#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
CPSF3L	54973	hgsc.bcm.edu	37	1	1248497	1248497	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:1248497A>G	ENST00000435064.1	-	11	1131	c.1049T>C	c.(1048-1050)aTg>aCg	p.M350T	CPSF3L_ENST00000421495.2_Missense_Mutation_p.M92T|CPSF3L_ENST00000540437.1_Missense_Mutation_p.M356T|CPSF3L_ENST00000419704.1_Missense_Mutation_p.M249T|CPSF3L_ENST00000450926.2_Missense_Mutation_p.M328T|CPSF3L_ENST00000411962.1_Missense_Mutation_p.M252T|CPSF3L_ENST00000545578.1_Missense_Mutation_p.M321T|CPSF3L_ENST00000462432.1_5'UTR	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	350					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-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;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GTAGCCGGGCATGATGACCTG	0.677																																					p.M356T		Atlas-SNP	.											.	CPSF3L	33	.	0			c.T1067C						PASS	.						22.0	21.0	21.0					1																	1248497		2196	4288	6484	SO:0001583	missense	54973	exon13			CCGGGCATGATGA	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"""integrator complex subunit 11"""	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.1049T>C	chr1.hg19:g.1248497A>G	ENSP00000413493:p.Met350Thr	37.0	0.0	.		31.0	12.0	.	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Missense_Mutation	SNP	ENST00000435064.1	hg19	CCDS21.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295485	0.60086	.	.	ENSG00000127054	ENST00000435064;ENST00000411962;ENST00000294579;ENST00000419704;ENST00000540437;ENST00000450926;ENST00000545578	T;T;T;T;T	0.46451	0.95;0.95;0.95;0.95;0.87	5.48	5.48	0.80851	Beta-Casp domain (1);	0.000000	0.85682	D	0.000000	T	0.62085	0.2399	M	0.78049	2.395	0.80722	D	1	P;P;P;P;P;P	0.51933	0.696;0.741;0.949;0.936;0.837;0.741	P;P;P;P;P;P	0.57960	0.535;0.665;0.83;0.738;0.617;0.665	T	0.67632	-0.5621	10	0.87932	D	0	-54.7181	15.5355	0.75998	1.0:0.0:0.0:0.0	.	328;321;252;249;356;350	Q5TA45-3;B4DM87;C9IYS7;Q5TA45-2;G3V1S5;Q5TA45	.;.;.;.;.;INT11_HUMAN	T	350;252;243;249;356;328;321	ENSP00000413493:M350T;ENSP00000404886:M249T;ENSP00000445001:M356T;ENSP00000392848:M328T;ENSP00000444672:M321T	ENSP00000294579:M243T	M	-	2	0	CPSF3L	1238360	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.568000	0.90741	2.077000	0.62373	0.460000	0.39030	ATG	.	.	.	none		0.677	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871	
PLCH2	9651	hgsc.bcm.edu	37	1	2430213	2430213	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:2430213A>G	ENST00000419816.2	+	18	2654	c.2380A>G	c.(2380-2382)Att>Gtt	p.I794V	PLCH2_ENST00000449969.1_Missense_Mutation_p.I767V|PLCH2_ENST00000378486.3_Missense_Mutation_p.I794V|PLCH2_ENST00000288766.5_Missense_Mutation_p.I82V|PLCH2_ENST00000378488.3_Missense_Mutation_p.I758V			O75038	PLCH2_HUMAN	phospholipase C, eta 2	794	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		GGTGGAGATCATTGGGCTCCC	0.657																																					p.I794V		Atlas-SNP	.											.	PLCH2	131	.	0			c.A2380G						PASS	.						28.0	32.0	31.0					1																	2430213		2068	4190	6258	SO:0001583	missense	9651	exon18			GAGATCATTGGGC	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"""EF-hand domain containing"""	29037	protein-coding gene	gene with protein product		612836	"""phospholipase C-like 4"""	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.2380A>G	chr1.hg19:g.2430213A>G	ENSP00000389803:p.Ile794Val	39.0	0.0	.		31.0	14.0	.	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.104041	0.76983	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488;ENST00000288766;ENST00000378483;ENST00000343889;ENST00000278878	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.93	4.93	0.64822	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.25005	0.0607	L	0.28400	0.85	0.48632	D	0.999685	P;P;D;P	0.69078	0.938;0.938;0.997;0.938	P;P;D;P	0.77557	0.679;0.842;0.99;0.842	T	0.01661	-1.1301	10	0.52906	T	0.07	.	13.39	0.60818	1.0:0.0:0.0:0.0	.	641;546;767;794	B9DI81;B9DI82;O75038-2;O75038	.;.;.;PLCH2_HUMAN	V	767;794;758;82;80;641;546	ENSP00000397289:I767V;ENSP00000367747:I794V;ENSP00000367749:I758V;ENSP00000288766:I82V	ENSP00000278878:I546V	I	+	1	0	PLCH2	2420073	1.000000	0.71417	0.993000	0.49108	0.499000	0.33736	5.860000	0.69546	1.845000	0.53610	0.459000	0.35465	ATT	.	.	.	none		0.657	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638	
HMGB4	127540	hgsc.bcm.edu	37	1	34329977	34329977	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:34329977C>T	ENST00000522796.1	+	4	2090	c.185C>T	c.(184-186)gCc>gTc	p.A62V	CSMD2_ENST00000373381.4_Intron|HMGB4_ENST00000519684.1_Missense_Mutation_p.A62V|HMGB4_ENST00000425537.1_3'UTR			Q8WW32	HMGB4_HUMAN	high mobility group box 4	62						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAATATGAAGCCCTGGCCAAA	0.463																																					p.A62V		Atlas-SNP	.											.	HMGB4	27	.	0			c.C185T						PASS	.						120.0	135.0	130.0					1																	34329977		2203	4300	6503	SO:0001583	missense	127540	exon2			ATGAAGCCCTGGC		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"""High-mobility group / Canonical"""	24954	protein-coding gene	gene with protein product			"""high-mobility group box 4"""				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.185C>T	chr1.hg19:g.34329977C>T	ENSP00000430919:p.Ala62Val	189.0	0.0	.		133.0	55.0	.	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542128	0.65198	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	T;T	0.14144	2.53;2.53	5.58	0.467	0.16721	.	0.232725	0.37053	N	0.002268	T	0.18002	0.0432	M	0.68317	2.08	0.31177	N	0.702474	P	0.40931	0.733	P	0.46758	0.526	T	0.09662	-1.0664	10	0.87932	D	0	.	4.817	0.13372	0.4359:0.4072:0.0:0.1569	.	62	B2R4X7	.	V	62	ENSP00000429214:A62V;ENSP00000430919:A62V	ENSP00000429214:A62V	A	+	2	0	HMGB4	34102564	0.991000	0.36638	0.082000	0.20525	0.854000	0.48673	2.434000	0.44802	-0.049000	0.13379	-0.192000	0.12808	GCC	.	.	.	none		0.463	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205	
SSBP3	23648	hgsc.bcm.edu	37	1	54870254	54870254	+	Nonsense_Mutation	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:54870254C>T	ENST00000371320.3	-	3	596	c.186G>A	c.(184-186)tgG>tgA	p.W62*	SSBP3_ENST00000371319.3_Nonsense_Mutation_p.W62*|SSBP3_ENST00000357475.4_Nonsense_Mutation_p.W62*|SSBP3_ENST00000417664.2_De_novo_Start_OutOfFrame	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	62					head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						CTTACCACCACCACGAGTGCA	0.507																																					p.W62X		Atlas-SNP	.											.	SSBP3	65	.	0			c.G186A						PASS	.						88.0	76.0	80.0					1																	54870254		2203	4300	6503	SO:0001587	stop_gained	23648	exon3			CCACCACCACGAG		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"""single-stranded DNA-binding protein 3"""			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.186G>A	chr1.hg19:g.54870254C>T	ENSP00000360371:p.Trp62*	149.0	0.0	.		68.0	19.0	.	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Nonsense_Mutation	SNP	ENST00000371320.3	hg19	CCDS591.1	.	.	.	.	.	.	.	.	.	.	C	43	10.209365	0.99360	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	5.03	5.03	0.67393	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2803	18.3392	0.90299	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000350067:W62X	W	-	3	0	SSBP3	54642842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.556000	0.82233	2.502000	0.84385	0.561000	0.74099	TGG	.	.	.	none		0.507	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070	
COLGALT2	23127	hgsc.bcm.edu	37	1	183944269	183944269	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:183944269G>C	ENST00000361927.4	-	3	825	c.454C>G	c.(454-456)Ctt>Gtt	p.L152V	COLGALT2_ENST00000546159.1_Missense_Mutation_p.L152V	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	152					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										GCAGTTCGAAGGGCTGCCTGT	0.438																																					p.L152V		Atlas-SNP	.											.	.	.	.	0			c.C454G						PASS	.						119.0	113.0	115.0					1																	183944269		2203	4300	6503	SO:0001583	missense	23127	exon3			TTCGAAGGGCTGC	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 17"", ""glycosyltransferase 25 domain containing 2"""	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.454C>G	chr1.hg19:g.183944269G>C	ENSP00000354960:p.Leu152Val	150.0	0.0	.		99.0	35.0	.	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519102	0.85495	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.62364	0.03;0.03	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.80889	0.4710	M	0.89840	3.065	0.80722	D	1	D;D	0.67145	0.993;0.996	P;D	0.67725	0.873;0.953	D	0.84426	0.0574	10	0.87932	D	0	.	12.479	0.55831	0.0768:0.0:0.9232:0.0	.	152;152	F5H3T5;Q8IYK4	.;GT252_HUMAN	V	152	ENSP00000439112:L152V;ENSP00000354960:L152V	ENSP00000354960:L152V	L	-	1	0	GLT25D2	182210892	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.705000	0.84606	2.583000	0.87209	0.650000	0.86243	CTT	.	.	.	none		0.438	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101	
HMCN1	83872	hgsc.bcm.edu	37	1	186083139	186083139	+	Silent	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:186083139G>A	ENST00000271588.4	+	73	11389	c.11160G>A	c.(11158-11160)caG>caA	p.Q3720Q	HMCN1_ENST00000367492.2_Silent_p.Q3720Q	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3720	Ig-like C2-type 36.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGGGCCCCCAGAGCCTTGTAA	0.423																																					p.Q3720Q		Atlas-SNP	.											.	HMCN1	797	.	0			c.G11160A						PASS	.						114.0	133.0	127.0					1																	186083139		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon73			CCCCCAGAGCCTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11160G>A	chr1.hg19:g.186083139G>A		278.0	0.0	.		208.0	69.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
GCC2	9648	hgsc.bcm.edu	37	2	109109239	109109239	+	Silent	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:109109239C>T	ENST00000309863.6	+	19	5154	c.4440C>T	c.(4438-4440)acC>acT	p.T1480T		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1480					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						ATGAACCGACCACAAGAAGTA	0.373																																					p.T1480T		Atlas-SNP	.											.	GCC2	129	.	0			c.C4440T						PASS	.						85.0	85.0	85.0					2																	109109239		2203	4300	6503	SO:0001819	synonymous_variant	9648	exon19			ACCGACCACAAGA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.4440C>T	chr2.hg19:g.109109239C>T		73.0	0.0	.		45.0	21.0	.	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	hg19	CCDS33268.1																																																																																			.	.	.	none		0.373	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
