#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
SLC35E2	9906	hgsc.bcm.edu	37	1	1670432	1670432	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:1670432T>A	ENST00000246421.4	-	3	802	c.387A>T	c.(385-387)ttA>ttT	p.L129F	SLC35E2_ENST00000355439.2_Missense_Mutation_p.L129F|SLC35E2_ENST00000400924.1_Missense_Mutation_p.L129F|RP1-283E3.8_ENST00000598846.1_RNA	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	129						integral component of membrane (GO:0016021)				endometrium(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGTGCTGATATAAACAGCAAG	0.537																																					p.L129F		Atlas-SNP	.											SLC35E2,NS,carcinoma,0,1	SLC35E2	13	.	0			c.A387T						PASS	.						108.0	140.0	129.0					1																	1670432		2203	4298	6501	SO:0001583	missense	9906	exon3			CTGATATAAACAG	AB007916	CCDS33.1, CCDS55560.1	1p36.33	2013-05-22			ENSG00000215790	ENSG00000215790		"""Solute carriers"""	20863	protein-coding gene	gene with protein product							Standard	NM_182838		Approved	KIAA0447	uc001aia.2	P0CK97	OTTHUMG00000000823	ENST00000246421.4:c.387A>T	chr1.hg19:g.1670432T>A	ENSP00000246421:p.Leu129Phe	1349.0	0.0	.		790.0	101.0	.	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Missense_Mutation	SNP	ENST00000246421.4	hg19	CCDS33.1	.	.	.	.	.	.	.	.	.	.	t	18.64	3.666694	0.67814	.	.	ENSG00000215790	ENST00000355439;ENST00000400924;ENST00000246421	D;D;D	0.95447	-3.71;-3.71;-3.71	2.89	-3.2	0.05156	Drug/metabolite transporter (1);	0.000000	0.56097	U	0.000040	D	0.94932	0.8361	M	0.67953	2.075	0.22954	N	0.998514	D;D	0.57899	0.957;0.981	P;P	0.54889	0.727;0.763	D	0.91334	0.5092	10	0.49607	T	0.09	-21.6831	11.2951	0.49274	0.0:0.8127:0.0:0.1873	.	129;129	P0CK97;P0CK97-2	S35E2_HUMAN;.	F	129	ENSP00000347614:L129F;ENSP00000383714:L129F;ENSP00000246421:L129F	ENSP00000246421:L129F	L	-	3	2	SLC35E2	1660292	0.925000	0.31364	0.949000	0.38748	0.955000	0.61496	0.050000	0.14120	-0.786000	0.04516	0.433000	0.28618	TTA	.	T|1.000;|0.000	.	alt		0.537	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733	
ICMT	23463	hgsc.bcm.edu	37	1	6285207	6285207	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:6285207T>A	ENST00000343813.5	-	5	816	c.788A>T	c.(787-789)tAc>tTc	p.Y263F	ICMT_ENST00000495791.1_5'Flank	NM_012405.3	NP_036537.1	O60725	ICMT_HUMAN	isoprenylcysteine carboxyl methyltransferase	263					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|positive regulation of cell proliferation (GO:0008284)|protein targeting to membrane (GO:0006612)|regulation of Ras protein signal transduction (GO:0046578)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cAMP response element binding protein binding (GO:0008140)|protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity (GO:0004671)			NS(1)|endometrium(2)	3	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		ATACTCCAGGTACTCCTCTCC	0.562																																					p.Y263F		Atlas-SNP	.											.	ICMT	13	.	0			c.A788T						PASS	.						99.0	106.0	104.0					1																	6285207		2203	4300	6503	SO:0001583	missense	23463	exon5			TCCAGGTACTCCT	AF064084	CCDS61.1	1p36	2010-04-29			ENSG00000116237	ENSG00000116237	2.1.1.100		5350	protein-coding gene	gene with protein product	"""protein-S-isoprenylcysteine O-methyltransferase"""	605851				9614111, 10441503	Standard	XM_005263437		Approved	PCCMT, HSTE14, PPMT	uc001amk.3	O60725	OTTHUMG00000001254	ENST00000343813.5:c.788A>T	chr1.hg19:g.6285207T>A	ENSP00000343552:p.Tyr263Phe	61.0	0.0	.		41.0	17.0	.	NM_012405	Q6FHT0	Missense_Mutation	SNP	ENST00000343813.5	hg19	CCDS61.1	.	.	.	.	.	.	.	.	.	.	T	33	5.239596	0.95240	.	.	ENSG00000116237	ENST00000343813;ENST00000535068	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.84056	0.5388	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86757	0.1964	9	0.72032	D	0.01	.	15.482	0.75534	0.0:0.0:0.0:1.0	.	263	O60725	ICMT_HUMAN	F	263;167	.	ENSP00000343552:Y263F	Y	-	2	0	ICMT	6207794	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.438000	0.80431	2.246000	0.74042	0.533000	0.62120	TAC	.	.	.	none		0.562	ICMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003681.1	NM_012405	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808387	18808387	+	Silent	SNP	C	C	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:18808387C>A	ENST00000400664.1	+	1	964	c.912C>A	c.(910-912)ggC>ggA	p.G304G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	304						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TCTTCCAGGGCAGGCTGGCTC	0.632																																					p.G304G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C912A						PASS	.						48.0	46.0	47.0					1																	18808387		2203	4300	6503	SO:0001819	synonymous_variant	127707	exon1			CCAGGGCAGGCTG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.912C>A	chr1.hg19:g.18808387C>A		121.0	0.0	.		61.0	28.0	.	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	hg19	CCDS185.2																																																																																			.	.	.	none		0.632	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
LEPRE1	64175	hgsc.bcm.edu	37	1	43224941	43224941	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:43224941C>T	ENST00000296388.5	-	3	790	c.739G>A	c.(739-741)Gaa>Aaa	p.E247K	LEPRE1_ENST00000236040.4_Missense_Mutation_p.E247K|LEPRE1_ENST00000397054.3_Missense_Mutation_p.E247K			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	247					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TAGGGCCCTTCGCAGAGGGCA	0.577																																					p.E247K		Atlas-SNP	.											.	LEPRE1	130	.	0			c.G739A						PASS	.						112.0	102.0	106.0					1																	43224941		2203	4300	6503	SO:0001583	missense	64175	exon3			GCCCTTCGCAGAG	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.739G>A	chr1.hg19:g.43224941C>T	ENSP00000296388:p.Glu247Lys	199.0	0.0	.		121.0	7.0	.	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.	.	.	.	.	.	.	.	.	.	C	36	5.747510	0.96882	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027;ENST00000372526	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.85410	0.5690	M	0.89715	3.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.87957	0.2727	10	0.87932	D	0	-23.3075	17.3244	0.87243	0.0:1.0:0.0:0.0	.	247;112;247	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	K	247;247;247;112;204	ENSP00000380245:E247K;ENSP00000236040:E247K;ENSP00000296388:E247K;ENSP00000361604:E204K	ENSP00000236040:E247K	E	-	1	0	LEPRE1	42997528	1.000000	0.71417	0.995000	0.50966	0.867000	0.49689	7.298000	0.78815	2.682000	0.91365	0.563000	0.77884	GAA	.	.	.	none		0.577	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
BCAR3	8412	hgsc.bcm.edu	37	1	94048486	94048486	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:94048486G>C	ENST00000370244.1	-	9	1346	c.1058C>G	c.(1057-1059)tCg>tGg	p.S353W	BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370247.3_Missense_Mutation_p.S262W|BCAR3_ENST00000260502.6_Missense_Mutation_p.S353W|BCAR3_ENST00000539242.1_Missense_Mutation_p.S29W|BCAR3_ENST00000370243.1_Missense_Mutation_p.S353W	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	353					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GTCCACACCCGAGGACTGAGG	0.567																																					p.S353W		Atlas-SNP	.											.	BCAR3	62	.	0			c.C1058G						PASS	.						35.0	37.0	36.0					1																	94048486		2199	4296	6495	SO:0001583	missense	8412	exon7			ACACCCGAGGACT	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"""SH2 domain containing"""	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.1058C>G	chr1.hg19:g.94048486G>C	ENSP00000359264:p.Ser353Trp	22.0	0.0	.		11.0	5.0	.	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	hg19	CCDS745.1	.	.	.	.	.	.	.	.	.	.	G	7.432	0.638822	0.14386	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243;ENST00000539242	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	5.16	2.18	0.27775	.	0.617466	0.17140	N	0.185513	T	0.19565	0.0470	N	0.19112	0.55	0.09310	N	1	P;P;D	0.54772	0.923;0.95;0.968	B;P;B	0.49085	0.346;0.6;0.346	T	0.03514	-1.1029	10	0.72032	D	0.01	-11.4446	5.4129	0.16358	0.1485:0.0:0.5671:0.2844	.	133;353;262	B3KNL6;O75815;Q5TEW3	.;BCAR3_HUMAN;.	W	262;353;353;353;29	ENSP00000359267:S262W;ENSP00000260502:S353W;ENSP00000359264:S353W;ENSP00000359263:S353W;ENSP00000441343:S29W	ENSP00000260502:S353W	S	-	2	0	BCAR3	93821074	0.175000	0.23083	0.004000	0.12327	0.179000	0.23085	1.152000	0.31663	0.657000	0.30906	0.655000	0.94253	TCG	.	.	.	none		0.567	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987953	154987953	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:154987953T>A	ENST00000368426.3	+	3	954	c.817T>A	c.(817-819)Tat>Aat	p.Y273N	ZBTB7B_ENST00000292176.2_Missense_Mutation_p.Y273N|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.Y307N|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.Y273N	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	273					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CTACGAACCCTATGAGGGTGA	0.672																																					p.Y307N		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.T919A						PASS	.						35.0	36.0	35.0					1																	154987953		2201	4300	6501	SO:0001583	missense	51043	exon4			GAACCCTATGAGG	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.817T>A	chr1.hg19:g.154987953T>A	ENSP00000357411:p.Tyr273Asn	154.0	0.0	.		102.0	47.0	.	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	hg19	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.494967	0.26774	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.09350	3.02;3.02;2.99;3.02	4.3	4.3	0.51218	.	0.830066	0.10696	N	0.644657	T	0.02848	0.0085	N	0.24115	0.695	0.18873	N	0.999987	B;B;B	0.22604	0.021;0.072;0.021	B;B;B	0.19666	0.026;0.018;0.026	T	0.40232	-0.9574	10	0.30078	T	0.28	.	11.4451	0.50118	0.0:0.0:0.0:1.0	.	273;273;307	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	N	273;273;307;273	ENSP00000438647:Y273N;ENSP00000357411:Y273N;ENSP00000406286:Y307N;ENSP00000292176:Y273N	ENSP00000292176:Y273N	Y	+	1	0	ZBTB7B	153254577	0.000000	0.05858	0.824000	0.32777	0.815000	0.46073	-0.170000	0.09897	1.808000	0.52836	0.379000	0.24179	TAT	.	.	.	none		0.672	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
RC3H1	149041	hgsc.bcm.edu	37	1	173921219	173921219	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:173921219A>G	ENST00000367696.2	-	14	2779	c.2428T>C	c.(2428-2430)Tac>Cac	p.Y810H	RC3H1_ENST00000258349.4_Missense_Mutation_p.Y810H|RC3H1_ENST00000367694.2_Missense_Mutation_p.Y810H			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	810					B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						CAGGGAGAGTATTGGCTATAA	0.393																																					p.Y810H		Atlas-SNP	.											.	RC3H1	110	.	0			c.T2428C						PASS	.						141.0	126.0	131.0					1																	173921219		2203	4300	6503	SO:0001583	missense	149041	exon13			GAGAGTATTGGCT	AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	29434	protein-coding gene	gene with protein product	"""KIAA2025 protein"""	609424	"""ring finger and CCCH-type zinc finger domains 1"""			15917799	Standard	XM_005244918		Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.2428T>C	chr1.hg19:g.173921219A>G	ENSP00000356669:p.Tyr810His	70.0	0.0	.		45.0	19.0	.	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	hg19	CCDS30940.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209630	0.79240	.	.	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	T;T;T	0.61158	0.14;0.14;0.13	5.92	4.77	0.60923	.	0.162470	0.56097	D	0.000025	T	0.62134	0.2403	L	0.55481	1.735	0.53005	D	0.999963	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.85130	0.994;0.994;0.997;0.994	T	0.67252	-0.5717	10	0.66056	D	0.02	-8.6265	12.306	0.54902	0.873:0.0:0.0:0.127	.	810;810;810;810	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	H	810	ENSP00000356669:Y810H;ENSP00000258349:Y810H;ENSP00000356667:Y810H	ENSP00000258349:Y810H	Y	-	1	0	RC3H1	172187842	1.000000	0.71417	0.728000	0.30774	0.978000	0.69477	8.962000	0.93254	1.011000	0.39340	0.477000	0.44152	TAC	.	.	.	none		0.393	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071	
LRRN2	10446	hgsc.bcm.edu	37	1	204587083	204587083	+	Missense_Mutation	SNP	G	G	A	rs535832685		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:204587083G>A	ENST00000367175.1	-	1	4250	c.2038C>T	c.(2038-2040)Cgg>Tgg	p.R680W	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367176.3_Missense_Mutation_p.R680W|LRRN2_ENST00000367177.3_Missense_Mutation_p.R680W|LRRN2_ENST00000496057.1_5'Flank			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	680					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GACACAACCCGGACAGAAGGG	0.632													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14704	0.0		0.0	False		,,,				2504	0.0				p.R680W		Atlas-SNP	.											.	LRRN2	81	.	0			c.C2038T						PASS	.						70.0	77.0	75.0					1																	204587083		2203	4300	6503	SO:0001583	missense	10446	exon3			CAACCCGGACAGA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.2038C>T	chr1.hg19:g.204587083G>A	ENSP00000356143:p.Arg680Trp	203.0	0.0	.		116.0	44.0	.	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390987	0.62066	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.62364	0.03;0.03;0.03	4.94	4.03	0.46877	.	0.240456	0.21555	N	0.072663	T	0.41119	0.1145	N	0.08118	0	0.43390	D	0.9955	B	0.19073	0.033	B	0.15484	0.013	T	0.35822	-0.9773	10	0.72032	D	0.01	.	10.4288	0.44395	0.0917:0.0:0.9083:0.0	.	680	O75325	LRRN2_HUMAN	W	680	ENSP00000356144:R680W;ENSP00000356145:R680W;ENSP00000356143:R680W	ENSP00000356143:R680W	R	-	1	2	LRRN2	202853706	0.731000	0.28111	0.820000	0.32676	0.525000	0.34531	4.080000	0.57620	1.316000	0.45131	0.561000	0.74099	CGG	.	.	.	none		0.632	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
