					X																	70674056		2203	4300	6503	SO:0001583	missense	6872	exon33			AGGAGATTGTGAA		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.4787T>C	chrX.hg19:g.70674056T>C	ENSP00000362895:p.Ile1596Thr	104.0	0.0		78.0	66.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.877669	0.72294	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000276072	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	4.84	4.84	0.62591	Bromodomain (3);	0.000000	0.85682	D	0.000000	T	0.63224	0.2493	M	0.77712	2.385	0.80722	D	1	D;D;D;D	0.67145	0.988;0.994;0.978;0.996	P;D;P;P	0.69307	0.882;0.963;0.818;0.871	T	0.68522	-0.5386	10	0.87932	D	0	.	12.6958	0.57003	0.0:0.0:0.0:1.0	.	250;1596;1596;1617	A5CVC9;P21675-4;P21675;P21675-2	.;.;TAF1_HUMAN;.	T	1596;1596;1617;302;1617	ENSP00000362895:I1596T;ENSP00000389000:I1596T;ENSP00000406549:I1617T;ENSP00000276072:I1617T	ENSP00000276072:I1617T	I	+	2	0	TAF1	70590781	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.636000	0.74299	1.789000	0.52484	0.345000	0.21793	ATT	.	.		0.403	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
USP26	83844	hgsc.bcm.edu	37	X	132159790	132159790	+	Missense_Mutation	SNP	C	C	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chrX:132159790C>A	ENST00000511190.1	-	6	2928	c.2459G>T	c.(2458-2460)gGa>gTa	p.G820V	USP26_ENST00000370832.1_Missense_Mutation_p.G820V|USP26_ENST00000406273.1_Missense_Mutation_p.G820V	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	820	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GGTATGATCTCCCTTATCATC	0.383																																					p.G820V	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.G2459T						.						179.0	161.0	167.0					X																	132159790		2203	4300	6503	SO:0001583	missense	83844	exon1			TGATCTCCCTTAT	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2459G>T	chrX.hg19:g.132159790C>A	ENSP00000423390:p.Gly820Val	16.0	0.0		52.0	11.0	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	hg19	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.623327	0.28889	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.30182	1.54;1.54;1.54	3.75	-5.55	0.02536	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	3.009010	0.01261	N	0.009165	T	0.42630	0.1211	L	0.46157	1.445	0.09310	N	1	D	0.59767	0.986	P	0.62089	0.898	T	0.55173	-0.8182	10	0.62326	D	0.03	2.8848	7.9187	0.29833	0.0:0.1744:0.1333:0.6923	.	820	Q9BXU7	UBP26_HUMAN	V	820	ENSP00000359869:G820V;ENSP00000423390:G820V;ENSP00000384360:G820V	ENSP00000359869:G820V	G	-	2	0	USP26	131987456	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.215000	0.01222	-1.639000	0.01527	-0.503000	0.04515	GGA	.	.		0.383	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
USP9Y	8287	hgsc.bcm.edu	37	Y	14951877	14951877	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chrY:14951877G>T	ENST00000338981.3	+	36	6370	c.5425G>T	c.(5425-5427)Gaa>Taa	p.E1809*	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	1809	USP.				BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CTGGGAAAGAGAATGTGCAAT	0.388																																					p.E1809X		Atlas-SNP	.											.	USP9Y	49	.	0			c.G5425T						.						54.0	50.0	51.0					Y																	14951877		599	1932	2531	SO:0001587	stop_gained	8287	exon36			GAAAGAGAATGTG	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"""Ubiquitin-specific peptidases"""	12633	protein-coding gene	gene with protein product	"""fat facets-like homolog (Drosophila)"""	400005	"""ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"""			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.5425G>T	chrY.hg19:g.14951877G>T	ENSP00000342812:p.Glu1809*	82.0	0.0		35.0	28.0	NM_004654	O14601	Nonsense_Mutation	SNP	ENST00000338981.3	hg19	CCDS14781.1																																																																																			.	.		0.388	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654	