TTN	7273	hgsc.bcm.edu	37	2	179611391	179611391	+	Intron	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:179611391G>C	ENST00000591111.1	-	46	10585				TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.Q5246E|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			TCTCCTTTTTGAATGTTAGAA	0.388																																					p.Q5246E		Atlas-SNP	.											.	TTN	18412	.	0			c.C15736G						PASS	.						136.0	129.0	131.0					2																	179611391		2203	4300	6503	SO:0001627	intron_variant	7273	exon46			CTTTTTGAATGTT	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.10361-4743C>G	chr2.hg19:g.179611391G>C		63.0	0.0	.		92.0	40.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	3.110	-0.182790	0.06340	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.65916	-0.18	5.95	5.95	0.96441	.	.	.	.	.	T	0.48352	0.1495	L	0.49778	1.585	0.80722	D	1	P	0.39282	0.666	B	0.28916	0.096	T	0.53063	-0.8491	9	0.02654	T	1	.	15.7227	0.77724	0.0:0.0:0.802:0.198	.	5246	Q8WZ42-6	.	E	5246;527	ENSP00000354117:Q5246E	ENSP00000304714:Q527E	Q	-	1	0	TTN	179319636	0.997000	0.39634	0.984000	0.44739	0.974000	0.67602	2.850000	0.48294	2.825000	0.97269	0.655000	0.94253	CAA	.	.	.	none		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GPR1	2825	hgsc.bcm.edu	37	2	207040930	207040930	+	Silent	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:207040930G>A	ENST00000407325.2	-	3	1404	c.1042C>T	c.(1042-1044)Ctg>Ttg	p.L348L	GPR1_ENST00000437420.1_Silent_p.L348L	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	348					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		AGGAGACACAGATTCTTGGTT	0.428																																					p.L348L		Atlas-SNP	.											GPR1,NS,carcinoma,0,1	GPR1	38	.	0			c.C1042T						PASS	.						64.0	61.0	62.0					2																	207040930		2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			GACACAGATTCTT		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.1042C>T	chr2.hg19:g.207040930G>A		63.0	0.0	.		46.0	17.0	.	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	hg19	CCDS2368.1																																																																																			.	.	.	none		0.428	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
RBM44	375316	hgsc.bcm.edu	37	2	238722326	238722326	+	Splice_Site	SNP	G	G	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:238722326G>T	ENST00000444524.2	+	2	201		c.e2+1		RBM44_ENST00000409864.1_Splice_Site|RBM44_ENST00000316997.4_Splice_Site			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44							cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		CTCCAAAAAGGTAAGGGTCTA	0.448																																					.		Atlas-SNP	.											.	RBM44	167	.	0			c.76+1G>T						PASS	.						55.0	57.0	57.0					2																	238722326		1917	4134	6051	SO:0001630	splice_region_variant	375316	exon2			AAAAAGGTAAGGG	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000444524.2:c.201+1G>T	chr2.hg19:g.238722326G>T		51.0	0.0	.		31.0	16.0	.	NM_001080504	A0AUW3	Splice_Site	SNP	ENST00000444524.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.22	1.289839	0.23478	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	.	.	.	4.25	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4628	0.55741	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM44	238387065	1.000000	0.71417	0.956000	0.39512	0.166000	0.22503	3.694000	0.54742	2.660000	0.90430	0.655000	0.94253	.	.	.	.	none		0.448	RBM44-003	PUTATIVE	basic|exp_conf	processed_transcript	protein_coding	OTTHUMT00000400909.1	NM_001080504	Intron
RAD54L2	23132	hgsc.bcm.edu	37	3	51697207	51697207	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:51697207C>G	ENST00000409535.2	+	22	4300	c.4175C>G	c.(4174-4176)tCc>tGc	p.S1392C	RAD54L2_ENST00000296477.3_Missense_Mutation_p.S1086C	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1392						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		CCACTCCTGTCCGAGCCGAGG	0.567																																					p.S1392C		Atlas-SNP	.											.	RAD54L2	94	.	0			c.C4175G						PASS	.						153.0	132.0	139.0					3																	51697207		2203	4300	6503	SO:0001583	missense	23132	exon22			TCCTGTCCGAGCC	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.4175C>G	chr3.hg19:g.51697207C>G	ENSP00000386520:p.Ser1392Cys	183.0	0.0	.		123.0	48.0	.	NM_015106	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	hg19	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	C	17.44	3.390512	0.62066	.	.	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.94092	-3.24;-3.35	5.56	5.56	0.83823	.	0.324591	0.28927	N	0.013698	D	0.85643	0.5744	N	0.08118	0	0.80722	D	1	P;P	0.46327	0.661;0.876	B;B	0.36289	0.221;0.221	D	0.88801	0.3285	10	0.72032	D	0.01	-4.0774	18.5281	0.90980	0.0:1.0:0.0:0.0	.	1392;981	Q9Y4B4;B3KV54	ARIP4_HUMAN;.	C	1392;1086	ENSP00000386520:S1392C;ENSP00000296477:S1086C	ENSP00000296477:S1086C	S	+	2	0	RAD54L2	51672247	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.158000	0.58150	2.609000	0.88269	0.655000	0.94253	TCC	.	.	.	none		0.567	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106	
MITF	4286	hgsc.bcm.edu	37	3	69928532	69928532	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:69928532A>T	ENST00000448226.2	+	2	479	c.352A>T	c.(352-354)Aag>Tag	p.K118*	MITF_ENST00000314589.5_Nonsense_Mutation_p.K102*|MITF_ENST00000352241.4_Nonsense_Mutation_p.K118*|MITF_ENST00000394355.2_Nonsense_Mutation_p.K93*|MITF_ENST00000328528.6_Nonsense_Mutation_p.K117*|MITF_ENST00000472437.1_Nonsense_Mutation_p.K66*			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	118					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GGAAGTCCTTAAGGTACGTGA	0.478			A		melanoma		"""Waardenburg syndrome type 2, Tietz syndrome"""																														p.K118X	Melanoma(29;269 969 31479 41502 42961)	Atlas-SNP	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF	156	.	0			c.A352T						PASS	.						53.0	59.0	57.0					3																	69928532		2104	4227	6331	SO:0001587	stop_gained	4286	exon2			GTCCTTAAGGTAC		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"""Basic helix-loop-helix proteins"""	7105	protein-coding gene	gene with protein product	"""homolog of mouse microphthalmia"""	156845	"""Waardenburg syndrome, type 2A"""	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.352A>T	chr3.hg19:g.69928532A>T	ENSP00000391803:p.Lys118*	35.0	0.0	.		35.0	19.0	.	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Nonsense_Mutation	SNP	ENST00000448226.2	hg19		.	.	.	.	.	.	.	.	.	.	A	33	5.248140	0.95305	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000429090;ENST00000433517;ENST00000472437;ENST00000457080;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355	.	.	.	6.02	6.02	0.97574	.	0.088619	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	.	.	.	X	118;118;66;66;66;117;117;102;102;93	.	.	K	+	1	0	MITF	70011222	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.923000	0.92808	2.311000	0.77944	0.533000	0.62120	AAG	.	.	.	none		0.478	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159	
NXPE3	91775	hgsc.bcm.edu	37	3	101520832	101520832	+	Splice_Site	SNP	A	A	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:101520832A>T	ENST00000491511.2	+	5	1803	c.847A>T	c.(847-849)Agt>Tgt	p.S283C	NXPE3_ENST00000273347.5_Splice_Site_p.S283C|NXPE3_ENST00000422132.1_Splice_Site_p.S283C|NXPE3_ENST00000477909.1_Splice_Site_p.S283C	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	283						extracellular region (GO:0005576)											TTTCTTCCAGAGGTATGTACT	0.443																																					p.S283C		Atlas-SNP	.											.	.	.	.	0			c.A847T						PASS	.						92.0	98.0	96.0					3																	101520832		2177	4287	6464	SO:0001630	splice_region_variant	91775	exon5			TTCCAGAGGTATG	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member C"""	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.848+1A>T	chr3.hg19:g.101520832A>T		233.0	0.0	.		174.0	65.0	.	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	hg19	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677582	0.88445	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	5.8	5.8	0.92144	.	0.197973	0.64402	D	0.000006	T	0.37461	0.1004	M	0.69823	2.125	0.58432	D	0.999999	D	0.76494	0.999	D	0.71656	0.974	T	0.10941	-1.0608	10	0.66056	D	0.02	-3.0682	16.1475	0.81580	1.0:0.0:0.0:0.0	.	283	Q969Y0	FA55C_HUMAN	C	283	ENSP00000273347:S283C;ENSP00000417485:S283C;ENSP00000418369:S283C;ENSP00000396421:S283C	ENSP00000273347:S283C	S	+	1	0	FAM55C	103003522	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.300000	0.96151	2.213000	0.71641	0.528000	0.53228	AGT	.	.	.	none		0.443	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	Missense_Mutation
AP2M1	1173	hgsc.bcm.edu	37	3	183898969	183898969	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:183898969T>C	ENST00000292807.5	+	7	810	c.662T>C	c.(661-663)gTt>gCt	p.V221A	AP2M1_ENST00000439647.1_Missense_Mutation_p.V219A|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Missense_Mutation_p.V219A|AP2M1_ENST00000411763.2_Missense_Mutation_p.V246A|AP2M1_ENST00000461733.1_3'UTR	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	221	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACAAGATTGTTATTGAAAAG	0.562																																					p.V219A		Atlas-SNP	.											.	AP2M1	35	.	0			c.T656C						PASS	.						145.0	153.0	151.0					3																	183898969		2060	4205	6265	SO:0001583	missense	1173	exon6			AGATTGTTATTGA	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.662T>C	chr3.hg19:g.183898969T>C	ENSP00000292807:p.Val221Ala	257.0	0.0	.		197.0	87.0	.	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	hg19	CCDS43177.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963122	0.53507	.	.	ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000439647	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	6.07	4.91	0.64330	Clathrin adaptor, mu subunit, C-terminal (3);	0.164876	0.53938	D	0.000053	T	0.33059	0.0850	M	0.67569	2.06	0.58432	D	0.999999	B;B;B;B	0.26602	0.003;0.076;0.154;0.127	B;B;B;B	0.41174	0.039;0.349;0.198;0.125	T	0.09122	-1.0689	10	0.46703	T	0.11	.	12.1758	0.54184	0.0:0.0663:0.0:0.9337	.	111;91;221;219	B7Z4N2;B4DTI4;Q96CW1;Q96CW1-2	.;.;AP2M1_HUMAN;.	A	219;246;221;161;206;219	ENSP00000371894:V219A;ENSP00000403362:V246A;ENSP00000292807:V221A;ENSP00000409081:V219A	ENSP00000292807:V221A	V	+	2	0	AP2M1	185381663	1.000000	0.71417	0.993000	0.49108	0.920000	0.55202	7.375000	0.79646	1.119000	0.41883	-0.256000	0.11100	GTT	.	.	.	none		0.562	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	