OBSCN	84033	hgsc.bcm.edu	37	1	228509045	228509045	+	Splice_Site	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:228509045G>A	ENST00000422127.1	+	55	14547	c.14503G>A	c.(14503-14505)Gtt>Att	p.V4835I	OBSCN_ENST00000570156.2_Splice_Site_p.V5792I|OBSCN_ENST00000366709.4_Splice_Site_p.V1954I|OBSCN_ENST00000366707.4_Splice_Site_p.V2469I|OBSCN_ENST00000284548.11_Splice_Site_p.V4835I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4835					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGCCCACAGGTTGGGGCCCC	0.632																																					p.V5792I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G17374A						PASS	.						17.0	18.0	18.0					1																	228509045		1977	4147	6124	SO:0001630	splice_region_variant	84033	exon66			CCACAGGTTGGGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.14503-1G>A	chr1.hg19:g.228509045G>A		83.0	0.0	.		36.0	10.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.565516	0.45694	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.62364	0.42;0.03;0.06;0.56	4.68	1.25	0.21368	.	1.586350	0.03728	N	0.252908	T	0.47002	0.1422	N	0.19112	0.55	0.19300	N	0.999973	B;B	0.06786	0.001;0.001	B;B	0.10450	0.002;0.005	T	0.23154	-1.0196	9	.	.	.	.	7.4965	0.27492	0.0967:0.4639:0.4394:0.0	.	4835;4835	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	4835;4835;2469;1954	ENSP00000284548:V4835I;ENSP00000409493:V4835I;ENSP00000355668:V2469I;ENSP00000355670:V1954I	.	V	+	1	0	OBSCN	226575668	0.647000	0.27304	0.073000	0.20177	0.062000	0.15995	0.764000	0.26532	0.057000	0.16193	0.563000	0.77884	GTT	.	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	Missense_Mutation
SPTBN1	6711	hgsc.bcm.edu	37	2	54873419	54873419	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:54873419T>G	ENST00000356805.4	+	23	4954	c.4673T>G	c.(4672-4674)cTc>cGc	p.L1558R	SPTBN1_ENST00000333896.5_Missense_Mutation_p.L1545R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1558					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGCAGCAGCCTCAGCGCTGAG	0.597																																					p.L1558R		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T4673G						PASS	.						59.0	64.0	62.0					2																	54873419		2203	4300	6503	SO:0001583	missense	6711	exon23			GCAGCCTCAGCGC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.4673T>G	chr2.hg19:g.54873419T>G	ENSP00000349259:p.Leu1558Arg	188.0	0.0	.		105.0	6.0	.	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	T	8.805	0.933832	0.18206	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.49432	0.78;0.78	5.8	0.634	0.17718	.	0.327233	0.33496	N	0.004851	T	0.35128	0.0921	L	0.42245	1.32	0.26816	N	0.968888	B;B	0.17465	0.0;0.022	B;B	0.24006	0.0;0.05	T	0.28235	-1.0050	10	0.15952	T	0.53	.	10.3045	0.43672	0.0:0.379:0.0:0.621	.	1545;1558	Q01082-3;Q01082	.;SPTB2_HUMAN	R	1558;1545	ENSP00000349259:L1558R;ENSP00000334156:L1545R	ENSP00000334156:L1545R	L	+	2	0	SPTBN1	54726923	0.578000	0.26717	0.502000	0.27614	0.792000	0.44763	1.002000	0.29796	-0.101000	0.12219	-0.366000	0.07423	CTC	.	.	.	none		0.597	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
POLR1A	25885	hgsc.bcm.edu	37	2	86297161	86297161	+	Nonsense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:86297161G>A	ENST00000263857.6	-	13	2224	c.1846C>T	c.(1846-1848)Cag>Tag	p.Q616*	POLR1A_ENST00000409681.1_Nonsense_Mutation_p.Q616*			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	616					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						AGGTACTGCTGATCAGTGCAG	0.577																																					p.Q616X		Atlas-SNP	.											.	POLR1A	137	.	0			c.C1846T						PASS	.						36.0	39.0	38.0					2																	86297161		2051	4179	6230	SO:0001587	stop_gained	25885	exon13			ACTGCTGATCAGT	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1846C>T	chr2.hg19:g.86297161G>A	ENSP00000263857:p.Gln616*	27.0	0.0	.		21.0	9.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Nonsense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	G	42	9.370452	0.99151	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	.	.	.	5.3	4.4	0.53042	.	0.172789	0.51477	D	0.000098	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-22.8516	8.3408	0.32243	0.0:0.3834:0.4874:0.1292	.	.	.	.	X	616	.	ENSP00000263857:Q616X	Q	-	1	0	POLR1A	86150672	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	4.626000	0.61269	2.479000	0.83701	0.655000	0.94253	CAG	.	.	.	none		0.577	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
CHMP3	51652	hgsc.bcm.edu	37	2	86769412	86769412	+	Missense_Mutation	SNP	T	T	C	rs540948421		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:86769412T>C	ENST00000263856.4	-	2	197	c.69A>G	c.(67-69)atA>atG	p.I23M	CHMP3_ENST00000439940.2_Missense_Mutation_p.I52M|CHMP3_ENST00000409225.2_Intron|CHMP3_ENST00000409727.1_Missense_Mutation_p.I23M|RNF103-CHMP3_ENST00000604011.1_Missense_Mutation_p.I52M	NM_001193517.1|NM_016079.3	NP_001180446.1|NP_057163.1	Q9Y3E7	CHMP3_HUMAN	charged multivesicular body protein 3	23	Intramolecular interaction with C- terminus.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)											TTTCCTTTCTTATCTTCAATG	0.323																																					p.I52M		Atlas-SNP	.											.	.	.	.	0			c.A156G						PASS	.						119.0	113.0	115.0					2																	86769412		2203	4298	6501	SO:0001583	missense	100526767	exon4			CTTTCTTATCTTC	AF219226	CCDS33236.1, CCDS42707.1, CCDS54375.1	2p11.2	2011-09-21	2011-09-21	2011-09-21	ENSG00000115561	ENSG00000115561		"""Charged multivesicular body proteins"""	29865	protein-coding gene	gene with protein product		610052	"""vacuolar protein sorting 24 (yeast)"", ""vacuolar protein sorting 24 homolog (S. cerevisiae)"""	VPS24		11549700, 12878588	Standard	NM_016079		Approved	NEDF, CGI-149		Q9Y3E7	OTTHUMG00000153189	ENST00000263856.4:c.69A>G	chr2.hg19:g.86769412T>C	ENSP00000263856:p.Ile23Met	227.0	0.0	.		142.0	64.0	.	NM_001198954	A8K3W0|B4DG34|B8ZZM0|B8ZZX5|Q3ZTS9|Q53S71|Q53SU5|Q9NZ51	Missense_Mutation	SNP	ENST00000263856.4	hg19	CCDS33236.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.397581	0.42512	.	.	ENSG00000115561;ENSG00000115561;ENSG00000115561;ENSG00000249884	ENST00000263856;ENST00000409727;ENST00000439940;ENST00000440757	T;D;T;T	0.89196	-0.73;-2.48;-0.73;-0.73	5.39	-0.595	0.11660	.	0.045218	0.85682	D	0.000000	D	0.87180	0.6113	L	0.56280	1.765	0.51767	D	0.999938	B;P;B	0.43701	0.159;0.815;0.064	B;P;B	0.46389	0.091;0.515;0.065	D	0.84790	0.0778	10	0.51188	T	0.08	-27.6725	12.7264	0.57173	0.0:0.0:0.5733:0.4267	.	52;23;23	Q9Y3E7-3;Q9Y3E7-4;Q9Y3E7	.;.;CHMP3_HUMAN	M	23;23;52;130	ENSP00000263856:I23M;ENSP00000387045:I23M;ENSP00000405575:I52M;ENSP00000392995:I130M	ENSP00000392995:I130M	I	-	3	3	VPS24;RNF103-VPS24	86622923	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	0.593000	0.23999	0.049000	0.15920	0.533000	0.62120	ATA	.	.	.	none		0.323	CHMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330015.2	NM_016079	
MERTK	10461	hgsc.bcm.edu	37	2	112686995	112686995	+	Silent	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:112686995T>G	ENST00000295408.4	+	2	617	c.360T>G	c.(358-360)ccT>ccG	p.P120P	RN7SL297P_ENST00000483161.2_RNA|MERTK_ENST00000421804.2_Silent_p.P120P|MERTK_ENST00000409780.1_Intron			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	120	Ig-like C2-type 1.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						TCAGTGTACCTAATATATACC	0.393																																					p.P120P		Atlas-SNP	.											.	MERTK	112	.	0			c.T360G						PASS	.						116.0	107.0	110.0					2																	112686995		2203	4300	6503	SO:0001819	synonymous_variant	10461	exon2			TGTACCTAATATA	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.360T>G	chr2.hg19:g.112686995T>G		188.0	0.0	.		116.0	41.0	.	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	hg19	CCDS2094.1																																																																																			.	.	.	none		0.393	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
AMER3	205147	hgsc.bcm.edu	37	2	131519874	131519874	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:131519874G>A	ENST00000423981.1	+	2	339	c.229G>A	c.(229-231)Gga>Aga	p.G77R	AMER3_ENST00000321420.4_Missense_Mutation_p.G77R	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	77					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.G77R(1)									CCCCAAAGGGGGACCCGCAGC	0.647																																					p.G77R		Atlas-SNP	.											FAM123C,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.G229A						PASS	.						18.0	27.0	24.0					2																	131519874		2197	4299	6496	SO:0001583	missense	205147	exon2			AAAGGGGGACCCG	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.229G>A	chr2.hg19:g.131519874G>A	ENSP00000392700:p.Gly77Arg	140.0	0.0	.		80.0	4.0	.	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	hg19	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689763	0.48097	.	.	ENSG00000178171	ENST00000321420;ENST00000431758;ENST00000458606;ENST00000423981	T;T	0.47528	0.84;0.84	4.89	1.02	0.19986	.	0.000000	0.47455	D	0.000240	T	0.38374	0.1038	L	0.29908	0.895	0.09310	N	1	P	0.48162	0.906	P	0.49752	0.621	T	0.17961	-1.0352	10	0.40728	T	0.16	.	6.6426	0.22917	0.3965:0.0:0.6035:0.0	.	77	Q8N944	F123C_HUMAN	R	77	ENSP00000314914:G77R;ENSP00000392700:G77R	ENSP00000314914:G77R	G	+	1	0	FAM123C	131236344	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.726000	0.25984	0.213000	0.20722	-0.291000	0.09656	GGA	.	.	.	none		0.647	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
SCN9A	6335	hgsc.bcm.edu	37	2	167094694	167094694	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:167094694G>T	ENST00000409435.1	-	19	3710	c.3711C>A	c.(3709-3711)ttC>ttA	p.F1237L	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.F1238L|SCN9A_ENST00000409672.1_Missense_Mutation_p.F1226L|SCN9A_ENST00000375387.4_Missense_Mutation_p.F1238L			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1237					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTCCAGAATGAAGATGTAAG	0.333																																					p.F1226L		Atlas-SNP	.											.	SCN9A	296	.	0			c.C3678A						PASS	.						49.0	50.0	50.0					2																	167094694		2158	4288	6446	SO:0001583	missense	6335	exon20			CAGAATGAAGATG	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.3711C>A	chr2.hg19:g.167094694G>T	ENSP00000386330:p.Phe1237Leu	301.0	0.0	.		136.0	51.0	.	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.084556	0.76642	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3	5.25	3.44	0.39384	.	0.000000	0.64402	D	0.000007	D	0.99423	0.9796	H	0.97732	4.065	0.50467	D	0.999872	D	0.69078	0.997	D	0.71870	0.975	D	0.98781	1.0732	10	0.87932	D	0	.	8.1778	0.31292	0.3304:0.0:0.6696:0.0	.	1226	E7EUN6	.	L	1226;1238;1238;1237	ENSP00000386306:F1226L;ENSP00000364536:F1238L;ENSP00000304748:F1238L;ENSP00000386330:F1237L	ENSP00000304748:F1238L	F	-	3	2	SCN9A	166802940	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.781000	0.38644	0.599000	0.29845	0.655000	0.94253	TTC	.	.	.	none		0.333	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
ATP5G3	518	hgsc.bcm.edu	37	2	176043935	176043935	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:176043935A>G	ENST00000284727.4	-	4	3188	c.164T>C	c.(163-165)cTa>cCa	p.L55P	ATP5G3_ENST00000392541.3_Missense_Mutation_p.L55P|ATP5G3_ENST00000409194.1_Missense_Mutation_p.L55P|Y_RNA_ENST00000363251.1_RNA	NM_001002258.4|NM_001689.4	NP_001002258.1|NP_001680.1	P48201	AT5G3_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9)	55					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.147)			CCTTTGGATTAGCTGAGACAC	0.448																																					p.L55P	GBM(30;387 605 18606 28805 47989)	Atlas-SNP	.											.	ATP5G3	11	.	0			c.T164C						PASS	.						90.0	83.0	85.0					2																	176043935		2203	4300	6503	SO:0001583	missense	518	exon4			TGGATTAGCTGAG	BC106881	CCDS2263.1	2q31.1	2012-10-12	2010-06-11		ENSG00000154518	ENSG00000154518		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	843	protein-coding gene	gene with protein product		602736	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9) isoform 3"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)"""			7698763	Standard	NM_001002258		Approved		uc002ujz.4	P48201	OTTHUMG00000132425	ENST00000284727.4:c.164T>C	chr2.hg19:g.176043935A>G	ENSP00000284727:p.Leu55Pro	69.0	0.0	.		52.0	21.0	.	NM_001190329	B2R4Z0|D3DPF0|Q4ZFX7	Missense_Mutation	SNP	ENST00000284727.4	hg19	CCDS2263.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.886484	0.51908	.	.	ENSG00000154518	ENST00000284727;ENST00000409194;ENST00000392541	T;T;T	0.25250	1.81;1.81;1.81	5.79	4.63	0.57726	.	0.131340	0.51477	D	0.000083	T	0.20333	0.0489	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.02042	-1.1224	10	0.45353	T	0.12	-13.4739	13.1837	0.59670	0.8669:0.1331:0.0:0.0	.	55	P48201	AT5G3_HUMAN	P	55	ENSP00000284727:L55P;ENSP00000387317:L55P;ENSP00000376324:L55P	ENSP00000284727:L55P	L	-	2	0	ATP5G3	175752181	0.999000	0.42202	0.999000	0.59377	0.993000	0.82548	2.870000	0.48451	1.010000	0.39314	0.455000	0.32223	CTA	.	.	.	none		0.448	ATP5G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255563.1	NM_001689	
TTN	7273	hgsc.bcm.edu	37	2	179644087	179644087	+	Nonsense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:179644087T>A	ENST00000591111.1	-	23	4056	c.3832A>T	c.(3832-3834)Aag>Tag	p.K1278*	RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.K1278*|TTN_ENST00000359218.5_Nonsense_Mutation_p.K1232*|TTN_ENST00000460472.2_Nonsense_Mutation_p.K1232*|TTN_ENST00000360870.5_Nonsense_Mutation_p.K1278*|TTN_ENST00000589042.1_Nonsense_Mutation_p.K1278*|TTN_ENST00000342175.6_Nonsense_Mutation_p.K1232*			Q8WZ42	TITIN_HUMAN	titin	33471					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)			ACTGCCATCTTTTCTTCTCCA	0.318																																					p.K1278X		Atlas-SNP	.											.	TTN	18412	.	0			c.A3832T						PASS	.						41.0	40.0	41.0					2																	179644087		2203	4297	6500	SO:0001587	stop_gained	7273	exon23			CCATCTTTTCTTC	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.3832A>T	chr2.hg19:g.179644087T>A	ENSP00000465570:p.Lys1278*	135.0	0.0	.		105.0	47.0	.	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	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	44	10.638742	0.99442	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.2813	0.82687	0.0:0.0:0.0:1.0	.	.	.	.	X	1278;1232;1232;1232;1232;1278	.	ENSP00000340554:K1232X	K	-	1	0	TTN	179352332	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.478000	0.66806	2.244000	0.73946	0.533000	0.62120	AAG	.	.	.	none		0.318	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF589	51385	hgsc.bcm.edu	37	3	48309513	48309513	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr3:48309513A>G	ENST00000354698.3	+	4	404	c.332A>G	c.(331-333)cAt>cGt	p.H111R	ZNF589_ENST00000412564.1_Intron|ZNF589_ENST00000440261.2_Missense_Mutation_p.H110R|ZNF589_ENST00000427617.2_Intron	NM_016089.2	NP_057173.2	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	111					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCAGGTTTCCATGCAGGAAAT	0.507																																					p.H111R	Colon(9;319 328 25374 27611 50948)	Atlas-SNP	.											.	ZNF589	20	.	0			c.A332G						PASS	.						70.0	71.0	71.0					3																	48309513		1983	4185	6168	SO:0001583	missense	51385	exon4			GTTTCCATGCAGG	AF114816	CCDS43085.1	3p21	2013-01-08			ENSG00000164048	ENSG00000164048		"""Zinc fingers, C2H2-type"", ""-"""	16747	protein-coding gene	gene with protein product						10029171	Standard	NM_016089		Approved	SZF1	uc003csl.4	Q86UQ0	OTTHUMG00000156833	ENST00000354698.3:c.332A>G	chr3.hg19:g.48309513A>G	ENSP00000346729:p.His111Arg	64.0	0.0	.		31.0	26.0	.	NM_016089	Q86UC9|Q9BRI6|Q9BRY3|Q9Y611|Q9Y612	Missense_Mutation	SNP	ENST00000354698.3	hg19	CCDS43085.1	.	.	.	.	.	.	.	.	.	.	A	5.998	0.368098	0.11352	.	.	ENSG00000164048	ENST00000354698;ENST00000440261;ENST00000296437	T;T	0.05996	3.36;4.89	1.17	-0.0169	0.13970	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	P;P;B	0.36712	0.566;0.523;0.389	B;B;B	0.34180	0.177;0.023;0.01	T	0.42716	-0.9435	9	0.25106	T	0.35	.	2.8669	0.05604	0.543:0.0:0.457:0.0	.	110;108;111	B4DQF9;Q86UQ0-2;Q86UQ0	.;.;ZN589_HUMAN	R	111;110;108	ENSP00000346729:H111R;ENSP00000408719:H110R	ENSP00000296437:H108R	H	+	2	0	ZNF589	48284517	0.000000	0.05858	0.001000	0.08648	0.532000	0.34746	0.801000	0.27055	-0.015000	0.14150	0.383000	0.25322	CAT	.	.	.	none		0.507	ZNF589-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346124.1	NM_016089	