ST5	6764	hgsc.bcm.edu	37	11	8752447	8752447	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr11:8752447delG	ENST00000534127.1	-	6	775	c.390delC	c.(388-390)gccfs	p.A130fs	ST5_ENST00000526757.1_Intron|ST5_ENST00000530438.1_Intron|ST5_ENST00000357665.1_Frame_Shift_Del_p.A130fs|ST5_ENST00000313726.6_Frame_Shift_Del_p.A130fs	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	130					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GGGGGAGGCAGGCAGCGACCC	0.667																																					p.C131fs		Atlas-INDEL	.											.	ST5	85	.	0			c.391delT						.						46.0	54.0	51.0					11																	8752447		2201	4296	6497	SO:0001589	frameshift_variant	6764	exon3			.	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.390delC	chr11.hg19:g.8752447delG	ENSP00000433528:p.Ala130fs	47.0	0.0		22.0	12.0	NM_213618	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Frame_Shift_Del	DEL	ENST00000534127.1	hg19	CCDS7791.1																																																																																			.	.		0.667	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
COL15A1	1306	hgsc.bcm.edu	37	9	101798606	101798607	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr9:101798606_101798607insT	ENST00000375001.3	+	21	2760_2761	c.2337_2338insT	c.(2338-2340)atgfs	p.M780fs		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	780	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				GAGAAAGGGGGATGGATGGAGC	0.54																																					p.G779fs		Atlas-INDEL	.											.	COL15A1	211	.	0			c.2337_2338insT						.																																			SO:0001589	frameshift_variant	1306	exon21			.	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	Exception_encountered	chr9.hg19:g.101798606_101798607insT	ENSP00000364140:p.Met780fs	96.0	0.0		49.0	11.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Frame_Shift_Ins	INS	ENST00000375001.3	hg19	CCDS35081.1																																																																																			.	.		0.540	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
RGPD3	653489	hgsc.bcm.edu	37	2	107051593	107051593	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:107051593delC	ENST00000409886.3	-	13	1911	c.1824delG	c.(1822-1824)aagfs	p.K609fs	RGPD3_ENST00000304514.7_Frame_Shift_Del_p.K609fs	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	609					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GCAAAACTTTCTTCCAATAAT	0.323																																					p.K609fs		Atlas-INDEL	.											.	RGPD3	316	.	0			c.1825delA						.																																			SO:0001589	frameshift_variant	653489	exon13			.		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.1824delG	chr2.hg19:g.107051593delC	ENSP00000386588:p.Lys609fs	602.0	0.0		479.0	82.0	NM_001144013	B8ZZM4	Frame_Shift_Del	DEL	ENST00000409886.3	hg19	CCDS46379.1																																																																																			.	.		0.323	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
ALB	213	hgsc.bcm.edu	37	4	74272392	74272393	+	Frame_Shift_Ins	INS	-	-	ATCA	rs560085213		TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr4:74272392_74272393insATCA	ENST00000295897.4	+	3	273_274	c.184_185insATCA	c.(184-186)gatfs	p.-62fs	ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_5'UTR|ALB_ENST00000509063.1_Frame_Shift_Ins_p.-62fs|ALB_ENST00000401494.3_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCCATTTGAAGATCATGTAAAA	0.322																																					p.D62fs		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.184_185insATCA						.																																			SO:0001589	frameshift_variant	213	exon3			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.185_188dupATCA	chr4.hg19:g.74272393_74272396dupATCA	ENSP00000295897:p.Asp62fs	71.0	0.0		45.0	29.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.322	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	