FIP1L1	81608	hgsc.bcm.edu	37	4	54266007	54266007	+	Splice_Site	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr4:54266007G>C	ENST00000337488.6	+	10	1009		c.e10+1		FIP1L1_ENST00000306932.6_Splice_Site|FIP1L1_ENST00000507922.1_Splice_Site|FIP1L1_ENST00000507166.1_Splice_Site|FIP1L1_ENST00000358575.5_Splice_Site	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1						mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CACCGAGCAGGTTAGTTACAT	0.363			T	PDGFRA	idiopathic hypereosinophilic syndrome																																.		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.701+1G>C						PASS	.						132.0	128.0	129.0					4																	54266007		2203	4300	6503	SO:0001630	splice_region_variant	81608	exon8			GAGCAGGTTAGTT	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.815+1G>C	chr4.hg19:g.54266007G>C		142.0	0.0	.		76.0	31.0	.	NM_001134938	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Splice_Site	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.122802	0.56613	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5077	0.95125	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FIP1L1	53960764	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	7.864000	0.87037	2.683000	0.91414	0.655000	0.94253	.	.	.	.	none		0.363	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	Intron
PLRG1	5356	hgsc.bcm.edu	37	4	155465648	155465648	+	Silent	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr4:155465648T>C	ENST00000499023.2	-	7	669	c.543A>G	c.(541-543)aaA>aaG	p.K181K	PLRG1_ENST00000302078.5_Silent_p.K172K|PLRG1_ENST00000393905.2_Silent_p.K181K|RNU6-1285P_ENST00000363480.1_RNA	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	181					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTGTAGGGGCTTTTTTAGCCA	0.408																																					p.K181K		Atlas-SNP	.											.,1	PLRG1	43	.	0			c.A543G						PASS	.						139.0	140.0	139.0					4																	155465648		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon7			AGGGGCTTTTTTA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.543A>G	chr4.hg19:g.155465648T>C		97.0	0.0	.		66.0	25.0	.	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	hg19	CCDS34083.1																																																																																			.	.	.	none		0.408	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
PCSK1	5122	hgsc.bcm.edu	37	5	95761622	95761622	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr5:95761622C>G	ENST00000311106.3	-	3	535	c.298G>C	c.(298-300)Gaa>Caa	p.E100Q	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.E53Q	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	100					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TACTGTTGTTCAGCCCATATC	0.383																																					p.E100Q		Atlas-SNP	.											.	PCSK1	93	.	0			c.G298C						PASS	.						141.0	129.0	133.0					5																	95761622		2203	4300	6503	SO:0001583	missense	5122	exon3			GTTGTTCAGCCCA		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.298G>C	chr5.hg19:g.95761622C>G	ENSP00000308024:p.Glu100Gln	50.0	0.0	.		40.0	16.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	hg19	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305017	0.81247	.	.	ENSG00000175426	ENST00000311106;ENST00000508626;ENST00000509190	T;T;T	0.33216	1.42;1.42;2.19	5.63	5.63	0.86233	Proteinase inhibitor, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.35740	0.0942	L	0.39633	1.23	0.58432	D	0.999997	D	0.53312	0.959	P	0.49887	0.625	T	0.01613	-1.1312	10	0.15066	T	0.55	-30.1455	19.6351	0.95728	0.0:1.0:0.0:0.0	.	100	P29120	NEC1_HUMAN	Q	100;53;100	ENSP00000308024:E100Q;ENSP00000421600:E53Q;ENSP00000427294:E100Q	ENSP00000308024:E100Q	E	-	1	0	PCSK1	95787378	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.393000	0.79851	2.805000	0.96524	0.655000	0.94253	GAA	.	.	.	none		0.383	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
FAM71B	153745	hgsc.bcm.edu	37	5	156590018	156590018	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr5:156590018G>C	ENST00000302938.4	-	2	1353	c.1258C>G	c.(1258-1260)Ccc>Gcc	p.P420A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	420						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCAGCACTGGGCTGGGAAACT	0.488																																					p.P420A		Atlas-SNP	.											.	FAM71B	145	.	0			c.C1258G						PASS	.						102.0	103.0	102.0					5																	156590018		2203	4300	6503	SO:0001583	missense	153745	exon2			CACTGGGCTGGGA		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1258C>G	chr5.hg19:g.156590018G>C	ENSP00000305596:p.Pro420Ala	137.0	0.0	.		113.0	54.0	.	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.631608	0.00813	.	.	ENSG00000170613	ENST00000302938	T	0.17528	2.27	4.4	-1.91	0.07641	.	0.847983	0.09952	N	0.734546	T	0.10035	0.0246	L	0.48877	1.53	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.42849	-0.9427	10	0.07482	T	0.82	-0.6432	2.0469	0.03562	0.1:0.2599:0.2424:0.3977	.	420	Q8TC56	FA71B_HUMAN	A	420	ENSP00000305596:P420A	ENSP00000305596:P420A	P	-	1	0	FAM71B	156522596	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.057000	0.11768	-0.177000	0.10690	-0.291000	0.09656	CCC	.	.	.	none		0.488	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
DDO	8528	hgsc.bcm.edu	37	6	110734538	110734538	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:110734538G>A	ENST00000368924.3	-	2	227	c.212C>T	c.(211-213)aCc>aTc	p.T71I	DDO_ENST00000368923.3_Missense_Mutation_p.T71I	NM_003649.2	NP_003640.2	Q99489	OXDD_HUMAN	D-aspartate oxidase	43					aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|D-amino acid catabolic process (GO:0019478)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insemination (GO:0007320)|oxidation-reduction process (GO:0055114)	peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-aspartate oxidase activity (GO:0008445)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|pancreas(1)|skin(3)	24		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		CACATCACTGGTGGTATCTGG	0.493																																					p.T71I		Atlas-SNP	.											.	DDO	51	.	0			c.C212T						PASS	.						133.0	116.0	122.0					6																	110734538		2203	4300	6503	SO:0001583	missense	8528	exon2			TCACTGGTGGTAT	D89858	CCDS5082.1, CCDS5083.1	6q22.1	2008-02-05			ENSG00000203797	ENSG00000203797	1.4.3.1		2727	protein-coding gene	gene with protein product		124450				9163533	Standard	NM_003649		Approved		uc003puc.3	Q99489	OTTHUMG00000015360	ENST00000368924.3:c.212C>T	chr6.hg19:g.110734538G>A	ENSP00000357920:p.Thr71Ile	207.0	0.0	.		125.0	53.0	.	NM_004032	A8KAG4|Q5JXM4|Q5JXM5|Q5JXM6|Q8N552	Missense_Mutation	SNP	ENST00000368924.3	hg19	CCDS5082.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287509	0.80803	.	.	ENSG00000203797	ENST00000368924;ENST00000368923;ENST00000368925	D;D;D	0.83250	-1.7;-1.7;-1.7	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.94221	0.8145	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95581	0.8646	10	0.72032	D	0.01	-21.4422	19.187	0.93648	0.0:0.0:1.0:0.0	.	71;71	Q99489-4;Q99489-3	.;.	I	71;71;43	ENSP00000357920:T71I;ENSP00000357919:T71I;ENSP00000357921:T43I	ENSP00000357919:T71I	T	-	2	0	DDO	110841231	1.000000	0.71417	0.997000	0.53966	0.546000	0.35178	7.120000	0.77153	2.614000	0.88457	0.655000	0.94253	ACC	.	.	.	none		0.493	DDO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041796.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152631610	152631610	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:152631610G>A	ENST00000367255.5	-	89	17541	c.16940C>T	c.(16939-16941)gCc>gTc	p.A5647V	SYNE1_ENST00000423061.1_Missense_Mutation_p.A5576V|SYNE1_ENST00000356820.4_Missense_Mutation_p.A171V|SYNE1_ENST00000265368.4_Missense_Mutation_p.A5647V|SYNE1_ENST00000341594.5_Missense_Mutation_p.A5259V|SYNE1_ENST00000448038.1_Missense_Mutation_p.A5576V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5647					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.A5647V(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGCTCCAAGGCAGCTTGTAA	0.433										HNSCC(10;0.0054)																											p.A5647V		Atlas-SNP	.											SYNE1_ENST00000265368,caecum,carcinoma,0,2	SYNE1	3227	.	2	Substitution - Missense(2)	large_intestine(2)	c.C16940T						PASS	.						104.0	103.0	103.0					6																	152631610		2203	4300	6503	SO:0001583	missense	23345	exon89			TCCAAGGCAGCTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16940C>T	chr6.hg19:g.152631610G>A	ENSP00000356224:p.Ala5647Val	86.0	0.0	.		50.0	19.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327610	0.81690	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50548	1.38;1.38;1.38;1.38;0.74;1.38	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000009	T	0.64136	0.2571	M	0.72118	2.19	0.53688	D	0.99997	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.961;0.961;0.983	T	0.57963	-0.7720	10	0.39692	T	0.17	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	5647;5647;5576	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	V	5647;5576;5647;5576;5259;171	ENSP00000356224:A5647V;ENSP00000396024:A5576V;ENSP00000265368:A5647V;ENSP00000390975:A5576V;ENSP00000341887:A5259V;ENSP00000349276:A171V	ENSP00000265368:A5647V	A	-	2	0	SYNE1	152673303	1.000000	0.71417	0.811000	0.32455	0.720000	0.41350	7.876000	0.87215	2.882000	0.98803	0.655000	0.94253	GCC	.	.	.	none		0.433	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
ACTB	60	hgsc.bcm.edu	37	7	5568977	5568977	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:5568977T>C	ENST00000331789.5	-	3	369	c.178A>G	c.(178-180)Agc>Ggc	p.S60G	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	60					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		CCTCTCTTGCTCTGGGCCTCG	0.587																																					p.S60G		Atlas-SNP	.											.	ACTB	45	.	0			c.A178G						PASS	.						71.0	73.0	73.0					7																	5568977		2203	4298	6501	SO:0001583	missense	60	exon3			TCTTGCTCTGGGC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.178A>G	chr7.hg19:g.5568977T>C	ENSP00000349960:p.Ser60Gly	181.0	0.0	.		178.0	97.0	.	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	hg19	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870663	0.51695	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72	4.91	4.91	0.64330	Actin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.92704	0.7681	M	0.81497	2.545	0.45594	D	0.998536	P	0.35033	0.481	P	0.45195	0.473	D	0.93247	0.6631	10	0.87932	D	0	.	12.5141	0.56021	0.0:0.0:0.0:1.0	.	60	P60709	ACTB_HUMAN	G	60;60;60;60;63;60	ENSP00000349960:S60G;ENSP00000407473:S60G;ENSP00000393951:S60G;ENSP00000399487:S63G;ENSP00000401032:S60G	ENSP00000349960:S60G	S	-	1	0	ACTB	5535503	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.816000	0.86201	1.837000	0.53436	0.460000	0.39030	AGC	.	.	.	none		0.587	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101	