RBM27	54439	hgsc.bcm.edu	37	5	145583374	145583374	+	Silent	SNP	T	T	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr5:145583374T>C	ENST00000265271.5	+	1	212	c.46T>C	c.(46-48)Tta>Cta	p.L16L	RBM27_ENST00000506502.1_Silent_p.L16L	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	16					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTGGCCAAGTTACTGGAGCC	0.711																																					p.L16L		Atlas-SNP	.											.	RBM27	119	.	0			c.T46C						PASS	.						11.0	13.0	12.0					5																	145583374		1260	2948	4208	SO:0001819	synonymous_variant	54439	exon1			GCCAAGTTACTGG	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.46T>C	chr5.hg19:g.145583374T>C		202.0	0.0	.		106.0	35.0	.	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.	.	none		0.711	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
PPP1R3G	648791	hgsc.bcm.edu	37	6	5086761	5086761	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:5086761A>G	ENST00000405617.2	+	1	1042	c.1042A>G	c.(1042-1044)Acg>Gcg	p.T348A		NM_001145115.1	NP_001138587.1	B7ZBB8	PP13G_HUMAN	protein phosphatase 1, regulatory subunit 3G	348	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				glucose homeostasis (GO:0042593)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)	cytoplasm (GO:0005737)	glycogen binding (GO:2001069)			kidney(2)	2						CGCCAACTACACGCTGCGCTA	0.692																																					p.T348A		Atlas-SNP	.											.	PPP1R3G	11	.	0			c.A1042G						PASS	.						7.0	9.0	8.0					6																	5086761		683	1575	2258	SO:0001583	missense	648791	exon1			AACTACACGCTGC		CCDS47366.1	6p25.1	2012-04-17	2011-10-04		ENSG00000219607	ENSG00000219607		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14945	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3G"""			11948623	Standard	NM_001145115		Approved		uc011dia.1	B7ZBB8	OTTHUMG00000014172	ENST00000405617.2:c.1042A>G	chr6.hg19:g.5086761A>G	ENSP00000393832:p.Thr348Ala	56.0	0.0	.		27.0	11.0	.	NM_001145115		Missense_Mutation	SNP	ENST00000405617.2	hg19	CCDS47366.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.017186	0.54576	.	.	ENSG00000219607	ENST00000405617	T	0.63417	-0.04	4.44	4.44	0.53790	Putative phosphatase regulatory subunit (2);	.	.	.	.	T	0.52964	0.1767	L	0.42487	1.325	0.29476	N	0.856727	D	0.76494	0.999	D	0.74674	0.984	T	0.40515	-0.9559	9	0.08599	T	0.76	.	11.2137	0.48815	1.0:0.0:0.0:0.0	.	348	B7ZBB8	PP13G_HUMAN	A	348	ENSP00000393832:T348A	ENSP00000393832:T348A	T	+	1	0	PPP1R3G	5031760	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	2.519000	0.45546	1.871000	0.54225	0.459000	0.35465	ACG	.	.	.	none		0.692	PPP1R3G-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039740.3	NM_001145115	
OR10C1	442194	hgsc.bcm.edu	37	6	29408295	29408295	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:29408295G>A	ENST00000444197.2	+	1	1213	c.503G>A	c.(502-504)tGc>tAc	p.C168Y	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TTGCCCTTCTGCGGCCCCAAT	0.592																																					p.C168Y		Atlas-SNP	.											.	OR10C1	58	.	0			c.G503A						PASS	.						121.0	135.0	130.0					6																	29408295		1509	2709	4218	SO:0001583	missense	442194	exon1			CCTTCTGCGGCCC		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.503G>A	chr6.hg19:g.29408295G>A	ENSP00000419119:p.Cys168Tyr	36.0	0.0	.		34.0	13.0	.	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	hg19	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.346866	0.41599	.	.	ENSG00000206474	ENST00000444197	T	0.00245	8.45	3.53	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42548	D	0.000681	T	0.00440	0.0014	H	0.94462	3.54	0.41362	D	0.987435	D	0.89917	1.0	D	0.97110	1.0	T	0.54728	-0.8250	10	0.72032	D	0.01	.	12.0891	0.53715	0.0:0.1749:0.8251:0.0	.	168	Q96KK4	O10C1_HUMAN	Y	168	ENSP00000419119:C168Y	ENSP00000419119:C168Y	C	+	2	0	OR10C1	29516274	1.000000	0.71417	1.000000	0.80357	0.309000	0.27889	5.166000	0.64965	1.805000	0.52779	0.508000	0.49915	TGC	.	.	.	none		0.592	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
MICA	100507436	hgsc.bcm.edu	37	6	31379810	31379810	+	Missense_Mutation	SNP	A	A	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:31379810A>T	ENST00000449934.2	+	4	754	c.700A>T	c.(700-702)Aat>Tat	p.N234Y	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CTATCCCCGGAATATCATACT	0.582																																					p.N234Y		Atlas-SNP	.											.	MICA	21	.	0			c.A700T						PASS	.						16.0	19.0	18.0					6																	31379810		692	1589	2281	SO:0001583	missense	100507436	exon4			CCCCGGAATATCA	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.700A>T	chr6.hg19:g.31379810A>T	ENSP00000413079:p.Asn234Tyr	88.0	0.0	.		63.0	25.0	.	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	hg19	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	N	13.54	2.268509	0.40095	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.14640	2.49;2.49	2.52	-1.33	0.09172	.	0.698014	0.11634	U	0.544522	T	0.17662	0.0424	M	0.83774	2.66	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.949	T	0.04065	-1.0980	10	0.87932	D	0	.	3.5133	0.07716	0.33:0.2458:0.4242:0.0	.	96;234	Q5SS58;Q96QC4	.;.	Y	96;234;191;234;125	ENSP00000413079:N234Y;ENSP00000402410:N125Y	ENSP00000365394:N234Y	N	+	1	0	MICA	31487789	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.220000	0.17660	-0.118000	0.11851	0.365000	0.22127	AAT	.	.	.	none		0.582	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
BAI3	577	hgsc.bcm.edu	37	6	69772840	69772840	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:69772840T>A	ENST00000370598.1	+	16	3169	c.2348T>A	c.(2347-2349)aTt>aAt	p.I783N		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	783					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TATACTGTCATTAATTCCAAA	0.353																																					p.I783N		Atlas-SNP	.											.	BAI3	451	.	0			c.T2348A						PASS	.						102.0	95.0	97.0					6																	69772840		2203	4300	6503	SO:0001583	missense	577	exon16			CTGTCATTAATTC	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2348T>A	chr6.hg19:g.69772840T>A	ENSP00000359630:p.Ile783Asn	79.0	0.0	.		63.0	30.0	.	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.416826	0.62511	.	.	ENSG00000135298	ENST00000370598	T	0.09817	2.94	5.54	5.54	0.83059	Domain of unknown function DUF3497 (1);	0.132236	0.50627	D	0.000118	T	0.08891	0.0220	L	0.34521	1.04	0.80722	D	1	P	0.41188	0.741	P	0.47528	0.549	T	0.03875	-1.0996	10	0.87932	D	0	.	15.6727	0.77292	0.0:0.0:0.0:1.0	.	783	O60242	BAI3_HUMAN	N	783	ENSP00000359630:I783N	ENSP00000359630:I783N	I	+	2	0	BAI3	69829561	1.000000	0.71417	0.965000	0.40720	0.934000	0.57294	6.725000	0.74752	2.094000	0.63399	0.397000	0.26171	ATT	.	.	.	none		0.353	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377132	168377132	+	lincRNA	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:168377132G>A	ENST00000538528.1	-	0	487																											CCCCTGCAGTGTGTTGGGAGG	0.617																																					p.H67H		Atlas-SNP	.											.	.	.	.	0			c.C201T						PASS	.						5.0	6.0	6.0					6																	168377132		656	1543	2199			0	exon1			TGCAGTGTGTTGG																													chr6.hg19:g.168377132G>A		263.0	0.0	.		197.0	8.0	.	NM_001129895		Silent	SNP	ENST00000538528.1	hg19																																																																																				.	.	.	none		0.617	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
ITGB8	3696	hgsc.bcm.edu	37	7	20449400	20449400	+	Splice_Site	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:20449400A>G	ENST00000222573.4	+	13	2870	c.2186A>G	c.(2185-2187)aAg>aGg	p.K729R	ITGB8_ENST00000537992.1_Splice_Site_p.K594R	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	729					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						GCCTCAAAAAAGGTCAGTGAA	0.318																																					p.K729R		Atlas-SNP	.											.	ITGB8	159	.	0			c.A2186G						PASS	.						73.0	79.0	77.0					7																	20449400		2203	4299	6502	SO:0001630	splice_region_variant	3696	exon13			CAAAAAAGGTCAG		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.2187+1A>G	chr7.hg19:g.20449400A>G		113.0	0.0	.		64.0	25.0	.	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749231	0.69533	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	T;T	0.51071	0.72;0.72	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000002	T	0.36744	0.0978	L	0.47716	1.5	0.53005	D	0.999961	P	0.42409	0.779	B	0.32149	0.141	T	0.37197	-0.9716	10	0.56958	D	0.05	.	10.8727	0.46894	0.9303:0.0:0.0697:0.0	.	729	P26012	ITB8_HUMAN	R	594;729	ENSP00000441561:K594R;ENSP00000222573:K729R	ENSP00000222573:K729R	K	+	2	0	ITGB8	20415925	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.810000	0.62598	2.324000	0.78689	0.533000	0.62120	AAG	.	.	.	none		0.318	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	Missense_Mutation
URGCP	55665	hgsc.bcm.edu	37	7	43917041	43917041	+	Missense_Mutation	SNP	C	C	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:43917041C>A	ENST00000453200.1	-	6	2514	c.2021G>T	c.(2020-2022)tGg>tTg	p.W674L	URGCP_ENST00000336086.6_Missense_Mutation_p.W631L|URGCP_ENST00000223341.7_Missense_Mutation_p.W631L|URGCP_ENST00000402306.3_Missense_Mutation_p.W665L|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000443736.1_Missense_Mutation_p.W631L|URGCP_ENST00000447717.3_Missense_Mutation_p.W631L			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	674					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCCTGTGACCCAGCGGACGGG	0.642																																					p.W674L		Atlas-SNP	.											.	URGCP	170	.	0			c.G2021T						PASS	.						29.0	33.0	32.0					7																	43917041		2118	4226	6344	SO:0001583	missense	55665	exon6			GTGACCCAGCGGA		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2021G>T	chr7.hg19:g.43917041C>A	ENSP00000396918:p.Trp674Leu	42.0	0.0	.		24.0	12.0	.	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	hg19	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068660	0.76301	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.22134	2.01;2.01;1.98;2.01;1.97;2.01	5.97	5.97	0.96955	.	0.056596	0.85682	D	0.000000	T	0.52403	0.1732	M	0.84082	2.675	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.54583	-0.8272	10	0.87932	D	0	-31.708	17.9218	0.88969	0.0:1.0:0.0:0.0	.	665;674	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	L	631;631;665;631;674;631	ENSP00000223341:W631L;ENSP00000336872:W631L;ENSP00000384955:W665L;ENSP00000392136:W631L;ENSP00000396918:W674L;ENSP00000402803:W631L	ENSP00000223341:W631L	W	-	2	0	URGCP	43883566	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	7.262000	0.78410	2.837000	0.97791	0.655000	0.94253	TGG	.	.	.	none		0.642	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
MDH2	4191	hgsc.bcm.edu	37	7	75693752	75693752	+	Silent	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:75693752A>G	ENST00000315758.5	+	7	823	c.729A>G	c.(727-729)ggA>ggG	p.G243G	MDH2_ENST00000432020.2_Silent_p.G201G|MDH2_ENST00000443006.1_Silent_p.G136G	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	243					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CTAAAGCCGGAGCAGGTAGAG	0.647																																					p.G243G		Atlas-SNP	.											.	MDH2	35	.	0			c.A729G						PASS	.						25.0	25.0	25.0					7																	75693752		2198	4299	6497	SO:0001819	synonymous_variant	4191	exon7			AGCCGGAGCAGGT		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.729A>G	chr7.hg19:g.75693752A>G		121.0	0.0	.		79.0	37.0	.	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	hg19	CCDS5581.1																																																																																			.	.	.	none		0.647	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
KMT2E	55904	hgsc.bcm.edu	37	7	104742604	104742604	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:104742604T>G	ENST00000311117.3	+	17	2704	c.2159T>G	c.(2158-2160)cTt>cGt	p.L720R	KMT2E_ENST00000334914.7_5'UTR|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334877.4_Missense_Mutation_p.L720R|KMT2E_ENST00000257745.4_Missense_Mutation_p.L720R	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	720					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										GTTCCAGCACTTAATAAATGT	0.299																																					p.L720R		Atlas-SNP	.											.	MLL5	173	.	0			c.T2159G						PASS	.						67.0	72.0	70.0					7																	104742604		2202	4298	6500	SO:0001583	missense	55904	exon16			CAGCACTTAATAA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2159T>G	chr7.hg19:g.104742604T>G	ENSP00000312379:p.Leu720Arg	141.0	0.0	.		81.0	23.0	.	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.687786	0.29962	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745	D;D;D	0.92048	-2.96;-2.59;-2.96	5.75	5.75	0.90469	.	0.461581	0.23362	N	0.049019	D	0.84741	0.5539	L	0.29908	0.895	0.80722	D	1	P	0.36199	0.543	B	0.34452	0.183	T	0.81824	-0.0755	10	0.10636	T	0.68	.	11.188	0.48669	0.137:0.0:0.0:0.863	.	720	Q8IZD2	MLL5_HUMAN	R	720;720;720;640;720	ENSP00000312379:L720R;ENSP00000335599:L720R;ENSP00000257745:L720R	ENSP00000257745:L720R	L	+	2	0	MLL5	104529840	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.598000	0.54038	2.201000	0.70794	0.533000	0.62120	CTT	.	.	.	none		0.299	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