RANBP2	5903	hgsc.bcm.edu	37	2	109369517	109369517	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr2:109369517delA	ENST00000283195.6	+	13	1945	c.1819delA	c.(1819-1821)aagfs	p.K608fs		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	608					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TCATTATTGGAAGAAAGTTTT	0.323																																					p.W606X		Atlas-INDEL	.											.	RANBP2	488	.	0			c.1818delG						.						18.0	19.0	19.0					2																	109369517		1806	3961	5767	SO:0001589	frameshift_variant	5903	exon13			.	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1819delA	chr2.hg19:g.109369517delA	ENSP00000283195:p.Lys608fs	641.0	0.0		511.0	114.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Frame_Shift_Del	DEL	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.		0.323	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
KCNJ4	3761	hgsc.bcm.edu	37	22	38823369	38823377	+	In_Frame_Del	DEL	ACACCAGGA	ACACCAGGA	-			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	ACACCAGGA	ACACCAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr22:38823369_38823377delACACCAGGA	ENST00000303592.3	-	2	1019_1027	c.761_769delTCCTGGTGT	c.(760-771)ttcctggtgtcg>tcg	p.FLV254del	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	254					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					ATGATGGGCGACACCAGGAAGATGCGGTC	0.603																																					p.254_257del		Atlas-Indel,Pindel	.											.	KCNJ4	74	.	0			c.762_770del						.																																			SO:0001651	inframe_deletion	3761	exon2			.	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.761_769delTCCTGGTGT	chr22.hg19:g.38823369_38823377delACACCAGGA	ENSP00000306497:p.Phe254_Val256del	182.0	0.0		145.0	28.0	NM_004981	Q14D44	In_Frame_Del	DEL	ENST00000303592.3	hg19	CCDS13971.1																																																																																			.	.		0.603	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981	
AXIN1	8312	hgsc.bcm.edu	37	16	348096	348097	+	Frame_Shift_Ins	INS	-	-	A			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr16:348096_348097insA	ENST00000262320.3	-	6	1780_1781	c.1409_1410insT	c.(1408-1410)atcfs	p.I470fs	AXIN1_ENST00000354866.3_Frame_Shift_Ins_p.I470fs|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	470	Interaction with CTNNB1. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GCTCGTCCAGGATGCTCTCAGG	0.688											OREG0003699	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.I470fs		Atlas-Indel,Pindel	.											.	AXIN1	290	.	0			c.1410_1411insT						.																																			SO:0001589	frameshift_variant	8312	exon6			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1410dupT	chr16.hg19:g.348097_348097dupA	ENSP00000262320:p.Ile470fs	67.0	0.0	587	21.0	14.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Ins	INS	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.688	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41807519	41807519	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CC-A5UE-01A-11D-A28X-10	TCGA-CC-A5UE-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	02ae91b2-04c4-42aa-a17e-acc1cd567538	94ab9c19-5161-421e-8816-59e46a6af947	g.chr19:41807519delC	ENST00000392006.3	+	11	1770	c.1597delC	c.(1597-1599)cccfs	p.P533fs	HNRNPUL1_ENST00000602130.1_Frame_Shift_Del_p.P533fs|HNRNPUL1_ENST00000595018.1_Frame_Shift_Del_p.P433fs|HNRNPUL1_ENST00000352456.3_Frame_Shift_Del_p.P433fs|HNRNPUL1_ENST00000378215.4_Frame_Shift_Del_p.P419fs|HNRNPUL1_ENST00000593587.1_Frame_Shift_Del_p.P433fs|HNRNPUL1_ENST00000263367.3_Frame_Shift_Del_p.P444fs	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	533	Necessary for interaction with BRD7 and transcriptional activation.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TGTAATTTGTCCCACTGACGA	0.448																																					p.C532fs		Pindel	.											.	HNRNPUL1	73	.	0			c.1596delT						.						149.0	132.0	138.0					19																	41807519		2203	4300	6503	SO:0001589	frameshift_variant	11100	exon11			.	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1597delC	chr19.hg19:g.41807519delC	ENSP00000375863:p.Pro533fs	103.0	0.0		67.0	28.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Frame_Shift_Del	DEL	ENST00000392006.3	hg19	CCDS12576.1																																																																																			.	.		0.448	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