ANKMY2	57037	hgsc.bcm.edu	37	7	16650259	16650260	+	Missense_Mutation	DNP	TC	TC	CT			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:16650259_16650260TC>CT	ENST00000306999.2	-	6	903_904	c.660_661GA>AG	c.(658-663)atGAag>atAGag	p.220_221MK>IE		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	220						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TAATGCATCTTCATAGCCAATA	0.351																																					p.K221E|p.M220I		Atlas-SNP	.											.	ANKMY2	46	.	0			c.A661G|c.G660A						PASS	.																																			SO:0001583	missense	57037	exon6			GCATCTTCATAGC|CATCTTCATAGCC	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.660_661delinsCT	chr7.hg19:g.16650259_16650260delinsCT	ENSP00000303570:p.M220_K221delinsIE	94.0|96.0	0.0	.		74.0|73.0	35.0|34.0	.	NM_020319	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	hg19	CCDS5361.1																																																																																			.	.	.	none		0.351	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
PCLO	27445	hgsc.bcm.edu	37	7	82584714	82584714	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:82584714T>A	ENST00000333891.9	-	5	5892	c.5555A>T	c.(5554-5556)cAt>cTt	p.H1852L	PCLO_ENST00000423517.2_Missense_Mutation_p.H1852L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGAAGATCTATGGAGCTCCTC	0.408																																					p.H1852L		Atlas-SNP	.											.	PCLO	1506	.	0			c.A5555T						PASS	.						178.0	163.0	168.0					7																	82584714		1858	4097	5955	SO:0001583	missense	27445	exon5			GATCTATGGAGCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5555A>T	chr7.hg19:g.82584714T>A	ENSP00000334319:p.His1852Leu	159.0	0.0	.		202.0	67.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.390651	0.25118	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19938	2.11;2.12	5.57	5.57	0.84162	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.80722	D	1	P;P	0.41848	0.763;0.763	B;B	0.39185	0.293;0.293	T	0.02860	-1.1101	9	0.87932	D	0	.	15.7247	0.77747	0.0:0.0:0.0:1.0	.	1852;1852	Q9Y6V0-5;Q9Y6V0-6	.;.	L	1783;1852;1852	ENSP00000334319:H1852L;ENSP00000388393:H1852L	ENSP00000334319:H1852L	H	-	2	0	PCLO	82422650	0.995000	0.38212	0.924000	0.36721	0.989000	0.77384	2.626000	0.46460	2.116000	0.64780	0.533000	0.62120	CAT	.	.	.	none		0.408	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
WDR91	29062	hgsc.bcm.edu	37	7	134871027	134871027	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:134871027A>T	ENST00000354475.4	-	15	2151	c.2120T>A	c.(2119-2121)cTa>cAa	p.L707Q	WDR91_ENST00000423565.1_Missense_Mutation_p.L672Q|WDR91_ENST00000344400.5_3'UTR	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	707										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GTGGCCACCTAGGCTCAAGCA	0.587																																					p.L707Q		Atlas-SNP	.											.	WDR91	82	.	0			c.T2120A						PASS	.						73.0	60.0	65.0					7																	134871027		2203	4300	6503	SO:0001583	missense	29062	exon15			CCACCTAGGCTCA	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.2120T>A	chr7.hg19:g.134871027A>T	ENSP00000346466:p.Leu707Gln	50.0	0.0	.		69.0	36.0	.	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	A	31	5.060981	0.93846	.	.	ENSG00000105875	ENST00000354475;ENST00000423565	T;T	0.68479	-0.33;-0.33	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82174	-0.0588	10	0.87932	D	0	-16.5822	15.6802	0.77360	1.0:0.0:0.0:0.0	.	707	A4D1P6	WDR91_HUMAN	Q	707;672	ENSP00000346466:L707Q;ENSP00000392555:L672Q	ENSP00000346466:L707Q	L	-	2	0	WDR91	134521567	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.103000	0.63969	0.533000	0.62120	CTA	.	.	.	none		0.587	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79578395	79578395	+	Silent	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr8:79578395G>C	ENST00000263849.4	+	1	114	c.12G>C	c.(10-12)ctG>ctC	p.L4L	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	4							metal ion binding (GO:0046872)										TGGAGGGACTGGAAGGTGAGG	0.672																																					p.L4L		Atlas-SNP	.											.	.	.	.	0			c.G12C						PASS	.						112.0	84.0	93.0					8																	79578395		2187	4279	6466	SO:0001819	synonymous_variant	51101	exon1			GGGACTGGAAGGT		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"""Zinc fingers, C2HC-type containing"""	24277	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 70"", ""family with sequence similarity 164, member A"""	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.12G>C	chr8.hg19:g.79578395G>C		2.0	0.0	.		10.0	6.0	.	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	hg19	CCDS6223.1																																																																																			.	.	.	none		0.672	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010	
EFR3A	23167	hgsc.bcm.edu	37	8	132968018	132968018	+	Silent	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr8:132968018C>T	ENST00000254624.5	+	7	867	c.642C>T	c.(640-642)cgC>cgT	p.R214R	EFR3A_ENST00000519656.1_Silent_p.R178R|EFR3A_ENST00000334503.4_Silent_p.R214R	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	214						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTTTTAGTCGCATAGGCCCTC	0.358																																					p.R214R		Atlas-SNP	.											.	EFR3A	96	.	0			c.C642T						PASS	.						108.0	111.0	110.0					8																	132968018		2203	4300	6503	SO:0001819	synonymous_variant	23167	exon7			TAGTCGCATAGGC	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.642C>T	chr8.hg19:g.132968018C>T		112.0	0.0	.		86.0	26.0	.	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	hg19	CCDS34942.2																																																																																			.	.	.	none		0.358	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
USP20	10868	hgsc.bcm.edu	37	9	132623219	132623219	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr9:132623219T>C	ENST00000315480.4	+	7	492	c.334T>C	c.(334-336)Tcc>Ccc	p.S112P	USP20_ENST00000372429.3_Missense_Mutation_p.S112P|USP20_ENST00000358355.1_Missense_Mutation_p.S112P			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	112					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				AACACAGGACTCCCCGCCACC	0.567																																					p.S112P		Atlas-SNP	.											.	USP20	186	.	0			c.T334C						PASS	.						146.0	150.0	149.0					9																	132623219		1918	4121	6039	SO:0001583	missense	10868	exon7			CAGGACTCCCCGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.334T>C	chr9.hg19:g.132623219T>C	ENSP00000313811:p.Ser112Pro	394.0	1.0	.		219.0	72.0	.	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.787014	0.31593	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.20463	2.07;2.07;2.07	5.66	1.8	0.24995	.	0.866856	0.10550	N	0.661611	T	0.16342	0.0393	L	0.46157	1.445	0.38108	D	0.937486	B	0.02656	0.0	B	0.04013	0.001	T	0.10337	-1.0634	10	0.30078	T	0.28	.	4.2306	0.10601	0.1241:0.0686:0.1298:0.6776	.	112	Q9Y2K6	UBP20_HUMAN	P	112	ENSP00000361506:S112P;ENSP00000313811:S112P;ENSP00000351122:S112P	ENSP00000313811:S112P	S	+	1	0	USP20	131663040	0.020000	0.18652	0.710000	0.30468	0.947000	0.59692	1.028000	0.30128	0.407000	0.25591	0.459000	0.35465	TCC	.	.	.	none		0.567	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
AKR1C3	8644	hgsc.bcm.edu	37	10	5139704	5139704	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr10:5139704G>C	ENST00000380554.3	+	3	983	c.331G>C	c.(331-333)Gtt>Ctt	p.V111L	AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.V88L|AKR1C3_ENST00000470862.2_3'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	111					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	ATTGGACTATGTTGACCTCTA	0.403																																					p.V111L		Atlas-SNP	.											.	AKR1C3	21	.	0			c.G331C						PASS	.						146.0	138.0	141.0					10																	5139704		2203	4300	6503	SO:0001583	missense	8644	exon3			GACTATGTTGACC	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.331G>C	chr10.hg19:g.5139704G>C	ENSP00000369927:p.Val111Leu	96.0	0.0	.		89.0	40.0	.	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	hg19	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.596157	0.00857	.	.	ENSG00000196139	ENST00000380554	T	0.47528	0.84	1.62	0.671	0.17929	NADP-dependent oxidoreductase domain (3);	0.237158	0.29558	N	0.011809	T	0.23410	0.0566	N	0.17564	0.495	0.80722	D	1	B;B;B	0.23249	0.082;0.005;0.005	B;B;B	0.30251	0.113;0.046;0.046	T	0.06972	-1.0797	10	0.07325	T	0.83	.	4.0982	0.10002	0.3926:0.0:0.6074:0.0	.	111;111;111	B4DKT3;P42330;Q2XPP3	.;AK1C3_HUMAN;.	L	111	ENSP00000369927:V111L	ENSP00000369927:V111L	V	+	1	0	AKR1C3	5129704	1.000000	0.71417	0.072000	0.20136	0.187000	0.23431	2.141000	0.42168	0.234000	0.21139	0.305000	0.20034	GTT	.	.	.	none		0.403	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
TACR2	6865	hgsc.bcm.edu	37	10	71175766	71175766	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr10:71175766A>T	ENST00000373306.4	-	1	857	c.314T>A	c.(313-315)tTc>tAc	p.F105Y		NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	105					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						GAAGTAGCAGAAGGCACGGCC	0.552																																					p.F105Y		Atlas-SNP	.											.	TACR2	37	.	0			c.T314A						PASS	.						92.0	81.0	85.0					10																	71175766		2203	4300	6503	SO:0001583	missense	6865	exon1			TAGCAGAAGGCAC		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.314T>A	chr10.hg19:g.71175766A>T	ENSP00000362403:p.Phe105Tyr	53.0	0.0	.		43.0	19.0	.	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	hg19	CCDS7293.1	.	.	.	.	.	.	.	.	.	.	A	7.919	0.738168	0.15574	.	.	ENSG00000075073	ENST00000373306	T	0.38240	1.15	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.063724	0.64402	D	0.000003	T	0.11922	0.0290	N	0.01493	-0.835	0.42246	D	0.99195	B	0.22146	0.065	B	0.20577	0.03	T	0.20140	-1.0284	10	0.02654	T	1	.	10.5582	0.45129	0.8559:0.0:0.0:0.1441	.	105	P21452	NK2R_HUMAN	Y	105	ENSP00000362403:F105Y	ENSP00000362403:F105Y	F	-	2	0	TACR2	70845772	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.205000	0.51090	2.093000	0.63338	0.460000	0.39030	TTC	.	.	.	none		0.552	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1		
MRPL17	63875	hgsc.bcm.edu	37	11	6703594	6703594	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:6703594G>A	ENST00000288937.6	-	3	387	c.283C>T	c.(283-285)Cct>Tct	p.P95S	MRPL17_ENST00000532676.1_5'UTR	NM_022061.3	NP_071344.1	Q9NRX2	RM17_HUMAN	mitochondrial ribosomal protein L17	95					translation (GO:0006412)	mitochondrial inner membrane (GO:0005743)|ribosome (GO:0005840)	protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			lung(4)	4		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTGTACCGAGGGGCCAGTACT	0.473																																					p.P95S		Atlas-SNP	.											.	MRPL17	11	.	0			c.C283T						PASS	.						115.0	114.0	114.0					11																	6703594		2201	4296	6497	SO:0001583	missense	63875	exon3			ACCGAGGGGCCAG	AB051620	CCDS31412.1	11p15.5-p15.4	2012-09-13				ENSG00000158042		"""Mitochondrial ribosomal proteins / large subunits"""	14053	protein-coding gene	gene with protein product		611830					Standard	NM_022061		Approved	RPML26, MRP-L26	uc001men.2	Q9NRX2		ENST00000288937.6:c.283C>T	chr11.hg19:g.6703594G>A	ENSP00000288937:p.Pro95Ser	197.0	0.0	.		141.0	48.0	.	NM_022061	D3DQU3|Q6IAH8|Q96Q53|Q9C066	Missense_Mutation	SNP	ENST00000288937.6	hg19	CCDS31412.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970737	0.74246	.	.	ENSG00000158042	ENST00000288937;ENST00000532203	.	.	.	5.73	5.73	0.89815	.	0.051442	0.85682	D	0.000000	D	0.83275	0.5219	M	0.85041	2.73	0.58432	D	0.999999	P	0.52061	0.95	D	0.65010	0.931	D	0.85197	0.1013	9	0.72032	D	0.01	-5.0434	17.4724	0.87649	0.0:0.0:1.0:0.0	.	95	Q9NRX2	RM17_HUMAN	S	95;72	.	ENSP00000288937:P95S	P	-	1	0	MRPL17	6660170	1.000000	0.71417	0.999000	0.59377	0.565000	0.35776	6.015000	0.70791	2.720000	0.93068	0.555000	0.69702	CCT	.	.	.	none		0.473	MRPL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384544.1	NM_022061	