WASL	8976	hgsc.bcm.edu	37	7	123332492	123332492	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:123332492A>G	ENST00000223023.4	-	9	1588	c.1256T>C	c.(1255-1257)cTa>cCa	p.L419P		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	419	WH2 1. {ECO:0000255|PROSITE- ProRule:PRU00406}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CACTTTTTTTAGCTGAGCACC	0.502																																					p.L419P		Atlas-SNP	.											.	WASL	70	.	0			c.T1256C						PASS	.						77.0	74.0	75.0					7																	123332492		2203	4300	6503	SO:0001583	missense	8976	exon9			TTTTTTAGCTGAG	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.1256T>C	chr7.hg19:g.123332492A>G	ENSP00000223023:p.Leu419Pro	73.0	0.0	.		44.0	14.0	.	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	hg19	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.192537	0.58017	.	.	ENSG00000106299	ENST00000223023	D	0.99849	-7.15	5.79	5.79	0.91817	Wiscott-Aldrich syndrome, C-terminal (1);Actin-binding WH2 (3);	0.000000	0.64402	D	0.000002	D	0.99832	0.9924	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96750	0.9553	10	0.72032	D	0.01	-17.53	16.1172	0.81314	1.0:0.0:0.0:0.0	.	419	O00401	WASL_HUMAN	P	419	ENSP00000223023:L419P	ENSP00000223023:L419P	L	-	2	0	WASL	123119728	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.884000	0.92432	2.201000	0.70794	0.528000	0.53228	CTA	.	.	.	none		0.502	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
BRAF	673	hgsc.bcm.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.V600E	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,NS,adenoma,0,1	BRAF	36346	.	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A						PASS	.						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	GATTTCACTGTAG	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	chr7.hg19:g.140453136A>T	ENSP00000288602:p.Val600Glu	55.0	0.0	.		50.0	19.0	.	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	hg19	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA	.	.	.	weak		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
NKX2-6	137814	hgsc.bcm.edu	37	8	23560587	23560587	+	Silent	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr8:23560587G>A	ENST00000325017.3	-	2	282	c.283C>T	c.(283-285)Ctg>Ttg	p.L95L	NKX2-6_ENST00000418222.1_Silent_p.L13L	NM_001136271.2	NP_001129743.2	A6NCS4	NKX26_HUMAN	NK2 homeobox 6	95					atrial cardiac muscle cell development (GO:0055014)|cell differentiation (GO:0030154)|digestive tract development (GO:0048565)|embryonic heart tube development (GO:0035050)|hypothalamus development (GO:0021854)|negative regulation of apoptotic process (GO:0043066)|pericardium development (GO:0060039)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCCGCGTTCAGGCCGGGCTCT	0.662																																					p.L95L		Atlas-SNP	.											.	NKX2-6	6	.	0			c.C283T						PASS	.						1.0	2.0	1.0					8																	23560587		410	1066	1476	SO:0001819	synonymous_variant	137814	exon2			CGTTCAGGCCGGG	CN272646		8p21.2	2012-03-09	2011-06-01			ENSG00000180053		"""Homeoboxes / ANTP class : NKL subclass"""	32940	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	611770	"""NK2 transcription factor related, locus 6 (Drosophila)"""			15649947	Standard	NM_001136271		Approved	CSX2, NKX4-2	uc011kzy.3	A6NCS4		ENST00000325017.3:c.283C>T	chr8.hg19:g.23560587G>A		69.0	0.0	.		36.0	33.0	.	NM_001136271		Silent	SNP	ENST00000325017.3	hg19																																																																																				.	.	.	none		0.662	NKX2-6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376057.4	NM_001136271	
INTS9	55756	hgsc.bcm.edu	37	8	28671112	28671113	+	Missense_Mutation	DNP	AG	AG	GA			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr8:28671112_28671113AG>GA	ENST00000521022.1	-	7	586_587	c.505_506CT>TC	c.(505-507)CTc>TCc	p.L169S	INTS9_ENST00000521777.1_Missense_Mutation_p.L145S|INTS9_ENST00000397363.4_Missense_Mutation_p.L63S|INTS9_ENST00000416984.2_Missense_Mutation_p.L148S	NM_018250.3	NP_060720.2	Q9NV88	INT9_HUMAN	integrator complex subunit 9	169					snRNA processing (GO:0016180)	cytoplasm (GO:0005737)|integrator complex (GO:0032039)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(2)	19		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		TGCATCCTTGAGAGGAGAAGGT	0.421																																					p.L169P|p.L169F		Atlas-SNP	.											.	INTS9	43	.	0			c.T506C|c.C505T						PASS	.																																			SO:0001583	missense	55756	exon7			TCCTTGAGAGGAG|CCTTGAGAGGAGA	BC025267	CCDS34873.1, CCDS55215.1, CCDS55216.1	8p21.1	2008-02-05			ENSG00000104299	ENSG00000104299			25592	protein-coding gene	gene with protein product		611352				16239144	Standard	NM_001172562		Approved	FLJ10871, CPSF2L, RC-74	uc011lav.2	Q9NV88	OTTHUMG00000164030	ENST00000521022.1:c.505_506delinsGA	chr8.hg19:g.28671112_28671113delinsGA	ENSP00000429065:p.Leu169Ser	145.0|142.0	0.0	.		71.0|72.0	61.0|62.0	.	NM_018250	B7Z560|B7Z6M5|O00224|Q8TB16	Missense_Mutation	SNP	ENST00000521022.1	hg19	CCDS34873.1																																																																																			.	.	.	none		0.421	INTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376846.1	NM_018250	
KCNB2	9312	hgsc.bcm.edu	37	8	73480085	73480085	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr8:73480085T>G	ENST00000523207.1	+	2	704	c.116T>G	c.(115-117)aTc>aGc	p.I39S		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	39					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	AGAGTTAAGATCAATGTGGGG	0.572																																					p.I39S		Atlas-SNP	.											.	KCNB2	228	.	0			c.T116G						PASS	.						80.0	81.0	80.0					8																	73480085		2203	4300	6503	SO:0001583	missense	9312	exon2			TTAAGATCAATGT	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.116T>G	chr8.hg19:g.73480085T>G	ENSP00000430846:p.Ile39Ser	106.0	0.0	.		55.0	42.0	.	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.552042	0.86127	.	.	ENSG00000182674	ENST00000523207	T	0.80393	-1.37	5.71	5.71	0.89125	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.329901	0.17562	U	0.169793	D	0.91402	0.7287	M	0.91354	3.2	0.51012	D	0.999906	D	0.59767	0.986	D	0.64687	0.928	D	0.92898	0.6337	10	0.87932	D	0	.	15.9958	0.80243	0.0:0.0:0.0:1.0	.	39	Q92953	KCNB2_HUMAN	S	39	ENSP00000430846:I39S	ENSP00000430846:I39S	I	+	2	0	KCNB2	73642639	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	7.841000	0.86834	2.188000	0.69820	0.533000	0.62120	ATC	.	.	.	none		0.572	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
ZCCHC7	84186	hgsc.bcm.edu	37	9	37349376	37349376	+	Missense_Mutation	SNP	A	A	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr9:37349376A>C	ENST00000336755.5	+	7	1116	c.1010A>C	c.(1009-1011)aAg>aCg	p.K337T	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_Missense_Mutation_p.K47T	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	337						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		CCACCCAAAAAGCCGAAGACC	0.413																																					p.K337T		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.A1010C						PASS	.						148.0	130.0	136.0					9																	37349376		2203	4300	6503	SO:0001583	missense	84186	exon7			CCAAAAAGCCGAA	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"""Zinc fingers, CCHC domain containing"""	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.1010A>C	chr9.hg19:g.37349376A>C	ENSP00000337839:p.Lys337Thr	110.0	0.0	.		52.0	21.0	.	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Missense_Mutation	SNP	ENST00000336755.5	hg19	CCDS6608.2	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047988	0.75846	.	.	ENSG00000147905	ENST00000336755;ENST00000534928	T;T	0.75821	-0.97;-0.97	5.7	4.36	0.52297	Zinc finger, CCHC retroviral-type (1);	0.284260	0.37053	N	0.002279	T	0.75443	0.3850	L	0.54323	1.7	0.38274	D	0.942228	D	0.63880	0.993	P	0.56343	0.796	T	0.76075	-0.3092	10	0.37606	T	0.19	-21.0409	6.5841	0.22610	0.7103:0.1622:0.1274:0.0	.	337	Q8N3Z6	ZCHC7_HUMAN	T	337;47	ENSP00000337839:K337T;ENSP00000443113:K47T	ENSP00000337839:K337T	K	+	2	0	ZCCHC7	37339376	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	0.957000	0.29215	2.176000	0.68965	0.445000	0.29226	AAG	.	.	.	none		0.413	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226	
C9orf3	84909	hgsc.bcm.edu	37	9	97767897	97767897	+	Splice_Site	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr9:97767897A>G	ENST00000375315.2	+	12	2114	c.2114A>G	c.(2113-2115)aAg>aGg	p.K705R	C9orf3_ENST00000297979.5_Splice_Site_p.K606R|C9orf3_ENST00000425634.2_Splice_Site_p.K67R|C9orf3_ENST00000433691.2_Splice_Site_p.K46R	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	705					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		GTGTTTGAAAAGGTAGGGGTT	0.493																																					p.K705R		Atlas-SNP	.											.	C9orf3	100	.	0			c.A2114G						PASS	.						99.0	104.0	102.0					9																	97767897		2203	4300	6503	SO:0001630	splice_region_variant	84909	exon12			TTGAAAAGGTAGG	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.2115+1A>G	chr9.hg19:g.97767897A>G		200.0	0.0	.		115.0	40.0	.	NM_001193329	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	hg19	CCDS55328.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.842859	0.71488	.	.	ENSG00000148120	ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313;ENST00000375316;ENST00000425634;ENST00000433691;ENST00000375314	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	4.11	4.11	0.48088	Peptidase M1, leukotriene A4 hydrolase, aminopeptidase C-terminal (1);Armadillo-type fold (1);	0.062989	0.64402	D	0.000008	T	0.57344	0.2047	M	0.65975	2.015	0.80722	D	1	P;D;D;P;P;D	0.76494	0.945;0.999;0.982;0.885;0.827;0.974	P;D;P;P;B;P	0.83275	0.703;0.996;0.832;0.666;0.359;0.806	T	0.54111	-0.8342	10	0.19147	T	0.46	-15.1115	11.2577	0.49063	1.0:0.0:0.0:0.0	.	46;67;124;705;606;606	B4DU39;B4DQU3;E9PF71;Q8N6M6;Q8N6M6-4;Q8N6M6-2	.;.;.;AMPO_HUMAN;.;.	R	606;705;429;487;124;67;46;69	ENSP00000297979:K606R;ENSP00000364464:K705R;ENSP00000402171:K429R;ENSP00000401854:K487R;ENSP00000411815:K67R;ENSP00000399365:K46R	ENSP00000297979:K606R	K	+	2	0	C9orf3	96807718	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	5.849000	0.69465	1.854000	0.53819	0.459000	0.35465	AAG	.	.	.	none		0.493	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823	Missense_Mutation
OAT	4942	hgsc.bcm.edu	37	10	126097337	126097337	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr10:126097337A>G	ENST00000368845.5	-	3	489	c.397T>C	c.(397-399)Tac>Cac	p.Y133H	OAT_ENST00000467675.1_5'UTR|OAT_ENST00000539214.1_5'UTR	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	133					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	ACTTTGTGGTAGTTGAAAAGT	0.284																																					p.Y133H		Atlas-SNP	.											.	OAT	25	.	0			c.T397C						PASS	.						68.0	71.0	70.0					10																	126097337		2203	4300	6503	SO:0001583	missense	4942	exon3			TGTGGTAGTTGAA	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"""Ornithine aminotransferase"", ""ornithine aminotransferase precursor"", ""gyrate atrophy"""	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.397T>C	chr10.hg19:g.126097337A>G	ENSP00000357838:p.Tyr133His	293.0	0.0	.		175.0	47.0	.	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Missense_Mutation	SNP	ENST00000368845.5	hg19	CCDS7639.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413753	0.83449	.	.	ENSG00000065154	ENST00000368845	D	0.86164	-2.08	5.0	5.0	0.66597	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.91882	0.7430	L	0.59967	1.855	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92611	0.6099	10	0.66056	D	0.02	0.1642	15.4281	0.75069	1.0:0.0:0.0:0.0	.	133	P04181	OAT_HUMAN	H	133	ENSP00000357838:Y133H	ENSP00000357838:Y133H	Y	-	1	0	OAT	126087327	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.959000	0.93110	2.195000	0.70347	0.455000	0.32223	TAC	.	.	.	none		0.284	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274	
CALCA	796	hgsc.bcm.edu	37	11	14992664	14992664	+	Silent	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:14992664T>A	ENST00000486207.1	-	1	83	c.75A>T	c.(73-75)gcA>gcT	p.A25A	CALCA_ENST00000361010.3_Silent_p.A25A|CALCA_ENST00000331587.4_Silent_p.A25A|CALCA_ENST00000396372.2_Silent_p.A25A|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000359642.3_Silent_p.A25A			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha	25					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|cytosolic calcium ion homeostasis (GO:0051480)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor internalization (GO:0002031)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of blood pressure (GO:0045776)|negative regulation of bone resorption (GO:0045779)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of osteoclast differentiation (GO:0045671)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of vasodilation (GO:0045909)|protein phosphorylation (GO:0006468)|receptor internalization (GO:0031623)|regulation of blood pressure (GO:0008217)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	protein complex binding (GO:0032403)|receptor binding (GO:0005102)			central_nervous_system(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	8						TGAATGGTGCTGCATGGAGGC	0.512																																					p.A25A		Atlas-SNP	.											.	CALCA	30	.	0			c.A75T						PASS	.						101.0	91.0	94.0					11																	14992664		2200	4294	6494	SO:0001819	synonymous_variant	796	exon2			TGGTGCTGCATGG	X00356, M64486	CCDS7819.1, CCDS31432.1	11p15.2	2014-09-17	2008-02-20		ENSG00000110680	ENSG00000110680		"""Endogenous ligands"""	1437	protein-coding gene	gene with protein product	"""calcitonin"""	114130	"""calcitonin 1"""	CALC1		6546550	Standard	NM_001033953		Approved		uc001mlw.1	P01258	OTTHUMG00000159731	ENST00000486207.1:c.75A>T	chr11.hg19:g.14992664T>A		53.0	0.0	.		32.0	10.0	.	NM_001033953	Q93048|Q9UCP0	Silent	SNP	ENST00000486207.1	hg19	CCDS31432.1																																																																																			.	.	.	none		0.512	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357068.1	NM_001741	
LTBP3	4054	hgsc.bcm.edu	37	11	65320922	65320922	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:65320922T>A	ENST00000301873.5	-	4	1212	c.944A>T	c.(943-945)aAg>aTg	p.K315M	LTBP3_ENST00000322147.4_Missense_Mutation_p.K315M|LTBP3_ENST00000536982.1_Intron	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	315	TB 1.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CTTGTGGCACTTGCTCTGGCC	0.667																																					p.K315M		Atlas-SNP	.											.	LTBP3	55	.	0			c.A944T						PASS	.						29.0	30.0	30.0					11																	65320922		2193	4291	6484	SO:0001583	missense	4054	exon4			TGGCACTTGCTCT	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"""Latent transforming growth factor, beta binding proteins"""	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.944A>T	chr11.hg19:g.65320922T>A	ENSP00000301873:p.Lys315Met	70.0	0.0	.		46.0	17.0	.	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396831	0.83120	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000530866;ENST00000530426	D;D;D;T	0.87887	-1.61;-1.68;-2.31;1.95	4.8	4.8	0.61643	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	D	0.000000	D	0.91019	0.7175	L	0.55481	1.735	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.91440	0.5173	10	0.62326	D	0.03	.	12.3307	0.55038	0.0:0.0:0.0:1.0	.	226;198;315;315	E9PKW1;B9EG76;Q9NS15;Q9NS15-2	.;.;LTBP3_HUMAN;.	M	315;315;226;36	ENSP00000326647:K315M;ENSP00000301873:K315M;ENSP00000435276:K226M;ENSP00000432476:K36M	ENSP00000301873:K315M	K	-	2	0	LTBP3	65077498	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.758000	0.55220	2.022000	0.59522	0.413000	0.27773	AAG	.	.	.	none		0.667	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070	
ABCG4	64137	hgsc.bcm.edu	37	11	119020846	119020846	+	Silent	SNP	A	A	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:119020846A>T	ENST00000449422.2	+	2	359	c.171A>T	c.(169-171)tcA>tcT	p.S57S	ABCG4_ENST00000307417.3_Silent_p.S57S|ABCG4_ENST00000531739.1_Silent_p.S57S	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	57					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CCAAGCGCTCAGCCGTGGACA	0.642																																					p.S57S		Atlas-SNP	.											.	ABCG4	77	.	0			c.A171T						PASS	.						80.0	86.0	84.0					11																	119020846		2200	4295	6495	SO:0001819	synonymous_variant	64137	exon2			GCGCTCAGCCGTG	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.171A>T	chr11.hg19:g.119020846A>T		92.0	0.0	.		58.0	31.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	hg19	CCDS8415.1																																																																																			.	.	.	none		0.642	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
CMAS	55907	hgsc.bcm.edu	37	12	22208120	22208120	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:22208120G>A	ENST00000229329.2	+	2	428	c.298G>A	c.(298-300)Gtg>Atg	p.V100M		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	100					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						AATTGAGAATGTGGCCAAACA	0.343																																					p.V100M		Atlas-SNP	.											.	CMAS	45	.	0			c.G298A						PASS	.						86.0	82.0	84.0					12																	22208120		2203	4300	6503	SO:0001583	missense	55907	exon2			GAGAATGTGGCCA	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"""CMP-Neu5Ac synthetase"""	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.298G>A	chr12.hg19:g.22208120G>A	ENSP00000229329:p.Val100Met	181.0	0.0	.		157.0	42.0	.	NM_018686	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	hg19	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.604159	0.87157	.	.	ENSG00000111726	ENST00000229329	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.85771	0.5774	M	0.91972	3.26	0.58432	D	0.999997	D	0.76494	0.999	D	0.79784	0.993	D	0.88715	0.3225	9	0.87932	D	0	-18.9373	17.6578	0.88182	0.0:0.0:1.0:0.0	.	100	Q8NFW8	NEUA_HUMAN	M	100	.	ENSP00000229329:V100M	V	+	1	0	CMAS	22099387	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.109000	0.94291	2.597000	0.87782	0.591000	0.81541	GTG	.	.	.	none		0.343	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686	
TPCN1	53373	hgsc.bcm.edu	37	12	113733831	113733831	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:113733831G>A	ENST00000335509.6	+	28	2715	c.2401G>A	c.(2401-2403)Gcc>Acc	p.A801T	TPCN1_ENST00000541517.1_Missense_Mutation_p.A873T|TPCN1_ENST00000550785.1_Missense_Mutation_p.A873T|TPCN1_ENST00000392569.4_Missense_Mutation_p.A733T	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	801					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						TGCAGCCCCCGCCGCCCAGCA	0.612																																					p.A873T		Atlas-SNP	.											TPCN1,colon,carcinoma,0,1	TPCN1	109	.	0			c.G2617A						PASS	.						26.0	32.0	30.0					12																	113733831		2202	4300	6502	SO:0001583	missense	53373	exon29			GCCCCCGCCGCCC	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.2401G>A	chr12.hg19:g.113733831G>A	ENSP00000335300:p.Ala801Thr	181.0	0.0	.		147.0	54.0	.	NM_001143819	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	hg19	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	G	0.084	-1.178598	0.01633	.	.	ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.33	-10.7	0.00240	.	2.170010	0.01720	N	0.028217	T	0.11965	0.0291	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.21348	-1.0248	10	0.02654	T	1	-1.6346	7.2145	0.25951	0.6415:0.1268:0.0874:0.1443	.	873;801	Q9ULQ1-3;Q9ULQ1	.;TPC1_HUMAN	T	801;873;873;733	ENSP00000335300:A801T;ENSP00000448083:A873T;ENSP00000438125:A873T;ENSP00000376350:A733T	ENSP00000335300:A801T	A	+	1	0	TPCN1	112218214	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.447000	0.01010	-1.860000	0.01154	-1.108000	0.02087	GCC	.	.	.	none		0.612	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
KNTC1	9735	hgsc.bcm.edu	37	12	123065184	123065184	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:123065184G>A	ENST00000333479.7	+	33	3126	c.2949G>A	c.(2947-2949)atG>atA	p.M983I	KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	983					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		GTGAAGAAATGTTGAAACTAT	0.303																																					p.M983I		Atlas-SNP	.											.	KNTC1	182	.	0			c.G2949A						PASS	.						83.0	77.0	79.0					12																	123065184		1851	4091	5942	SO:0001583	missense	9735	exon33			AGAAATGTTGAAA		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.2949G>A	chr12.hg19:g.123065184G>A	ENSP00000328236:p.Met983Ile	254.0	0.0	.		194.0	104.0	.	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	4.710	0.132087	0.08981	.	.	ENSG00000184445	ENST00000333479	T	0.13657	2.57	5.9	1.99	0.26369	.	1.288510	0.05264	N	0.516315	T	0.07503	0.0189	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35475	-0.9787	10	0.21014	T	0.42	4.0371	7.1155	0.25414	0.0:0.5751:0.255:0.1699	.	983	P50748	KNTC1_HUMAN	I	983	ENSP00000328236:M983I	ENSP00000328236:M983I	M	+	3	0	KNTC1	121631137	0.008000	0.16893	0.044000	0.18714	0.704000	0.40688	0.201000	0.17276	0.814000	0.34374	-0.519000	0.04390	ATG	.	.	.	none		0.303	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
FBRSL1	57666	hgsc.bcm.edu	37	12	133158846	133158846	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:133158846A>G	ENST00000434748.2	+	16	3344	c.2324A>G	c.(2323-2325)cAg>cGg	p.Q775R	FBRSL1_ENST00000261673.6_Missense_Mutation_p.Q702R	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	775							poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						AAGGAGGAGCAGGAACGGTGA	0.672																																					p.Q775R		Atlas-SNP	.											.	FBRSL1	47	.	0			c.A2324G						PASS	.						80.0	95.0	90.0					12																	133158846		692	1591	2283	SO:0001583	missense	57666	exon16			AGGAGCAGGAACG		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.2324A>G	chr12.hg19:g.133158846A>G	ENSP00000396160:p.Gln775Arg	130.0	0.0	.		115.0	63.0	.	NM_001142641	Q86XQ1	Missense_Mutation	SNP	ENST00000434748.2	hg19	CCDS45010.1	.	.	.	.	.	.	.	.	.	.	a	2.433	-0.330384	0.05314	.	.	ENSG00000112787	ENST00000434748;ENST00000261673	T;T	0.27557	1.66;1.68	3.63	0.498	0.16908	.	1.075130	0.07394	N	0.889670	T	0.09379	0.0231	N	0.00801	-1.175	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23833	-1.0177	10	0.40728	T	0.16	-1.0919	3.4263	0.07412	0.2285:0.0:0.5685:0.203	.	775	Q9HCM7	FBSL_HUMAN	R	775;702	ENSP00000396160:Q775R;ENSP00000261673:Q702R	ENSP00000261673:Q702R	Q	+	2	0	FBRSL1	131668919	0.635000	0.27199	0.069000	0.20011	0.118000	0.20060	0.523000	0.22925	-0.006000	0.14370	-0.549000	0.04216	CAG	.	.	.	none		0.672	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
COL4A1	1282	hgsc.bcm.edu	37	13	110844571	110844572	+	Missense_Mutation	DNP	GC	GC	AG			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr13:110844571_110844572GC>AG	ENST00000375820.4	-	24	1646_1647	c.1525_1526GC>CT	c.(1525-1527)GCa>CTa	p.A509L	COL4A1_ENST00000543140.1_Missense_Mutation_p.A509L	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	509	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TGGCACTCCTGCAACACCATCT	0.515																																					p.A509V|p.A509P		Atlas-SNP	.											.	COL4A1	372	.	0			c.C1526T|c.G1525C						PASS	.																																			SO:0001583	missense	1282	exon24			ACTCCTGCAACAC|CTCCTGCAACACC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.1525_1526delinsAG	chr13.hg19:g.110844571_110844572delinsAG	ENSP00000364979:p.Ala509Leu	64.0|65.0	0.0	.		33.0|34.0	9.0	.	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1																																																																																			.	.	.	none		0.515	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
DDHD1	80821	hgsc.bcm.edu	37	14	53522531	53522531	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr14:53522531T>G	ENST00000323669.5	-	10	2091	c.2092A>C	c.(2092-2094)Atg>Ctg	p.M698L	DDHD1_ENST00000357758.3_Missense_Mutation_p.M698L|DDHD1_ENST00000395606.1_Missense_Mutation_p.M705L|DDHD1_ENST00000555621.1_5'Flank	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	698	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					CTTGGCTTCATATGTTCATAA	0.408																																					p.M705L		Atlas-SNP	.											.	DDHD1	202	.	0			c.A2113C						PASS	.						207.0	201.0	203.0					14																	53522531		2203	4300	6503	SO:0001583	missense	80821	exon11			GCTTCATATGTTC	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"""phosphatidic acid-preferring phospholipase A1"""	614603	"""spastic paraplegia 28 (autosomal recessive)"""	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.2092A>C	chr14.hg19:g.53522531T>G	ENSP00000327104:p.Met698Leu	79.0	0.0	.		52.0	23.0	.	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	hg19	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.649974	0.47362	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	5.75	5.75	0.90469	DDHD (2);	0.043024	0.85682	D	0.000000	T	0.38134	0.1029	N	0.14661	0.345	0.46167	D	0.998908	B;B;B;B	0.11235	0.004;0.002;0.003;0.003	B;B;B;B	0.15052	0.007;0.007;0.012;0.004	T	0.32666	-0.9898	9	0.05351	T	0.99	-19.4471	16.0487	0.80740	0.0:0.0:0.0:1.0	.	94;705;698;698	Q2VYF2;G5E9D1;Q8NEL9;Q8NEL9-2	.;.;DDHD1_HUMAN;.	L	698;705;698;569	.	ENSP00000327104:M698L	M	-	1	0	DDHD1	52592281	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	3.384000	0.52478	2.189000	0.69895	0.533000	0.62120	ATG	.	.	.	none		0.408	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1		
ULK3	25989	hgsc.bcm.edu	37	15	75135403	75135403	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr15:75135403A>G	ENST00000440863.2	-	1	135	c.44T>C	c.(43-45)aTc>aCc	p.I15T	ULK3_ENST00000568667.1_5'Flank|ULK3_ENST00000569437.1_Missense_Mutation_p.I15T	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	15	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						CTCGGTGAGGATGAAGCCGTC	0.776																																					p.I15T		Atlas-SNP	.											.	ULK3	30	.	0			c.T44C						PASS	.						3.0	5.0	4.0					15																	75135403		1571	3479	5050	SO:0001583	missense	25989	exon1			GTGAGGATGAAGC	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"""unc-51-like kinase 3 (C. elegans)"""				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.44T>C	chr15.hg19:g.75135403A>G	ENSP00000400312:p.Ile15Thr	153.0	0.0	.		98.0	29.0	.	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Missense_Mutation	SNP	ENST00000440863.2	hg19	CCDS45305.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480633	0.44044	.	.	ENSG00000140474	ENST00000440863	T	0.23552	1.9	4.54	4.54	0.55810	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.117629	0.53938	D	0.000046	T	0.15262	0.0368	N	0.13272	0.32	0.80722	D	1	B;B	0.17038	0.002;0.02	B;B	0.24006	0.01;0.05	T	0.08534	-1.0717	10	0.14252	T	0.57	.	12.8187	0.57679	1.0:0.0:0.0:0.0	.	15;15	Q6PHR2;Q6PHR2-3	ULK3_HUMAN;.	T	15	ENSP00000400312:I15T	ENSP00000400312:I15T	I	-	2	0	ULK3	72922456	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.408000	0.80041	1.903000	0.55091	0.459000	0.35465	ATC	.	.	.	none		0.776	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518	
SLC28A1	9154	hgsc.bcm.edu	37	15	85476403	85476403	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr15:85476403T>A	ENST00000286749.3	+	12	1201	c.1111T>A	c.(1111-1113)Tct>Act	p.S371T	SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537216.1_Missense_Mutation_p.S371T|SLC28A1_ENST00000537624.1_Missense_Mutation_p.S371T|SLC28A1_ENST00000394573.1_Missense_Mutation_p.S371T			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	371					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GATTGCAGCCTCTGTGATGGC	0.572																																					p.S371T		Atlas-SNP	.											.	SLC28A1	118	.	0			c.T1111A						PASS	.						194.0	163.0	174.0					15																	85476403		2203	4299	6502	SO:0001583	missense	9154	exon13			GCAGCCTCTGTGA	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1111T>A	chr15.hg19:g.85476403T>A	ENSP00000286749:p.Ser371Thr	55.0	0.0	.		34.0	14.0	.	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	hg19	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395020	0.62066	.	.	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	4.4	3.27	0.37495	Na dependent nucleoside transporter, C-terminal (1);	0.112318	0.64402	D	0.000006	T	0.15869	0.0382	M	0.82823	2.61	0.80722	D	1	B;B;B	0.34264	0.432;0.446;0.432	B;B;B	0.40940	0.344;0.329;0.344	T	0.00837	-1.1546	10	0.49607	T	0.09	-10.8731	8.0882	0.30784	0.0:0.0977:0.0:0.9023	.	371;371;371	B7Z533;F5H560;O00337	.;.;S28A1_HUMAN	T	371	ENSP00000440546:S371T;ENSP00000444700:S371T;ENSP00000286749:S371T;ENSP00000378074:S371T	ENSP00000286749:S371T	S	+	1	0	SLC28A1	83277407	1.000000	0.71417	0.141000	0.22245	0.782000	0.44232	7.597000	0.82733	0.718000	0.32166	0.460000	0.39030	TCT	.	.	.	none		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