DCDC1	341019	hgsc.bcm.edu	37	11	30902745	30902745	+	Silent	SNP	G	G	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:30902745G>T	ENST00000597505.1	-	35	5183	c.5184C>A	c.(5182-5184)gtC>gtA	p.V1728V				P59894	DCDC1_HUMAN	doublecortin domain containing 1	234					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					ACACACAGATGACCATATCTC	0.453																																					p.V835V		Atlas-SNP	.											.	DCDC5	137	.	0			c.C2505A						PASS	.						113.0	109.0	110.0					11																	30902745		1954	4159	6113	SO:0001819	synonymous_variant	100506627	exon18			ACAGATGACCATA	AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000597505.1:c.5184C>A	chr11.hg19:g.30902745G>T		61.0	0.0	.		56.0	25.0	.	NM_020869	A6PVL6|B7WNX6|Q6ZU04	Silent	SNP	ENST00000597505.1	hg19																																																																																				.	.	.	none		0.453	DCDC1-010	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000463167.1	NM_181807	
FDXACB1	91893	hgsc.bcm.edu	37	11	111749725	111749725	+	Silent	SNP	A	A	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:111749725A>G	ENST00000260257.4	-	1	179	c.132T>C	c.(130-132)gaT>gaC	p.D44D	C11orf1_ENST00000529270.1_5'Flank|C11orf1_ENST00000528125.1_5'UTR|C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000524880.1_Silent_p.D44D|C11orf1_ENST00000260276.3_5'Flank|ALG9_ENST00000527377.1_5'Flank|FDXACB1_ENST00000542429.1_5'UTR	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	44					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						AGGCCAGTGGATCCCGAGCCA	0.667											OREG0021330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D44D		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T132C						PASS	.						16.0	22.0	20.0					11																	111749725		1936	4151	6087	SO:0001819	synonymous_variant	91893	exon1			CAGTGGATCCCGA		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"""hypothetical protein BC006136"""						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.132T>C	chr11.hg19:g.111749725A>G		28.0	0.0	.	1437	25.0	11.0	.	NM_138378	A0PJW7|B4DUU2	Silent	SNP	ENST00000260257.4	hg19	CCDS44729.1																																																																																			.	.	.	none		0.667	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378	
GUCY2C	2984	hgsc.bcm.edu	37	12	14772233	14772233	+	Silent	SNP	A	A	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:14772233A>C	ENST00000261170.3	-	24	2923	c.2787T>G	c.(2785-2787)gcT>gcG	p.A929A	RP11-695J4.2_ENST00000545424.1_RNA|RP11-695J4.2_ENST00000542401.1_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	929	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CAACTCCAGCAGCACAGGGAC	0.483																																					p.A929A		Atlas-SNP	.											.	GUCY2C	126	.	0			c.T2787G						PASS	.						95.0	93.0	93.0					12																	14772233		2203	4300	6503	SO:0001819	synonymous_variant	2984	exon24			TCCAGCAGCACAG		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.2787T>G	chr12.hg19:g.14772233A>C		82.0	0.0	.		91.0	29.0	.	NM_004963	B2RMY6	Silent	SNP	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.	.	none		0.483	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1		
CNTN1	1272	hgsc.bcm.edu	37	12	41316146	41316146	+	Nonsense_Mutation	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:41316146C>T	ENST00000551295.2	+	5	433	c.316C>T	c.(316-318)Cag>Tag	p.Q106*	CNTN1_ENST00000360099.3_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000348761.2_Nonsense_Mutation_p.Q95*|CNTN1_ENST00000347616.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000547702.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000547849.1_Nonsense_Mutation_p.Q106*	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	106	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				CCCTGACAAACAGAAAGATGC	0.398																																					p.Q106X		Atlas-SNP	.											CNTN1,NS,carcinoma,0,1	CNTN1	207	.	0			c.C316T						PASS	.						138.0	123.0	128.0					12																	41316146		2203	4300	6503	SO:0001587	stop_gained	1272	exon5			GACAAACAGAAAG	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.316C>T	chr12.hg19:g.41316146C>T	ENSP00000447006:p.Gln106*	69.0	0.0	.		84.0	38.0	.	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Nonsense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063249	0.76187	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	.	.	.	5.65	4.74	0.60224	.	0.687302	0.15218	N	0.274073	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	7.1246	0.25465	0.0:0.7637:0.0:0.2363	.	.	.	.	X	106;106;106;106;106;95	.	ENSP00000325660:Q106X	Q	+	1	0	CNTN1	39602413	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.250000	0.32850	2.833000	0.97629	0.585000	0.79938	CAG	.	.	.	none		0.398	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	
KIF5A	3798	hgsc.bcm.edu	37	12	57975209	57975209	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:57975209C>T	ENST00000455537.2	+	25	3041	c.2767C>T	c.(2767-2769)Cgg>Tgg	p.R923W	KIF5A_ENST00000286452.5_Missense_Mutation_p.R834W	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	923	Globular.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAAACCCGTCCGGCCTGGCCA	0.547																																					p.R923W		Atlas-SNP	.											.	KIF5A	143	.	0			c.C2767T						PASS	.						74.0	75.0	75.0					12																	57975209		2203	4300	6503	SO:0001583	missense	3798	exon25			CCCGTCCGGCCTG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"""Kinesins"""	6323	protein-coding gene	gene with protein product		602821	"""spastic paraplegia 10 (autosomal dominant)"""	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2767C>T	chr12.hg19:g.57975209C>T	ENSP00000408979:p.Arg923Trp	150.0	0.0	.		125.0	50.0	.	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159251	0.78226	.	.	ENSG00000155980	ENST00000455537;ENST00000286452;ENST00000547989	T;T	0.81078	-1.38;-1.45	4.52	3.59	0.41128	.	0.201593	0.32343	N	0.006224	D	0.86715	0.5999	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71184	0.972;0.972	D	0.87757	0.2596	10	0.87932	D	0	.	12.7339	0.57212	0.1717:0.8283:0.0:0.0	.	834;923	B7Z2M7;Q12840	.;KIF5A_HUMAN	W	923;834;17	ENSP00000408979:R923W;ENSP00000286452:R834W	ENSP00000286452:R834W	R	+	1	2	KIF5A	56261476	1.000000	0.71417	0.989000	0.46669	0.881000	0.50899	5.716000	0.68437	1.212000	0.43366	0.561000	0.74099	CGG	.	.	.	none		0.547	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984	
NAV3	89795	hgsc.bcm.edu	37	12	78604234	78604234	+	Silent	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:78604234C>T	ENST00000397909.2	+	40	7268	c.7095C>T	c.(7093-7095)tgC>tgT	p.C2365C	NAV3_ENST00000266692.7_Silent_p.C2166C|NAV3_ENST00000536525.2_Silent_p.C2343C|NAV3_ENST00000228327.6_Silent_p.C2343C|NAV3_ENST00000541270.1_Silent_p.C195C			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2365						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CACAAAGCTGCGACAGCGAAA	0.403										HNSCC(70;0.22)																											p.C2343C		Atlas-SNP	.											.	NAV3	506	.	0			c.C7029T						PASS	.						55.0	58.0	57.0					12																	78604234		1952	4172	6124	SO:0001819	synonymous_variant	89795	exon39			AAGCTGCGACAGC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.7095C>T	chr12.hg19:g.78604234C>T		59.0	0.0	.		71.0	26.0	.	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	C	0.069	-1.207030	0.01568	.	.	ENSG00000067798	ENST00000552895;ENST00000551162	.	.	.	5.35	-7.82	0.01205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.2288	19.8674	0.96824	0.0:0.1434:0.0:0.8566	.	.	.	.	X	1238;233	.	.	R	+	1	2	NAV3	77128365	0.348000	0.24861	0.594000	0.28785	0.129000	0.20672	-0.324000	0.07986	-1.610000	0.01583	-2.173000	0.00322	CGA	.	.	.	none		0.403	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
TBX5	6910	hgsc.bcm.edu	37	12	114793542	114793542	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:114793542C>G	ENST00000310346.4	-	9	2018	c.1352G>C	c.(1351-1353)gGa>gCa	p.G451A	TBX5_ENST00000405440.2_Missense_Mutation_p.G451A|TBX5_ENST00000349716.5_Missense_Mutation_p.G401A	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	451				MDRLPYQHFSAHFTSGPLVPRLAGMANHGSPQLGEGMFQHQ TS -> WTGYPTSTSPLTSPRGPWSLGWLAWQPWLPTAGRG NVPSTRPP (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.G451V(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		CATTCCCTCTCCCAGCTGTGG	0.662																																					p.G451A	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											TBX5,NS,carcinoma,0,1	TBX5	188	.	1	Substitution - Missense(1)	lung(1)	c.G1352C						PASS	.						27.0	29.0	28.0					12																	114793542		2203	4300	6503	SO:0001583	missense	6910	exon9			CCCTCTCCCAGCT	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1352G>C	chr12.hg19:g.114793542C>G	ENSP00000309913:p.Gly451Ala	41.0	0.0	.		43.0	2.0	.	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	hg19	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.817720	0.50633	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440	T;T;T	0.54279	0.58;0.58;0.58	5.27	5.27	0.74061	.	0.682044	0.14424	N	0.320472	T	0.45538	0.1347	L	0.32530	0.975	0.80722	D	1	B	0.12013	0.005	B	0.12837	0.008	T	0.28902	-1.0029	10	0.42905	T	0.14	.	15.949	0.79817	0.0:0.8652:0.1348:0.0	.	451	Q99593	TBX5_HUMAN	A	401;451;348;451	ENSP00000337723:G401A;ENSP00000309913:G451A;ENSP00000384152:G451A	ENSP00000309913:G451A	G	-	2	0	TBX5	113277925	0.959000	0.32827	0.383000	0.26132	0.922000	0.55478	2.879000	0.48522	2.463000	0.83235	0.655000	0.94253	GGA	.	.	.	none		0.662	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717	