PRR14	78994	hgsc.bcm.edu	37	16	30666905	30666905	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr16:30666905G>A	ENST00000542965.2	+	9	1853	c.1397G>A	c.(1396-1398)cGa>cAa	p.R466Q	PRR14_ENST00000571654.1_3'UTR|FBRS_ENST00000356166.6_5'Flank|PRR14_ENST00000300835.4_Missense_Mutation_p.R466Q			Q9BWN1	PRR14_HUMAN	proline rich 14	466										breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			GGACTGCCTCGACCAATCAGG	0.527																																					p.R466Q		Atlas-SNP	.											.	PRR14	45	.	0			c.G1397A						PASS	.						59.0	50.0	53.0					16																	30666905		2197	4300	6497	SO:0001583	missense	78994	exon10			TGCCTCGACCAAT	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.1397G>A	chr16.hg19:g.30666905G>A	ENSP00000441641:p.Arg466Gln	70.0	0.0	.		81.0	47.0	.	NM_024031	Q8WTX2	Missense_Mutation	SNP	ENST00000542965.2	hg19	CCDS10687.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870580	0.72065	.	.	ENSG00000156858	ENST00000287463;ENST00000300835;ENST00000542965	T;T	0.58060	0.36;0.36	4.9	4.9	0.64082	.	0.234286	0.32218	N	0.006402	T	0.69251	0.3090	M	0.61703	1.905	0.40056	D	0.975836	D	0.89917	1.0	D	0.81914	0.995	T	0.73528	-0.3954	10	0.72032	D	0.01	-5.1769	14.9896	0.71377	0.0:0.0:1.0:0.0	.	466	Q9BWN1	PRR14_HUMAN	Q	439;466;466	ENSP00000300835:R466Q;ENSP00000441641:R466Q	ENSP00000287463:R439Q	R	+	2	0	PRR14	30574406	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.651000	0.54431	2.289000	0.77006	0.467000	0.42956	CGA	.	.	.	none		0.527	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031	
VMO1	284013	hgsc.bcm.edu	37	17	4688689	4688689	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr17:4688689T>C	ENST00000328739.5	-	3	656	c.577A>G	c.(577-579)Aac>Gac	p.N193D	VMO1_ENST00000416307.2_3'UTR|VMO1_ENST00000441199.2_3'UTR|VMO1_ENST00000354194.4_3'UTR	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	193						extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						CGCGCGTCGTTCAGCGCAGTG	0.637																																					p.N193D		Atlas-SNP	.											.	VMO1	19	.	0			c.A577G						PASS	.						39.0	38.0	38.0					17																	4688689		2203	4300	6503	SO:0001583	missense	284013	exon3			CGTCGTTCAGCGC	AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.577A>G	chr17.hg19:g.4688689T>C	ENSP00000328397:p.Asn193Asp	41.0	0.0	.		29.0	5.0	.	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	hg19	CCDS11055.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614127	0.87359	.	.	ENSG00000182853	ENST00000328739	T	0.52983	0.64	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.67804	0.2932	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72414	-0.4301	10	0.87932	D	0	-28.9276	12.295	0.54840	0.0:0.0:0.0:1.0	.	193	Q7Z5L0	VMO1_HUMAN	D	193	ENSP00000328397:N193D	ENSP00000328397:N193D	N	-	1	0	VMO1	4635429	1.000000	0.71417	0.768000	0.31515	0.847000	0.48162	6.415000	0.73328	2.016000	0.59253	0.459000	0.35465	AAC	.	.	.	none		0.637	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566	
OMG	4974	hgsc.bcm.edu	37	17	29622689	29622689	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr17:29622689T>G	ENST00000247271.4	-	2	922	c.661A>C	c.(661-663)Acc>Ccc	p.T221P	NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron	NM_002544.4	NP_002535.3	P23515	OMGP_HUMAN	oligodendrocyte myelin glycoprotein	221					cell adhesion (GO:0007155)|negative regulation of axonogenesis (GO:0050771)|neuron projection regeneration (GO:0031102)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|regulation of collateral sprouting of intact axon in response to injury (GO:0048683)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.0?(8)|p.?(3)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|stomach(1)	13		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;1.81e-13)|Epithelial(4;4.04e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.49e-12)|GBM - Glioblastoma multiforme(4;0.121)		TTGTAAAGGGTTATCTCTTGC	0.383																																					p.T221P		Atlas-SNP	.											.	OMG	30	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A661C						PASS	.						168.0	160.0	163.0					17																	29622689		2203	4300	6503	SO:0001583	missense	4974	exon2			AAAGGGTTATCTC		CCDS11265.1	17q11-q12	2008-07-18			ENSG00000126861	ENSG00000126861			8135	protein-coding gene	gene with protein product		164345				1899288, 2277079	Standard	NM_002544		Approved	OMGP	uc002hgj.3	P23515	OTTHUMG00000132870	ENST00000247271.4:c.661A>C	chr17.hg19:g.29622689T>G	ENSP00000247271:p.Thr221Pro	100.0	0.0	.		79.0	23.0	.	NM_002544	E1P659	Missense_Mutation	SNP	ENST00000247271.4	hg19	CCDS11265.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.715414	0.48622	.	.	ENSG00000126861	ENST00000247271	T	0.58060	0.36	5.72	4.61	0.57282	.	0.092549	0.47093	D	0.000251	T	0.61413	0.2345	L	0.46157	1.445	0.80722	D	1	P	0.46142	0.873	P	0.59487	0.858	T	0.58228	-0.7673	10	0.37606	T	0.19	-3.0707	12.2612	0.54651	0.1274:0.0:0.0:0.8726	.	221	P23515	OMGP_HUMAN	P	221	ENSP00000247271:T221P	ENSP00000247271:T221P	T	-	1	0	OMG	26646815	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.403000	0.59729	1.055000	0.40461	0.528000	0.53228	ACC	.	.	.	none		0.383	OMG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256350.2	NM_002544	
BPTF	2186	hgsc.bcm.edu	37	17	65944312	65944312	+	Nonsense_Mutation	SNP	C	C	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr17:65944312C>T	ENST00000321892.4	+	25	8255	c.8194C>T	c.(8194-8196)Cag>Tag	p.Q2732*	BPTF_ENST00000306378.6_Nonsense_Mutation_p.Q2606*|BPTF_ENST00000335221.5_Nonsense_Mutation_p.Q2589*|RP11-855A2.3_ENST00000577385.1_RNA|BPTF_ENST00000424123.3_Nonsense_Mutation_p.Q2450*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2732					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACGTAGCAAGCAGAATGCCAC	0.453																																					p.Q2606X		Atlas-SNP	.											.	BPTF	415	.	0			c.C7816T						PASS	.						122.0	122.0	122.0					17																	65944312		2203	4300	6503	SO:0001587	stop_gained	2186	exon23			AGCAAGCAGAATG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8194C>T	chr17.hg19:g.65944312C>T	ENSP00000315454:p.Gln2732*	113.0	0.0	.		96.0	21.0	.	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Nonsense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	C	50	16.265582	0.99859	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892;ENST00000424123	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-7.5331	19.9341	0.97130	0.0:1.0:0.0:0.0	.	.	.	.	X	2606;2589;2732;260	.	ENSP00000307208:Q2606X	Q	+	1	0	BPTF	63374774	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.480000	0.45206	2.711000	0.92665	0.563000	0.77884	CAG	.	.	.	none		0.453	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
NPC1	4864	hgsc.bcm.edu	37	18	21112245	21112245	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr18:21112245G>T	ENST00000269228.5	-	25	4312	c.3758C>A	c.(3757-3759)cCa>cAa	p.P1253Q	NPC1_ENST00000412552.2_Missense_Mutation_p.P935Q	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	1253					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ATTTACTGATGGCCCTATGAG	0.483																																					p.P1253Q		Atlas-SNP	.											.	NPC1	114	.	0			c.C3758A						PASS	.						166.0	153.0	158.0					18																	21112245		2203	4300	6503	SO:0001583	missense	4864	exon25			ACTGATGGCCCTA	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.3758C>A	chr18.hg19:g.21112245G>T	ENSP00000269228:p.Pro1253Gln	66.0	0.0	.		67.0	22.0	.	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051325	0.75960	.	.	ENSG00000141458	ENST00000269228;ENST00000412552	D;D	0.94723	-3.5;-3.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.97362	0.9137	M	0.77616	2.38	0.80722	D	1	D;D	0.76494	0.992;0.999	D;D	0.72338	0.964;0.977	D	0.97027	0.9747	10	0.72032	D	0.01	-14.4897	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1264;1253	Q59GR1;O15118	.;NPC1_HUMAN	Q	1253;935	ENSP00000269228:P1253Q;ENSP00000408606:P935Q	ENSP00000269228:P1253Q	P	-	2	0	NPC1	19366243	1.000000	0.71417	0.585000	0.28666	0.304000	0.27724	8.841000	0.92131	2.941000	0.99782	0.655000	0.94253	CCA	.	.	.	none		0.483	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
KATNAL2	83473	hgsc.bcm.edu	37	18	44595931	44595931	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr18:44595931T>G	ENST00000245121.5	+	10	946	c.752T>G	c.(751-753)aTt>aGt	p.I251S	KATNAL2_ENST00000356157.7_Missense_Mutation_p.I323S|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						GCATCCACCATTGTCAGCAAA	0.358																																					p.I251S		Atlas-SNP	.											.	KATNAL2	64	.	0			c.T752G						PASS	.						92.0	88.0	89.0					18																	44595931		2203	4300	6503	SO:0001583	missense	83473	exon10			CCACCATTGTCAG	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.752T>G	chr18.hg19:g.44595931T>G	ENSP00000245121:p.Ile251Ser	109.0	0.0	.		62.0	35.0	.	NM_031303		Missense_Mutation	SNP	ENST00000245121.5	hg19	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.653075	0.88056	.	.	ENSG00000167216	ENST00000356157;ENST00000245121;ENST00000454462	D;D	0.95103	-3.61;-3.61	5.78	5.78	0.91487	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.96506	0.8860	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97051	0.9764	10	0.87932	D	0	-7.6939	16.1021	0.81178	0.0:0.0:0.0:1.0	.	323	Q8IYT4	KATL2_HUMAN	S	323;251;91	ENSP00000348478:I323S;ENSP00000245121:I251S	ENSP00000245121:I251S	I	+	2	0	KATNAL2	42849929	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	6.267000	0.72546	2.210000	0.71456	0.533000	0.62120	ATT	.	.	.	none		0.358	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303	
ALPK2	115701	hgsc.bcm.edu	37	18	56149190	56149190	+	Silent	SNP	T	T	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr18:56149190T>C	ENST00000361673.3	-	13	6591	c.6378A>G	c.(6376-6378)aaA>aaG	p.K2126K		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	2126	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GTCCCAGCATTTTGCAATACT	0.408																																					p.K2126K		Atlas-SNP	.											.	ALPK2	487	.	0			c.A6378G						PASS	.						178.0	163.0	168.0					18																	56149190		2203	4300	6503	SO:0001819	synonymous_variant	115701	exon13			CAGCATTTTGCAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.6378A>G	chr18.hg19:g.56149190T>C		113.0	0.0	.		56.0	23.0	.	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	hg19	CCDS11966.2																																																																																			.	.	.	none		0.408	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
SAFB	6294	hgsc.bcm.edu	37	19	5664085	5664085	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:5664085T>C	ENST00000292123.5	+	16	2313	c.2206T>C	c.(2206-2208)Tac>Cac	p.Y736H	SAFB_ENST00000454510.1_Missense_Mutation_p.Y667H|SAFB_ENST00000433404.1_Missense_Mutation_p.Y566H|SAFB_ENST00000592224.1_Missense_Mutation_p.Y735H|SAFB_ENST00000588852.1_Missense_Mutation_p.Y736H|SAFB_ENST00000538656.1_Missense_Mutation_p.Y578H	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	736	Arg-rich.|Interaction with POLR2A.|Interaction with SAFB2.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GGATGAGCGCTACCATTCTGA	0.622																																					p.Y736H	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.T2206C						PASS	.						48.0	47.0	47.0					19																	5664085		2203	4300	6503	SO:0001583	missense	6294	exon16			GAGCGCTACCATT	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.2206T>C	chr19.hg19:g.5664085T>C	ENSP00000292123:p.Tyr736His	47.0	0.0	.		38.0	19.0	.	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	hg19	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.496184	0.44352	.	.	ENSG00000160633	ENST00000454510;ENST00000540206;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.12039	2.75;2.9;2.72;2.73	4.99	4.99	0.66335	.	0.000000	0.45606	D	0.000353	T	0.15176	0.0366	M	0.76574	2.34	0.42698	D	0.993605	P;P;P;P;P;P;P	0.39759	0.56;0.56;0.687;0.56;0.56;0.56;0.56	B;B;B;B;B;B;B	0.37833	0.132;0.132;0.259;0.132;0.132;0.132;0.132	T	0.05131	-1.0904	10	0.12766	T	0.61	-20.0369	8.9747	0.35928	0.0:0.0842:0.0:0.9158	.	535;578;667;735;736;736;735	B7Z1C7;B7Z2F6;F5H0H3;B7ZLP5;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	H	667;631;566;736;578	ENSP00000415895:Y667H;ENSP00000404545:Y566H;ENSP00000292123:Y736H;ENSP00000438880:Y578H	ENSP00000292123:Y736H	Y	+	1	0	SAFB	5615085	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.510000	0.67018	2.008000	0.58898	0.460000	0.39030	TAC	.	.	.	none		0.622	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2		
MLLT1	4298	hgsc.bcm.edu	37	19	6270658	6270658	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:6270658C>T	ENST00000252674.7	-	2	288	c.125G>A	c.(124-126)tGt>tAt	p.C42Y		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	42	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CTGGATGTCACATTGCTCGGG	0.627			T	MLL	AL						OREG0025198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C42Y		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""		L	.	MLLT1	47	.	0			c.G125A						PASS	.						119.0	92.0	101.0					19																	6270658		2203	4300	6503	SO:0001583	missense	4298	exon2			ATGTCACATTGCT		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.125G>A	chr19.hg19:g.6270658C>T	ENSP00000252674:p.Cys42Tyr	52.0	0.0	.	632	36.0	19.0	.	NM_005934	Q14768	Missense_Mutation	SNP	ENST00000252674.7	hg19	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745359	0.49151	.	.	ENSG00000130382	ENST00000252674	.	.	.	5.41	5.41	0.78517	.	0.154638	0.64402	D	0.000013	T	0.29458	0.0734	N	0.08118	0	0.46317	D	0.998986	B	0.19200	0.034	B	0.17979	0.02	T	0.17471	-1.0368	9	0.15952	T	0.53	-10.324	10.1806	0.42965	0.0:0.9095:0.0:0.0905	.	42	Q03111	ENL_HUMAN	Y	42	.	ENSP00000252674:C42Y	C	-	2	0	MLLT1	6221658	0.991000	0.36638	0.969000	0.41365	0.970000	0.65996	6.004000	0.70709	2.537000	0.85549	0.561000	0.74099	TGT	.	.	.	none		0.627	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934	
MUC16	94025	hgsc.bcm.edu	37	19	9064158	9064158	+	Missense_Mutation	SNP	G	G	C	rs567112342		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:9064158G>C	ENST00000397910.4	-	3	23491	c.23288C>G	c.(23287-23289)aCa>aGa	p.T7763R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7765	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CACGGCTTCTGTATGTGCAGT	0.488													g|||	1	0.000199681	0.0	0.0	5008	,	,		22175	0.0		0.0	False		,,,				2504	0.001				p.T7763R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C23288G						PASS	.						370.0	348.0	355.0					19																	9064158		2079	4201	6280	SO:0001583	missense	94025	exon3			GCTTCTGTATGTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.23288C>G	chr19.hg19:g.9064158G>C	ENSP00000381008:p.Thr7763Arg	133.0	0.0	.		96.0	39.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.147	-0.175028	0.06421	.	.	ENSG00000181143	ENST00000397910	T	0.28666	1.6	1.52	1.52	0.23074	.	.	.	.	.	T	0.35335	0.0928	L	0.34521	1.04	.	.	.	D	0.71674	0.998	P	0.61328	0.887	T	0.45234	-0.9275	8	0.87932	D	0	.	6.441	0.21849	0.0:0.0:1.0:0.0	.	7763	B5ME49	.	R	7763	ENSP00000381008:T7763R	ENSP00000381008:T7763R	T	-	2	0	MUC16	8925158	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.908000	0.04063	1.138000	0.42230	0.195000	0.17529	ACA	.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRKCSH	5589	hgsc.bcm.edu	37	19	11558367	11558367	+	Silent	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:11558367G>A	ENST00000589838.1	+	10	963	c.963G>A	c.(961-963)gaG>gaA	p.E321E	PRKCSH_ENST00000592741.1_Silent_p.E321E|PRKCSH_ENST00000587327.1_Silent_p.E321E|PRKCSH_ENST00000412601.1_Silent_p.E321E|PRKCSH_ENST00000252455.2_Silent_p.E321E|PRKCSH_ENST00000591462.1_Silent_p.E321E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	321	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaggaagaag	0.632																																					p.E321E		Atlas-SNP	.											.	PRKCSH	55	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G963A						PASS	.						28.0	28.0	28.0					19																	11558367		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAGGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.963G>A	chr19.hg19:g.11558367G>A		108.0	0.0	.		74.0	9.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	none		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
AKAP8	10270	hgsc.bcm.edu	37	19	15483755	15483755	+	Silent	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:15483755G>A	ENST00000269701.2	-	5	828	c.768C>T	c.(766-768)taC>taT	p.Y256Y		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	256					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						CCATCACGCCGTAGTCGGGAG	0.692																																					p.Y256Y	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.C768T						PASS	.						16.0	17.0	17.0					19																	15483755		2202	4296	6498	SO:0001819	synonymous_variant	10270	exon5			CACGCCGTAGTCG	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.768C>T	chr19.hg19:g.15483755G>A		110.0	0.0	.		67.0	25.0	.	NM_005858		Silent	SNP	ENST00000269701.2	hg19	CCDS12329.1																																																																																			.	.	.	none		0.692	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858	
ATP1A3	478	hgsc.bcm.edu	37	19	42482815	42482815	+	Nonsense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:42482815T>A	ENST00000302102.5	-	12	1723	c.1573A>T	c.(1573-1575)Aag>Tag	p.K525*	ATP1A3_ENST00000545399.1_Nonsense_Mutation_p.K538*|ATP1A3_ENST00000602133.1_Nonsense_Mutation_p.K495*|ATP1A3_ENST00000543770.1_Nonsense_Mutation_p.K536*	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	525					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						AAGGCCTCCTTCATTTCCTCG	0.662																																					p.K538X		Atlas-SNP	.											.	ATP1A3	117	.	0			c.A1612T						PASS	.						79.0	73.0	75.0					19																	42482815		2203	4300	6503	SO:0001587	stop_gained	478	exon12			CCTCCTTCATTTC		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"""ATPases / P-type"""	801	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-3"", ""sodium pump subunit alpha-3"", ""sodium-potassium ATPase catalytic subunit alpha-3"""	182350	"""dystonia 12"""	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.1573A>T	chr19.hg19:g.42482815T>A	ENSP00000302397:p.Lys525*	48.0	0.0	.		36.0	18.0	.	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Nonsense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	T	40	8.091975	0.98648	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	.	.	.	4.02	4.02	0.46733	.	0.174631	0.48286	D	0.000184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2493	0.49015	0.0:0.0:0.0:1.0	.	.	.	.	X	525;525;538;495;269;536	.	ENSP00000302397:K525X	K	-	1	0	ATP1A3	47174655	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	2.706000	0.47135	1.833000	0.53350	0.459000	0.35465	AAG	.	.	.	none		0.662	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296	
APOC4	346	hgsc.bcm.edu	37	19	45448498	45448498	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:45448498G>A	ENST00000592954.1	+	3	360	c.320G>A	c.(319-321)aGc>aAc	p.S107N	APOC4-APOC2_ENST00000589057.1_Intron|APOC2_ENST00000591597.1_5'Flank|APOC4_ENST00000419266.2_Missense_Mutation_p.S107N|APOC2_ENST00000590360.1_5'Flank|APOC2_ENST00000252490.4_5'Flank|APOC2_ENST00000592257.1_5'Flank	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	107					lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		TCCAAAGACAGCCTCTTGAAG	0.577																																					p.S107N		Atlas-SNP	.											.	APOC4	6	.	0			c.G320A						PASS	.						180.0	178.0	179.0					19																	45448498		2203	4300	6503	SO:0001583	missense	346	exon3			AAGACAGCCTCTT	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"""Apolipoproteins"""	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.320G>A	chr19.hg19:g.45448498G>A	ENSP00000468236:p.Ser107Asn	88.0	0.0	.		39.0	15.0	.	NM_001646	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	hg19	CCDS12649.1	.	.	.	.	.	.	.	.	.	.	G	7.462	0.644959	0.14451	.	.	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.23348	1.91;1.91	4.26	-2.32	0.06745	.	1.088790	0.07066	N	0.834612	T	0.16041	0.0386	L	0.38838	1.175	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.34875	-0.9811	10	0.16420	T	0.52	-3.9741	4.8774	0.13664	0.4377:0.1779:0.3844:0.0	.	107	P55056	APOC4_HUMAN	N	107	ENSP00000406381:S107N;ENSP00000412935:S107N	ENSP00000406381:S107N	S	+	2	0	APOC4	50140338	0.001000	0.12720	0.422000	0.26621	0.142000	0.21351	0.285000	0.18883	-0.339000	0.08401	0.298000	0.19748	AGC	.	.	.	none		0.577	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453255.1	NM_001646	
MYH14	79784	hgsc.bcm.edu	37	19	50714027	50714028	+	Splice_Site	DNP	CG	CG	TC			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:50714027_50714028CG>TC	ENST00000596571.1	+	1	405	c.405_405CG>TC	c.(403-405)taCG>taTCg	p.Y135Y	MYH14_ENST00000601313.1_Splice_Site_p.Y135Y|MYH14_ENST00000440075.2_Splice_Site_p.Y135Y|MYH14_ENST00000376970.2_Splice_Site_p.Y135Y|MYH14_ENST00000425460.1_Splice_Site_p.Y135Y|MYH14_ENST00000598205.1_Splice_Site_p.Y135Y|MYH14_ENST00000262269.8_Splice_Site_p.Y135Y			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	135	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCCTCATCTACGTGAGTGGGCT	0.644																																					p.Y135Y|.		Atlas-SNP	.											.	MYH14	261	.	0			c.C405T|c.405+1G>C						PASS	.																																			SO:0001630	splice_region_variant	79784	exon2			CATCTACGTGAGT|ATCTACGTGAGTG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		Exception_encountered	chr19.hg19:g.50714027_50714028delinsTC		109.0|110.0	0.0	.		63.0|65.0	29.0|30.0	.	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent|Splice_Site	SNP	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.	.	none		0.644	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	Silent
PHF20	51230	hgsc.bcm.edu	37	20	34459634	34459634	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:34459634G>C	ENST00000374012.3	+	9	1294	c.1165G>C	c.(1165-1167)Ggg>Cgg	p.G389R	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	389					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CCACTCCTTTGGGGATGGATC	0.478																																					p.G389R		Atlas-SNP	.											.	PHF20	94	.	0			c.G1165C						PASS	.						120.0	122.0	121.0					20																	34459634		2203	4300	6503	SO:0001583	missense	51230	exon9			TCCTTTGGGGATG	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1165G>C	chr20.hg19:g.34459634G>C	ENSP00000363124:p.Gly389Arg	104.0	0.0	.		88.0	46.0	.	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	hg19	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374080	0.61735	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.45668	1.51;0.89;0.89	5.62	5.62	0.85841	.	0.181111	0.47455	D	0.000222	T	0.42653	0.1212	L	0.43152	1.355	0.80722	D	1	P;P	0.51933	0.845;0.949	P;P	0.49752	0.467;0.621	T	0.11227	-1.0596	10	0.11485	T	0.65	.	15.156	0.72743	0.0:0.0:1.0:0.0	.	389;389	Q9BVI0;Q66K49	PHF20_HUMAN;.	R	389	ENSP00000363124:G389R;ENSP00000341900:G389R;ENSP00000363112:G389R	ENSP00000341900:G389R	G	+	1	0	PHF20	33923048	1.000000	0.71417	0.987000	0.45799	0.629000	0.37895	4.775000	0.62346	2.652000	0.90054	0.591000	0.81541	GGG	.	.	.	none		0.478	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	
HELZ2	85441	hgsc.bcm.edu	37	20	62193551	62193551	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:62193551G>C	ENST00000467148.1	-	10	6472	c.6403C>G	c.(6403-6405)Ccc>Gcc	p.P2135A	HELZ2_ENST00000427522.2_Missense_Mutation_p.P1566A	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2135	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AACCTGCTGGGGATCACTGAG	0.672																																					p.P2135A		Atlas-SNP	.											.	.	.	.	0			c.C6403G						PASS	.						11.0	13.0	13.0					20																	62193551		2168	4244	6412	SO:0001583	missense	85441	exon11			TGCTGGGGATCAC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6403C>G	chr20.hg19:g.62193551G>C	ENSP00000417401:p.Pro2135Ala	69.0	0.0	.		73.0	19.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	9.651	1.141671	0.21205	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.80033	-1.33;-1.22	2.52	-1.22	0.09494	.	1.595590	0.03742	N	0.255101	T	0.72162	0.3426	L	0.47716	1.5	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.54629	-0.8265	10	0.66056	D	0.02	-10.8255	2.2456	0.04031	0.1157:0.1269:0.3287:0.4288	.	2135;1566	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	A	1566;2135	ENSP00000393257:P1566A;ENSP00000417401:P2135A	ENSP00000393257:P1566A	P	-	1	0	RP4-697K14.7	61663995	0.000000	0.05858	0.005000	0.12908	0.703000	0.40648	-0.571000	0.05889	-0.220000	0.09988	0.313000	0.20887	CCC	.	.	.	none		0.672	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
IL10RB	3588	hgsc.bcm.edu	37	21	34648956	34648956	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr21:34648956T>A	ENST00000290200.2	+	3	337	c.229T>A	c.(229-231)Tca>Aca	p.S77T	AP000295.9_ENST00000433395.2_Silent_p.S204S	NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	77	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						ATGTGATTTCTCAAGTCTTTC	0.413																																					p.S77T	Melanoma(67;315 1275 21667 21943 44564)	Atlas-SNP	.											.	IL10RB	37	.	0			c.T229A						PASS	.						226.0	201.0	209.0					21																	34648956		2203	4300	6503	SO:0001583	missense	3588	exon3			GATTTCTCAAGTC	U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"""Interleukins and interleukin receptors"", ""CD molecules"""	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.229T>A	chr21.hg19:g.34648956T>A	ENSP00000290200:p.Ser77Thr	91.0	0.0	.		52.0	20.0	.	NM_000628	Q9BUU4	Missense_Mutation	SNP	ENST00000290200.2	hg19	CCDS13623.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937266	0.52972	.	.	ENSG00000243646	ENST00000290200;ENST00000539894	T	0.69435	-0.4	5.73	4.55	0.56014	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.148799	0.44902	D	0.000416	T	0.71239	0.3316	L	0.55017	1.72	0.28360	N	0.920525	D;D;D;P	0.89917	1.0;1.0;1.0;0.947	D;D;D;P	0.75484	0.986;0.986;0.986;0.668	T	0.62647	-0.6810	10	0.02654	T	1	-5.4307	10.0206	0.42041	0.0:0.0:0.1697:0.8303	.	79;77;77;77	Q6ZVU9;Q08334;B4DSX5;F5H766	.;I10R2_HUMAN;.;.	T	77	ENSP00000290200:S77T	ENSP00000290200:S77T	S	+	1	0	IL10RB	33570826	1.000000	0.71417	0.957000	0.39632	0.271000	0.26615	4.110000	0.57831	1.066000	0.40716	0.533000	0.62120	TCA	.	.	.	none		0.413	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3		
COL18A1	80781	hgsc.bcm.edu	37	21	46896343	46896343	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr21:46896343G>A	ENST00000359759.4	+	5	2143	c.2122G>A	c.(2122-2124)Gat>Aat	p.D708N	COL18A1_ENST00000400337.2_Missense_Mutation_p.D293N|COL18A1_ENST00000355480.5_Missense_Mutation_p.D473N			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	708	Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CAGCACGGAAGATTCCAGAAG	0.627																																					p.D473N		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1417A						PASS	.						73.0	78.0	76.0					21																	46896343		2092	4213	6305	SO:0001583	missense	80781	exon5			ACGGAAGATTCCA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2122G>A	chr21.hg19:g.46896343G>A	ENSP00000352798:p.Asp708Asn	90.0	0.0	.		64.0	32.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	G	14.41	2.526689	0.44969	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90788	-2.73;-2.69;-2.6	3.85	2.95	0.34219	.	0.864751	0.10135	U	0.711574	D	0.86439	0.5933	L	0.39245	1.2	0.09310	N	0.999996	P;P;P	0.49961	0.884;0.93;0.827	B;P;B	0.44647	0.341;0.456;0.342	T	0.74811	-0.3538	10	0.30854	T	0.27	.	7.9022	0.29742	0.1233:0.0:0.8766:0.0	.	708;473;293	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	N	293;293;473;708;708	ENSP00000383191:D293N;ENSP00000347665:D473N;ENSP00000352798:D708N	ENSP00000347665:D473N	D	+	1	0	COL18A1	45720771	0.542000	0.26426	0.214000	0.23707	0.174000	0.22865	3.652000	0.54439	0.918000	0.36919	0.391000	0.25812	GAT	.	.	.	none		0.627	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