KCTD4	386618	hgsc.bcm.edu	37	13	45768535	45768535	+	Silent	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr13:45768535G>A	ENST00000379108.1	-	1	317	c.168C>T	c.(166-168)gaC>gaT	p.D56D	GTF2F2_ENST00000340473.6_Intron|KCTD4_ENST00000405872.1_Silent_p.D56D			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	56	BTB.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		CAAGGAAAGTGTCTGGGTACT	0.413																																					p.D56D		Atlas-SNP	.											.	KCTD4	18	.	0			c.C168T						PASS	.						266.0	265.0	265.0					13																	45768535		2203	4300	6503	SO:0001819	synonymous_variant	386618	exon2			GAAAGTGTCTGGG	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 4"""				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.168C>T	chr13.hg19:g.45768535G>A		288.0	0.0	.		182.0	55.0	.	NM_198404	Q5W0P9	Silent	SNP	ENST00000379108.1	hg19	CCDS9396.1																																																																																			.	.	.	none		0.413	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1		
NEMF	9147	hgsc.bcm.edu	37	14	50256253	50256253	+	Silent	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr14:50256253C>T	ENST00000298310.5	-	27	3107	c.2658G>A	c.(2656-2658)caG>caA	p.Q886Q	NEMF_ENST00000546046.1_Silent_p.Q865Q|NEMF_ENST00000545773.1_Silent_p.Q844Q|NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000382135.2_Silent_p.Q86Q			O60524	NEMF_HUMAN	nuclear export mediator factor	886					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						CTTCTTCATCCTGGTCTTTGT	0.328																																					p.Q886Q		Atlas-SNP	.											.	NEMF	79	.	0			c.G2658A						PASS	.						130.0	123.0	125.0					14																	50256253		2203	4300	6503	SO:0001819	synonymous_variant	9147	exon27			TTCATCCTGGTCT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"""serologically defined colon cancer antigen 1"""	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2658G>A	chr14.hg19:g.50256253C>T		89.0	0.0	.		63.0	17.0	.	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Silent	SNP	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.	.	none		0.328	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713	
VRK1	7443	hgsc.bcm.edu	37	14	97321567	97321567	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr14:97321567T>A	ENST00000216639.3	+	8	732	c.583T>A	c.(583-585)Ttg>Atg	p.L195M		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		ATAGGTGTACTTGGTAGATTA	0.388																																					p.L195M		Atlas-SNP	.											.	VRK1	34	.	0			c.T583A						PASS	.						199.0	195.0	196.0					14																	97321567		2203	4300	6503	SO:0001583	missense	7443	exon8			GTGTACTTGGTAG	AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.583T>A	chr14.hg19:g.97321567T>A	ENSP00000216639:p.Leu195Met	134.0	0.0	.		105.0	46.0	.	NM_003384	Q3SYL2	Missense_Mutation	SNP	ENST00000216639.3	hg19	CCDS9947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.34|19.34	3.808500|3.808500	0.70797|0.70797	.|.	.|.	ENSG00000100749|ENSG00000100749	ENST00000557222|ENST00000216639	.|T	.|0.72835	.|-0.69	5.95|5.95	1.04|1.04	0.20106|0.20106	.|Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.81024|0.81024	0.4737|0.4737	M|M	0.76938|0.76938	2.355|2.355	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.78823|0.78823	-0.2052|-0.2052	6|10	.|0.66056	.|D	.|0.02	-11.377|-11.377	9.4931|9.4931	0.38971|0.38971	0.0:0.2599:0.0:0.7401|0.0:0.2599:0.0:0.7401	.|.	.|195	.|Q99986	.|VRK1_HUMAN	H|M	51|195	.|ENSP00000216639:L195M	.|ENSP00000216639:L195M	L|L	+|+	2|1	0|2	VRK1|VRK1	96391320|96391320	0.992000|0.992000	0.36948|0.36948	0.995000|0.995000	0.50966|0.50966	0.985000|0.985000	0.73830|0.73830	0.976000|0.976000	0.29462|0.29462	-0.050000|-0.050000	0.13356|0.13356	0.533000|0.533000	0.62120|0.62120	CTT|TTG	.	.	.	none		0.388	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384	
DUOX1	53905	hgsc.bcm.edu	37	15	45456067	45456068	+	Missense_Mutation	DNP	GT	GT	TA			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:45456067_45456068GT>TA	ENST00000321429.4	+	34	4891_4892	c.4484_4485GT>TA	c.(4483-4485)cGT>cTA	p.R1495L	DUOX1_ENST00000561166.1_Missense_Mutation_p.R1141L|DUOX1_ENST00000389037.3_Missense_Mutation_p.R1495L|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1495					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CACTTTGGCCGTCCCCCCTTTG	0.55																																					p.R1495L|p.R1495R		Atlas-SNP	.											.	DUOX1	125	.	0			c.G4484T|c.T4485A						PASS	.																																			SO:0001583	missense	53905	exon34			TTGGCCGTCCCCC|TGGCCGTCCCCCC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		Exception_encountered	chr15.hg19:g.45456067_45456068delinsTA	ENSP00000317997:p.Arg1495Leu	212.0|213.0	0.0	.		132.0|134.0	56.0|58.0	.	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation|Silent	SNP	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.	.	none		0.550	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
ZNF609	23060	hgsc.bcm.edu	37	15	64791991	64791991	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:64791991T>C	ENST00000326648.3	+	1	501	c.373T>C	c.(373-375)Tca>Cca	p.S125P	ZNF609_ENST00000416172.1_Missense_Mutation_p.S125P	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	125						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCAGGGGCGCTCAGGAGATGG	0.567																																					p.S125P		Atlas-SNP	.											.	ZNF609	106	.	0			c.T373C						PASS	.						44.0	48.0	46.0					15																	64791991		2203	4300	6503	SO:0001583	missense	23060	exon1			GGGCGCTCAGGAG	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"""Zinc fingers, C2H2-type"""	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.373T>C	chr15.hg19:g.64791991T>C	ENSP00000316527:p.Ser125Pro	54.0	0.0	.		62.0	18.0	.	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	hg19	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	.	5.590	0.293619	0.10567	.	.	ENSG00000180357	ENST00000416172;ENST00000326648	T	0.42513	0.97	5.5	3.1	0.35709	.	0.722344	0.13093	N	0.414351	T	0.24699	0.0599	N	0.16368	0.405	0.40301	D	0.97861	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.05241	-1.0897	10	0.21540	T	0.41	-18.1137	8.0215	0.30412	0.0:0.0671:0.2567:0.6762	.	125;125	E7ERY8;O15014	.;ZN609_HUMAN	P	125	ENSP00000316527:S125P	ENSP00000316527:S125P	S	+	1	0	ZNF609	62579044	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	1.673000	0.37534	0.419000	0.25927	-0.322000	0.08575	TCA	.	.	.	none		0.567	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833	
CLCN7	1186	hgsc.bcm.edu	37	16	1505793	1505793	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:1505793C>T	ENST00000382745.4	-	11	1525	c.920G>A	c.(919-921)gGg>gAg	p.G307E	CLCN7_ENST00000448525.1_Missense_Mutation_p.G283E|CLCN7_ENST00000262318.8_Missense_Mutation_p.G283E	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	307					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GAACAGGACCCCACCTGGAAG	0.642																																					p.G307E		Atlas-SNP	.											.	CLCN7	53	.	0			c.G920A						PASS	.						89.0	74.0	79.0					16																	1505793		2199	4300	6499	SO:0001583	missense	1186	exon11			AGGACCCCACCTG	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.920G>A	chr16.hg19:g.1505793C>T	ENSP00000372193:p.Gly307Glu	63.0	0.0	.		73.0	43.0	.	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	hg19	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.854384	0.71719	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.98701	-5.08;-5.08	5.13	5.13	0.70059	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97845	1.0271	10	0.87932	D	0	-37.9855	17.1357	0.86739	0.0:1.0:0.0:0.0	.	283;307	E9PDB9;P51798	.;CLCN7_HUMAN	E	283;260;307;249	ENSP00000410907:G283E;ENSP00000372193:G307E	ENSP00000262318:G260E	G	-	2	0	CLCN7	1445794	1.000000	0.71417	0.996000	0.52242	0.531000	0.34715	7.468000	0.80943	2.387000	0.81309	0.313000	0.20887	GGG	.	.	.	none		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
SEPT1	1731	hgsc.bcm.edu	37	16	30393873	30393873	+	5'UTR	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:30393873T>C	ENST00000571393.1	-	0	162				SEPT1_ENST00000605106.1_5'Flank|SEPT1_ENST00000570039.1_5'Flank|SEPT1_ENST00000321367.3_Silent_p.A39A			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			TCACTGCACCTGCCGTCTCTC	0.647																																					p.A39A		Atlas-SNP	.											.	SEPT1	34	.	0			c.A117G						PASS	.						25.0	21.0	22.0					16																	30393873		2196	4299	6495	SO:0001623	5_prime_UTR_variant	1731	exon2			TGCACCTGCCGTC	AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984	ENST00000571393.1:c.-25A>G	chr16.hg19:g.30393873T>C		12.0	0.0	.		11.0	7.0	.	NM_052838	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Silent	SNP	ENST00000571393.1	hg19																																																																																				.	.	.	none		0.647	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
HEATR3	55027	hgsc.bcm.edu	37	16	50112741	50112741	+	Nonsense_Mutation	SNP	G	G	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:50112741G>T	ENST00000299192.7	+	7	1044	c.853G>T	c.(853-855)Gga>Tga	p.G285*	HEATR3_ENST00000285767.4_Nonsense_Mutation_p.G199*	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	285										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TGAAGTTTTGGGAATGGATGC	0.373																																					p.G285X		Atlas-SNP	.											.	HEATR3	59	.	0			c.G853T						PASS	.						79.0	78.0	78.0					16																	50112741		2198	4300	6498	SO:0001587	stop_gained	55027	exon7			GTTTTGGGAATGG	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.853G>T	chr16.hg19:g.50112741G>T	ENSP00000299192:p.Gly285*	75.0	0.0	.		91.0	5.0	.	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Nonsense_Mutation	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	39	7.589360	0.98374	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	.	.	.	5.61	4.66	0.58398	.	0.526535	0.23112	N	0.051781	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	10.9314	0.47220	0.1434:0.0:0.8566:0.0	.	.	.	.	X	199;285	.	ENSP00000285767:G199X	G	+	1	0	HEATR3	48670242	1.000000	0.71417	0.826000	0.32828	0.973000	0.67179	5.765000	0.68834	1.516000	0.48900	-0.277000	0.10078	GGA	.	.	.	none		0.373	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57463170	57463170	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:57463170C>T	ENST00000569979.1	-	6	699	c.653G>A	c.(652-654)cGc>cAc	p.R218H	CIAPIN1_ENST00000567518.1_Missense_Mutation_p.R271H|CIAPIN1_ENST00000568940.1_Silent_p.P245P|CIAPIN1_ENST00000569370.1_Silent_p.P245P|CIAPIN1_ENST00000569246.1_5'Flank|CIAPIN1_ENST00000394391.4_Missense_Mutation_p.R284H|CIAPIN1_ENST00000565961.1_Silent_p.P218P					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						GCTGGCACAGCGGAAGGCATC	0.532																																					p.R284H		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.G851A						PASS	.						56.0	57.0	57.0					16																	57463170		2015	4178	6193	SO:0001583	missense	57019	exon9			GCACAGCGGAAGG	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.653G>A	chr16.hg19:g.57463170C>T	ENSP00000458000:p.Arg218His	83.0	0.0	.		73.0	38.0	.	NM_020313		Missense_Mutation	SNP	ENST00000569979.1	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.381122	0.95945	.	.	ENSG00000005194	ENST00000394391	T	0.68181	-0.31	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.87184	0.6114	H	0.95539	3.685	0.53688	D	0.99997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91214	0.5001	10	0.72032	D	0.01	-16.045	17.0668	0.86561	0.0:1.0:0.0:0.0	.	271;284	Q6FI81-3;Q6FI81	.;CPIN1_HUMAN	H	284	ENSP00000377914:R284H	ENSP00000377914:R284H	R	-	2	0	CIAPIN1	56020671	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.141000	0.77330	2.347000	0.79759	0.561000	0.74099	CGC	.	.	.	none		0.532	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313	