TRMT2A	27037	hgsc.bcm.edu	37	22	20104104	20104104	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr22:20104104T>C	ENST00000252136.7	-	2	444	c.56A>G	c.(55-57)gAg>gGg	p.E19G	RANBP1_ENST00000331821.3_5'Flank|TRMT2A_ENST00000403707.3_Missense_Mutation_p.E19G|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000439169.2_Missense_Mutation_p.E19G|RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000404751.3_Missense_Mutation_p.E19G|RANBP1_ENST00000430524.1_Intron	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	19					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						ACTGCTGCTCTCCTGGCCACA	0.697																																					p.E19G		Atlas-SNP	.											.	TRMT2A	34	.	0			c.A56G						PASS	.						17.0	22.0	20.0					22																	20104104		2106	4119	6225	SO:0001583	missense	27037	exon2			CTGCTCTCCTGGC	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.56A>G	chr22.hg19:g.20104104T>C	ENSP00000252136:p.Glu19Gly	43.0	0.0	.		25.0	7.0	.	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	hg19	CCDS13774.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.180784	0.57800	.	.	ENSG00000099899	ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169;ENST00000445045	T;T;T	0.44083	0.93;0.93;0.93	5.01	5.01	0.66863	.	0.442996	0.22937	N	0.053835	T	0.31009	0.0783	L	0.29908	0.895	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.07947	-1.0746	10	0.36615	T	0.2	-5.047	11.3948	0.49836	0.0:0.0:0.0:1.0	.	19;19;19	B4E213;F2Z2W7;Q8IZ69	.;.;TRM2A_HUMAN	G	19;19;19;19;7	ENSP00000252136:E19G;ENSP00000385807:E19G;ENSP00000395738:E19G	ENSP00000252136:E19G	E	-	2	0	TRMT2A	18484104	0.543000	0.26434	0.144000	0.22314	0.089000	0.18198	0.964000	0.29306	2.023000	0.59567	0.402000	0.26972	GAG	.	.	.	none		0.697	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
PNPLA4	8228	hgsc.bcm.edu	37	X	7868821	7868821	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chrX:7868821A>G	ENST00000381042.4	-	7	838	c.668T>C	c.(667-669)cTt>cCt	p.L223P	PNPLA4_ENST00000444736.1_Missense_Mutation_p.L223P|PNPLA4_ENST00000537427.1_Missense_Mutation_p.L136P	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	223					lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				TGGGGGAAAAAGGGCTTGGTT	0.353																																					p.L223P		Atlas-SNP	.											.	PNPLA4	24	.	0			c.T668C						PASS	.						57.0	52.0	54.0					X																	7868821		2203	4299	6502	SO:0001583	missense	8228	exon7			GGAAAAAGGGCTT	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"""Patatin-like phospholipase domain containing"""	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.668T>C	chrX.hg19:g.7868821A>G	ENSP00000370430:p.Leu223Pro	240.0	0.0	.		148.0	6.0	.	NM_004650	A8K1H3|B4E362|Q8WW83	Missense_Mutation	SNP	ENST00000381042.4	hg19	CCDS14129.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.341460	0.41498	.	.	ENSG00000006757	ENST00000381042;ENST00000444736;ENST00000537427	T;T;T	0.81078	-1.45;-1.45;-1.45	4.38	4.38	0.52667	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.193685	0.33127	N	0.005243	D	0.89866	0.6839	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.90635	0.4570	10	0.87932	D	0	-22.634	9.3053	0.37872	1.0:0.0:0.0:0.0	.	223	P41247	PLPL4_HUMAN	P	223;223;136	ENSP00000370430:L223P;ENSP00000415245:L223P;ENSP00000443157:L136P	ENSP00000370430:L223P	L	-	2	0	PNPLA4	7828821	1.000000	0.71417	0.139000	0.22197	0.388000	0.30384	5.486000	0.66856	1.452000	0.47756	0.481000	0.45027	CTT	.	.	.	none		0.353	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650	
BCOR	54880	hgsc.bcm.edu	37	X	39930898	39930898	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chrX:39930898A>G	ENST00000378444.4	-	5	3271	c.3043T>C	c.(3043-3045)Tac>Cac	p.Y1015H	BCOR_ENST00000397354.3_Missense_Mutation_p.Y1015H|BCOR_ENST00000342274.4_Missense_Mutation_p.Y1015H|BCOR_ENST00000378455.4_Intron	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1015					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						ACCTCACAGTAAGCAGCGGGT	0.328			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.Y1015H		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.T3043C						PASS	.						82.0	77.0	79.0					X																	39930898		2202	4296	6498	SO:0001583	missense	54880	exon5			CACAGTAAGCAGC	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.3043T>C	chrX.hg19:g.39930898A>G	ENSP00000367705:p.Tyr1015His	234.0	0.0	.		148.0	126.0	.	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.002638	0.54254	.	.	ENSG00000183337	ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	5.87	5.87	0.94306	.	.	.	.	.	T	0.19087	0.0458	L	0.29908	0.895	0.34462	D	0.701845	D;P	0.57257	0.979;0.955	P;P	0.51487	0.671;0.542	T	0.14671	-1.0464	9	0.87932	D	0	-15.5403	15.4001	0.74834	1.0:0.0:0.0:0.0	.	1015;1015	Q6W2J9;Q6W2J9-2	BCOR_HUMAN;.	H	1015	ENSP00000380512:Y1015H;ENSP00000367705:Y1015H;ENSP00000345923:Y1015H;ENSP00000384485:Y1015H	ENSP00000345923:Y1015H	Y	-	1	0	BCOR	39815842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.170000	0.64990	2.088000	0.63022	0.486000	0.48141	TAC	.	.	.	none		0.328	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
MT-ND1	4535	hgsc.bcm.edu	37	M	3427	3427	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chrM:3427G>A	ENST00000361390.2	+	1	121	c.121G>A	c.(121-123)Ggc>Agc	p.G41S	MT-CO1_ENST00000361624.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-RNR1_ENST00000389680.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TC_ENST00000387405.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	41					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCAACGTTGTAGGCCCCTACG	0.483																																					p.G41S		Atlas-SNP	.											.	.	.	.	0			c.G121A						PASS	.																																			SO:0001583	missense	10625	exon1			GTTGTAGGCCCCT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.121G>A	chrM.hg19:g.3427G>A	ENSP00000354687:p.Gly41Ser	28.0	0.0	.		8.0	6.0	.	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	hg19																																																																																				.	.	.	none		0.483	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
SEMG2	6407	hgsc.bcm.edu	37	20	43850357	43850357	+	Frame_Shift_Del	DEL	A	A	-	rs372121807		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:43850357delA	ENST00000372769.3	+	2	174	c.84delA	c.(82-84)tcafs	p.S28fs		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	28					sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				CAGGTGGATCAAAAGGCCAAT	0.398																																					p.S28X		Atlas-Indel,Pindel	.											.	SEMG2	92	.	0			c.83delC						PASS	.						81.0	80.0	80.0					20																	43850357		2203	4300	6503	SO:0001589	frameshift_variant	6407	exon2			.		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.84delA	chr20.hg19:g.43850357delA	ENSP00000361855:p.Ser28fs	190.0	0.0	0		156.0	87.0	0.557692	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Frame_Shift_Del	DEL	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.	.	none		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
CTAGE5	4253	hgsc.bcm.edu	37	14	39777771	39777775	+	Frame_Shift_Del	DEL	AAATG	AAATG	-			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	AAATG	AAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr14:39777771_39777775delAAATG	ENST00000280083.3	+	13	1487_1491	c.1173_1177delAAATG	c.(1171-1179)gaaaatgaafs	p.ENE391fs	CTAGE5_ENST00000341502.5_Frame_Shift_Del_p.ENE391fs|CTAGE5_ENST00000396158.2_Frame_Shift_Del_p.ENE396fs|CTAGE5_ENST00000341749.3_Frame_Shift_Del_p.ENE379fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Del_p.ENE362fs|CTAGE5_ENST00000553352.1_Frame_Shift_Del_p.ENE362fs|CTAGE5_ENST00000396165.4_Frame_Shift_Del_p.ENE362fs|CTAGE5_ENST00000557038.1_Frame_Shift_Del_p.ENE311fs|CTAGE5_ENST00000556148.1_Frame_Shift_Del_p.ENE316fs|CTAGE5_ENST00000348007.3_Frame_Shift_Del_p.ENE391fs|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.ENE926fs			O15320	CTGE5_HUMAN	CTAGE family, member 5	391					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TATATCAAGAAAATGAAATGAAACT	0.293																																					p.396_397del		Atlas-Indel,Pindel	.											.	CTAGE5	75	.	0			c.1187_1191del						PASS	.																																			SO:0001589	frameshift_variant	4253	exon13			.	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1173_1177delAAATG	chr14.hg19:g.39777776_39777780delAAATG	ENSP00000280083:p.Glu391fs	312.0	0.0	0		211.0	46.0	0.218009	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Del	DEL	ENST00000280083.3	hg19	CCDS9674.1																																																																																			.	.	.	none		0.293	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
MUC2	4583	hgsc.bcm.edu	37	11	1092801	1092802	+	In_Frame_Ins	INS	-	-	CCTCCAACA	rs528672869|rs534872608	byFrequency	TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:1092801_1092802insCCTCCAACA	ENST00000441003.2	+	30	4647_4648	c.4620_4621insCCTCCAACA	c.(4621-4623)acc>CCTCCAACAacc	p.1540_1541insPPT	MUC2_ENST00000359061.5_In_Frame_Ins_p.1541_1542insPPT|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccactcccatcaccaccaccac	0.629																																					p.I1540delinsIPPT		Atlas-INDEL	.											.	MUC2	614	.	0			c.4620_4621insCCTCCAACA						PASS	.																																			SO:0001652	inframe_insertion	4583	exon30			.	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	Exception_encountered	chr11.hg19:g.1092801_1092802insCCTCCAACA	ENSP00000415183:p.Ile1540_Thr1541insProProThr	49.0	0.0	0		31.0	13.0	0.419355	NM_002457	Q14878	In_Frame_Ins	INS	ENST00000441003.2	hg19																																																																																				.	.	.	none		0.629	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ESF1	51575	hgsc.bcm.edu	37	20	13763764	13763765	+	Frame_Shift_Ins	INS	-	-	T			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:13763764_13763765insT	ENST00000202816.1	-	2	129_130	c.22_23insA	c.(22-24)atgfs	p.M8fs	NDUFAF5_ENST00000463598.1_5'Flank|NDUFAF5_ENST00000378106.5_5'Flank	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	8					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CTGGTCACTCATTATTTCTTGT	0.347																																					p.M8fs		Atlas-Indel,Pindel	.											.	ESF1	77	.	0			c.23_24insA						PASS	.																																			SO:0001589	frameshift_variant	51575	exon2			.		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.23dupA	chr20.hg19:g.13763766_13763766dupT	ENSP00000202816:p.Met8fs	57.0	0.0	0		60.0	17.0	0.283333	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Ins	INS	ENST00000202816.1	hg19	CCDS13117.1																																																																																			.	.	.	none		0.347	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649	
ALG3	10195	hgsc.bcm.edu	37	3	183958875	183958899	+	IGR	DEL	CCACTGTTGTCTACTCTAAAGGTAA	CCACTGTTGTCTACTCTAAAGGTAA	-			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	CCACTGTTGTCTACTCTAAAGGTAA	CCACTGTTGTCTACTCTAAAGGTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr3:183958875_183958899delCCACTGTTGTCTACTCTAAAGGTAA	ENST00000397676.3	-	0	1528				MIR1224_ENST00000408193.1_RNA|ALG3_ENST00000463495.1_5'Flank|VWA5B2_ENST00000426955.2_Splice_Site_p.PTVVYSKG981fs|EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Splice_Site_p.PTVVYSKG763fs	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)	p.P981H(1)		kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCTCCTCTGCCCACTGTTGTCTACTCTAAAGGTAACACCCAAAGG	0.596																																					p.981_988del		Atlas-Indel,Pindel	.											VWA5B2,NS,carcinoma,-1,1	VWA5B2	47	.	1	Substitution - Missense(1)	endometrium(1)	c.2941_2962del						PASS	.																																			SO:0001628	intergenic_variant	90113	exon17			.	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823		chr3.hg19:g.183958875_183958899delCCACTGTTGTCTACTCTAAAGGTAA		66.0	0.0	0		24.0	19.0	0.791667	NM_138345	A8JZZ6|Q9BT71	Frame_Shift_Del	DEL	ENST00000397676.3	hg19	CCDS46968.1																																																																																			.	.	.	none		0.596	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
DAZAP1	26528	hgsc.bcm.edu	37	19	1418337	1418342	+	In_Frame_Del	DEL	GCCAGC	GCCAGC	-			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	GCCAGC	GCCAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:1418337_1418342delGCCAGC	ENST00000233078.4	+	3	366_371	c.205_210delGCCAGC	c.(205-210)gccagcdel	p.AS69del	DAZAP1_ENST00000336761.6_In_Frame_Del_p.AS69del|DAZAP1_ENST00000586579.1_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	69	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACGGTGCTGGCCAGCAGACCGCACA	0.515																																					p.68_70del		Atlas-Indel,Pindel	.											.	DAZAP1	52	.	0			c.204_209del						PASS	.																																			SO:0001651	inframe_deletion	26528	exon3			.		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"""RNA binding motif (RRM) containing"""	2683	protein-coding gene	gene with protein product	"""deleted in azoospermia associated protein 1"""	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.205_210delGCCAGC	chr19.hg19:g.1418337_1418342delGCCAGC	ENSP00000233078:p.Ala69_Ser70del	56.0	0.0	0		40.0	14.0	0.35	NM_018959	Q96MJ3|Q9NRR9	In_Frame_Del	DEL	ENST00000233078.4	hg19	CCDS12065.1																																																																																			.	.	.	none		0.515	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711	
HIVEP1	3096	hgsc.bcm.edu	37	6	12123780	12123781	+	Frame_Shift_Ins	INS	-	-	C			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:12123780_12123781insC	ENST00000379388.2	+	4	4084_4085	c.3752_3753insC	c.(3751-3756)tgccatfs	p.H1252fs	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1252					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				GAAGCTCAATGCCATGATCAAG	0.475																																					p.C1251fs		Atlas-Indel,Pindel	.											.	HIVEP1	242	.	0			c.3752_3753insC						PASS	.																																			SO:0001589	frameshift_variant	3096	exon4			.	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.3754dupC	chr6.hg19:g.12123782_12123782dupC	ENSP00000368698:p.His1252fs	60.0	0.0	0		43.0	23.0	0.534884	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Frame_Shift_Ins	INS	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.	.	none		0.475	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