DNAH2	146754	hgsc.bcm.edu	37	17	7727461	7727461	+	Missense_Mutation	SNP	G	G	A	rs368019673		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:7727461G>A	ENST00000572933.1	+	76	12961	c.11501G>A	c.(11500-11502)cGa>cAa	p.R3834Q	DNAH2_ENST00000389173.2_Missense_Mutation_p.R3834Q			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3834	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TCAACCCCACGATCCCCACTC	0.597																																					p.R3834Q		Atlas-SNP	.											.	DNAH2	498	.	0			c.G11501A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	103.0	87.0	93.0		11501	4.1	0.2	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH2	NM_020877.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	3834/4428	7727461	1,13005	2203	4300	6503	SO:0001583	missense	146754	exon75			CCCCACGATCCCC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.11501G>A	chr17.hg19:g.7727461G>A	ENSP00000458355:p.Arg3834Gln	180.0	0.0	.		205.0	26.0	.	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.690038	0.29962	0.0	1.16E-4	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.08193	3.12	5.03	4.06	0.47325	Dynein heavy chain (1);	0.102365	0.48286	D	0.000190	T	0.04227	0.0117	N	0.25201	0.72	0.44985	D	0.998	B;B	0.32829	0.227;0.386	B;B	0.22753	0.024;0.041	T	0.42396	-0.9454	10	0.10111	T	0.7	.	8.878	0.35356	0.1665:0.0:0.8335:0.0	.	3795;3834	Q9P225-2;Q9P225	.;DYH2_HUMAN	Q	3795;3834	ENSP00000373825:R3834Q	ENSP00000353818:R3795Q	R	+	2	0	DNAH2	7668186	0.186000	0.23225	0.167000	0.22817	0.981000	0.71138	2.589000	0.46145	2.350000	0.79820	0.511000	0.50034	CGA	.	.	.	weak		0.597	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
EFCAB5	374786	hgsc.bcm.edu	37	17	28407885	28407885	+	Silent	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:28407885G>C	ENST00000394835.3	+	17	3504	c.3312G>C	c.(3310-3312)ctG>ctC	p.L1104L	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Silent_p.L980L	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1104							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GTTCATTCCTGGCTCTGCCTC	0.438																																					p.L1104L		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3312C						PASS	.						91.0	88.0	89.0					17																	28407885		1881	4112	5993	SO:0001819	synonymous_variant	374786	exon17			ATTCCTGGCTCTG	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3312G>C	chr17.hg19:g.28407885G>C		82.0	0.0	.		63.0	24.0	.	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	hg19	CCDS11254.2																																																																																			.	.	.	none		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
HELZ	9931	hgsc.bcm.edu	37	17	65214853	65214853	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:65214853T>G	ENST00000358691.5	-	4	234	c.68A>C	c.(67-69)gAa>gCa	p.E23A	HELZ_ENST00000580168.1_Missense_Mutation_p.E23A|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	23						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GAGGGCCATTTCATAGTCCTG	0.473																																					p.E23A		Atlas-SNP	.											.	HELZ	160	.	0			c.A68C						PASS	.						127.0	119.0	121.0					17																	65214853		1892	4130	6022	SO:0001583	missense	9931	exon4			GCCATTTCATAGT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.68A>C	chr17.hg19:g.65214853T>G	ENSP00000351524:p.Glu23Ala	120.0	0.0	.		142.0	34.0	.	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	t	15.08	2.728346	0.48833	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.75589	-0.95;-0.95	5.27	5.27	0.74061	.	0.046820	0.85682	D	0.000000	T	0.70692	0.3253	L	0.29908	0.895	0.58432	D	0.999999	B;P;B	0.48503	0.247;0.911;0.247	B;P;B	0.47941	0.078;0.562;0.078	T	0.75019	-0.3465	10	0.66056	D	0.02	-4.8435	15.1782	0.72931	0.0:0.0:0.0:1.0	.	23;23;23	B7ZLW2;F8WBX6;P42694	.;.;HELZ_HUMAN	A	23	ENSP00000351524:E23A;ENSP00000411144:E23A	ENSP00000351524:E23A	E	-	2	0	HELZ	62645315	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.414000	0.80117	1.980000	0.57719	0.455000	0.32223	GAA	.	.	.	none		0.473	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
COG1	9382	hgsc.bcm.edu	37	17	71199203	71199203	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:71199203C>A	ENST00000299886.4	+	8	2218	c.2138C>A	c.(2137-2139)gCc>gAc	p.A713D		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	713					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			CTGGCCACAGCCACCAGCTGG	0.512																																					p.A713D		Atlas-SNP	.											.	COG1	46	.	0			c.C2138A						PASS	.						80.0	74.0	76.0					17																	71199203		2203	4300	6503	SO:0001583	missense	9382	exon8			CCACAGCCACCAG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2138C>A	chr17.hg19:g.71199203C>A	ENSP00000299886:p.Ala713Asp	83.0	0.0	.		87.0	58.0	.	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	hg19	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.632096	0.67015	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.25414	1.8;1.81	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	M	0.75447	2.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.37572	-0.9700	10	0.35671	T	0.21	-30.898	20.8794	0.99867	0.0:1.0:0.0:0.0	.	713;713;713	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	D	713	ENSP00000400111:A713D;ENSP00000299886:A713D	ENSP00000299886:A713D	A	+	2	0	COG1	68710798	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.941000	0.99782	0.655000	0.94253	GCC	.	.	.	none		0.512	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
FDXR	2232	hgsc.bcm.edu	37	17	72861043	72861043	+	Missense_Mutation	SNP	A	A	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:72861043A>C	ENST00000293195.5	-	7	698	c.620T>G	c.(619-621)aTc>aGc	p.I207S	FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000420580.2_Missense_Mutation_p.I167S|FDXR_ENST00000583917.1_Missense_Mutation_p.I208S|FDXR_ENST00000582944.1_Missense_Mutation_p.I199S|FDXR_ENST00000455107.2_Missense_Mutation_p.I163S|FDXR_ENST00000544854.1_Missense_Mutation_p.I155S|FDXR_ENST00000413947.2_Missense_Mutation_p.I238S|FDXR_ENST00000581530.1_Missense_Mutation_p.I213S|FDXR_ENST00000442102.2_Missense_Mutation_p.I250S	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	207					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	TGCCTTCGTGATGTCCGTTCT	0.592											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I250S		Atlas-SNP	.											.	FDXR	68	.	0			c.T749G						PASS	.						96.0	80.0	86.0					17																	72861043		2203	4300	6503	SO:0001583	missense	2232	exon7			TTCGTGATGTCCG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.620T>G	chr17.hg19:g.72861043A>C	ENSP00000293195:p.Ile207Ser	80.0	0.0	.	1140	102.0	54.0	.	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	a	15.15	2.747032	0.49257	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89931	0.6858	H	0.94345	3.525	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.992;0.983;0.984;1.0;0.996;0.984;0.978;1.0;0.978;0.996	D	0.92675	0.6153	10	0.87932	D	0	-11.7911	15.4798	0.75517	1.0:0.0:0.0:0.0	.	167;250;238;205;155;238;207;199;207;213	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;B4DDI7;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;.;ADRO_HUMAN;.	S	167;155;213;163;250;238	ENSP00000414172:I167S;ENSP00000445432:I155S;ENSP00000390875:I163S;ENSP00000416515:I250S;ENSP00000408595:I238S	ENSP00000293195:I213S	I	-	2	0	FDXR	70372638	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.738000	0.68613	2.145000	0.66743	0.454000	0.30748	ATC	.	.	.	none		0.592	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
SGSH	6448	hgsc.bcm.edu	37	17	78197109	78197109	+	5'Flank	SNP	C	C	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:78197109C>G	ENST00000326317.6	-	0	0				SGSH_ENST00000570923.1_5'Flank|SGSH_ENST00000572208.1_5'Flank|SLC26A11_ENST00000361193.3_Silent_p.A162A|SLC26A11_ENST00000546047.2_Silent_p.A162A|SLC26A11_ENST00000411502.3_Silent_p.A162A|SLC26A11_ENST00000572725.1_Silent_p.A162A|SGSH_ENST00000534910.1_5'Flank	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase						carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CTGCTGCTGCCGTCACCATCG	0.622																																					p.A162A		Atlas-SNP	.											.	SLC26A11	60	.	0			c.C486G						PASS	.						95.0	67.0	76.0					17																	78197109		2203	4300	6503	SO:0001631	upstream_gene_variant	284129	exon5			TGCTGCCGTCACC	BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"""sulfamidase"", ""mucopolysaccharidosis type IIIA"""	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688			chr17.hg19:g.78197109C>G	Exception_encountered	84.0	0.0	.		82.0	4.0	.	NM_173626	A8K5E2	Silent	SNP	ENST00000326317.6	hg19	CCDS11770.1																																																																																			.	.	.	none		0.622	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199	
EMILIN2	84034	hgsc.bcm.edu	37	18	2913257	2913257	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:2913257G>T	ENST00000254528.3	+	8	3176	c.3017G>T	c.(3016-3018)gGg>gTg	p.G1006V	EMILIN2_ENST00000308080.5_3'UTR	NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	1006	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGGGGCCCGGGGGCATTCCAC	0.607																																					p.G1006V		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G3017T						PASS	.						41.0	43.0	43.0					18																	2913257		2203	4300	6503	SO:0001583	missense	84034	exon8			GCCCGGGGGCATT	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.3017G>T	chr18.hg19:g.2913257G>T	ENSP00000254528:p.Gly1006Val	76.0	0.0	.		49.0	13.0	.	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989478	0.53934	.	.	ENSG00000132205	ENST00000254528;ENST00000308080	T	0.74842	-0.88	5.61	5.61	0.85477	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79771	-0.1663	10	0.33940	T	0.23	-34.4219	20.0086	0.97443	0.0:0.0:1.0:0.0	.	1006	Q9BXX0	EMIL2_HUMAN	V	1006;283	ENSP00000254528:G1006V	ENSP00000254528:G1006V	G	+	2	0	EMILIN2	2903257	1.000000	0.71417	0.301000	0.25044	0.022000	0.10575	5.618000	0.67722	2.808000	0.96608	0.655000	0.94253	GGG	.	.	.	none		0.607	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048	
CCDC178	374864	hgsc.bcm.edu	37	18	30926327	30926327	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:30926327T>C	ENST00000383096.3	-	9	688	c.506A>G	c.(505-507)gAg>gGg	p.E169G	CCDC178_ENST00000403303.1_Missense_Mutation_p.E169G|CCDC178_ENST00000406524.2_Missense_Mutation_p.E169G|CCDC178_ENST00000402325.1_Missense_Mutation_p.E169G|CCDC178_ENST00000300227.8_Missense_Mutation_p.E169G|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000583930.1_Missense_Mutation_p.E169G|CCDC178_ENST00000579947.1_Missense_Mutation_p.E169G			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	169																	ACGAATGGCCTCTGAGAGCAA	0.343																																					p.E169G		Atlas-SNP	.											.	.	.	.	0			c.A506G						PASS	.						93.0	88.0	90.0					18																	30926327		2203	4300	6503	SO:0001583	missense	374864	exon8			ATGGCCTCTGAGA	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.506A>G	chr18.hg19:g.30926327T>C	ENSP00000372576:p.Glu169Gly	79.0	0.0	.		83.0	26.0	.	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	9.274	1.046438	0.19748	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.57107	1.82;1.82;1.83;1.82;1.83;0.42	5.59	4.36	0.52297	.	.	.	.	.	T	0.65133	0.2662	L	0.54323	1.7	0.31006	N	0.719736	D;D;D;D	0.89917	1.0;0.996;0.996;0.996	D;D;D;D	0.74674	0.984;0.944;0.944;0.944	T	0.65520	-0.6148	9	0.59425	D	0.04	-20.3796	10.1932	0.43039	0.0:0.0:0.1668:0.8332	.	169;169;169;169	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	G	169	ENSP00000385591:E169G;ENSP00000372576:E169G;ENSP00000300227:E169G;ENSP00000385867:E169G;ENSP00000385234:E169G;ENSP00000382130:E169G	ENSP00000300227:E169G	E	-	2	0	C18orf34	29180325	1.000000	0.71417	0.996000	0.52242	0.418000	0.31294	3.210000	0.51129	2.129000	0.65627	0.455000	0.32223	GAG	.	.	.	none		0.343	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	
MUC16	94025	hgsc.bcm.edu	37	19	9059472	9059472	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:9059472G>T	ENST00000397910.4	-	3	28177	c.27974C>A	c.(27973-27975)gCc>gAc	p.A9325D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9327	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						AGAAGAGATGGCTTCTGTCCT	0.507																																					p.A9325D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27974A						PASS	.						162.0	157.0	158.0					19																	9059472		1993	4179	6172	SO:0001583	missense	94025	exon3			GAGATGGCTTCTG	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.27974C>A	chr19.hg19:g.9059472G>T	ENSP00000381008:p.Ala9325Asp	199.0	0.0	.		143.0	69.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.093	0.202874	0.09704	.	.	ENSG00000181143	ENST00000397910	T	0.02812	4.15	2.43	-4.86	0.03132	.	.	.	.	.	T	0.02727	0.0082	N	0.19112	0.55	.	.	.	P	0.52316	0.952	P	0.50049	0.629	T	0.26677	-1.0096	8	0.87932	D	0	.	4.6628	0.12650	0.5463:0.176:0.2777:0.0	.	9325	B5ME49	.	D	9325	ENSP00000381008:A9325D	ENSP00000381008:A9325D	A	-	2	0	MUC16	8920472	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.962000	0.01514	-1.169000	0.02772	-0.382000	0.06688	GCC	.	.	.	none		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF317	57693	hgsc.bcm.edu	37	19	9271676	9271676	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:9271676G>A	ENST00000247956.6	+	7	1660	c.1355G>A	c.(1354-1356)gGg>gAg	p.G452E	ZNF317_ENST00000360385.3_Missense_Mutation_p.G420E	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GATCTCTGCGGGAAAGCTTTC	0.547																																					p.G452E		Atlas-SNP	.											.	ZNF317	61	.	0			c.G1355A						PASS	.						62.0	59.0	60.0					19																	9271676		2203	4300	6503	SO:0001583	missense	57693	exon7			TCTGCGGGAAAGC	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"""Zinc fingers, C2H2-type"", ""-"""	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.1355G>A	chr19.hg19:g.9271676G>A	ENSP00000247956:p.Gly452Glu	67.0	0.0	.		58.0	20.0	.	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	hg19	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.795593	0.70452	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.07114	3.22;3.22	3.04	3.04	0.35103	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43260	D	0.000600	T	0.22627	0.0546	L	0.59436	1.845	0.47009	D	0.999286	D;D	0.89917	1.0;0.994	D;D	0.83275	0.996;0.924	T	0.01013	-1.1481	10	0.59425	D	0.04	-30.6663	12.2796	0.54757	0.0:0.0:1.0:0.0	.	420;452	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	E	452;420	ENSP00000247956:G452E;ENSP00000353554:G420E	ENSP00000247956:G452E	G	+	2	0	ZNF317	9132676	0.999000	0.42202	0.881000	0.34555	0.542000	0.35054	3.149000	0.50655	2.031000	0.59945	0.491000	0.48974	GGG	.	.	.	none		0.547	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933	
C19orf57	79173	hgsc.bcm.edu	37	19	13996869	13996869	+	Splice_Site	SNP	C	C	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:13996869C>G	ENST00000586783.1	-	6	1668		c.e6-1		C19orf57_ENST00000591586.1_Splice_Site|C19orf57_ENST00000454313.1_Splice_Site|C19orf57_ENST00000346736.2_Splice_Site			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57						multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			AAGGAAAGAGCTGGAAAGAGA	0.632																																					.		Atlas-SNP	.											.	C19orf57	34	.	0			c.1669-1G>C						PASS	.						33.0	34.0	34.0					19																	13996869		2203	4300	6503	SO:0001630	splice_region_variant	79173	exon8			AAAGAGCTGGAAA	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.1669-1G>C	chr19.hg19:g.13996869C>G		58.0	0.0	.		58.0	21.0	.	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Splice_Site	SNP	ENST00000586783.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.061	0.994432	0.19043	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.45762	D	0.998659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7555	0.40500	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C19orf57	13857869	0.176000	0.23096	0.016000	0.15963	0.050000	0.14768	2.605000	0.46283	2.000000	0.58554	0.563000	0.77884	.	.	.	.	none		0.632	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	Intron
CD22	933	hgsc.bcm.edu	37	19	35828752	35828752	+	Silent	SNP	C	C	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:35828752C>T	ENST00000085219.5	+	5	879	c.813C>T	c.(811-813)aaC>aaT	p.N271N	CD22_ENST00000341773.6_Intron|CD22_ENST00000594250.1_Intron|CD22_ENST00000419549.2_Silent_p.N99N|CD22_ENST00000536635.2_Silent_p.N271N|CD22_ENST00000544992.2_Silent_p.N271N|CD22_ENST00000270311.6_Silent_p.N151N	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	271	Ig-like C2-type 2.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GCAGCAGCAACCCGGAGTACA	0.567																																					p.N271N	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.C813T						PASS	.						90.0	75.0	80.0					19																	35828752		2203	4300	6503	SO:0001819	synonymous_variant	933	exon5			CAGCAACCCGGAG	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.813C>T	chr19.hg19:g.35828752C>T		107.0	0.0	.		77.0	32.0	.	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	hg19	CCDS12457.1																																																																																			.	.	.	none		0.567	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
SCAF1	58506	hgsc.bcm.edu	37	19	50161552	50161552	+	Missense_Mutation	SNP	A	A	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:50161552A>C	ENST00000360565.3	+	11	3959	c.3835A>C	c.(3835-3837)Aag>Cag	p.K1279Q	IRF3_ENST00000599680.1_5'Flank	NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1279	Necessary for interaction with the CTD domain of POLR2A.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CTACTTCCGCAAGCACGGTCG	0.701																																					p.K1279Q		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3835C						PASS	.						20.0	18.0	19.0					19																	50161552		2196	4296	6492	SO:0001583	missense	58506	exon11			TTCCGCAAGCACG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3835A>C	chr19.hg19:g.50161552A>C	ENSP00000353769:p.Lys1279Gln	28.0	0.0	.		20.0	10.0	.	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749503	0.69533	.	.	ENSG00000126461	ENST00000360565	T	0.50548	0.74	4.94	4.94	0.65067	.	0.000000	0.41001	D	0.000978	T	0.62575	0.2439	L	0.52905	1.665	0.45076	D	0.998095	D	0.76494	0.999	D	0.71656	0.974	T	0.65800	-0.6080	10	0.72032	D	0.01	-23.9463	13.702	0.62616	1.0:0.0:0.0:0.0	.	1279	Q9H7N4	SFR19_HUMAN	Q	1279	ENSP00000353769:K1279Q	ENSP00000353769:K1279Q	K	+	1	0	SCAF1	54853364	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.499000	0.90494	2.064000	0.61679	0.533000	0.62120	AAG	.	.	.	none		0.701	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
LILRB1	10859	hgsc.bcm.edu	37	19	55144006	55144006	+	Silent	SNP	C	C	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:55144006C>A	ENST00000396331.1	+	7	1110	c.753C>A	c.(751-753)ggC>ggA	p.G251G	LILRB1_ENST00000396317.1_Silent_p.G251G|LILRB1_ENST00000396321.2_Silent_p.G251G|LILRB1_ENST00000418536.2_Silent_p.G251G|LILRB1_ENST00000324602.7_Silent_p.G251G|LILRB1_ENST00000396327.3_Silent_p.G251G|LILRB1_ENST00000427581.2_Silent_p.G287G|LILRB1_ENST00000396315.1_Silent_p.G251G|LILRB1_ENST00000448689.1_Silent_p.G251G|LILRB1_ENST00000396332.4_Silent_p.G251G|LILRB1_ENST00000434867.2_Silent_p.G251G	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	251	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CTGATGCTGGCTACAACAGAT	0.572										HNSCC(37;0.09)																											p.G251G		Atlas-SNP	.											.	LILRB1	140	.	0			c.C753A						PASS	.						100.0	105.0	103.0					19																	55144006		2203	4300	6503	SO:0001819	synonymous_variant	10859	exon6			TGCTGGCTACAAC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.753C>A	chr19.hg19:g.55144006C>A		173.0	0.0	.		110.0	44.0	.	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	hg19	CCDS42617.1																																																																																			.	.	.	none		0.572	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
ZNF543	125919	hgsc.bcm.edu	37	19	57839968	57839968	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:57839968G>A	ENST00000321545.4	+	4	1483	c.1138G>A	c.(1138-1140)Gca>Aca	p.A380T		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	380					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTGCGAGAGTGCAGACCTCAT	0.512																																					p.A380T		Atlas-SNP	.											.	ZNF543	61	.	0			c.G1138A						PASS	.						84.0	73.0	76.0					19																	57839968		2203	4300	6503	SO:0001583	missense	125919	exon4			GAGAGTGCAGACC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1138G>A	chr19.hg19:g.57839968G>A	ENSP00000322545:p.Ala380Thr	119.0	0.0	.		83.0	35.0	.	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	G	2.550	-0.304214	0.05495	.	.	ENSG00000178229	ENST00000321545	T	0.15139	2.45	3.14	-2.57	0.06248	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10337	0.0253	N	0.25825	0.765	0.09310	N	1	B	0.21071	0.051	B	0.14023	0.01	T	0.32188	-0.9916	9	0.42905	T	0.14	.	7.5755	0.27933	0.138:0.0:0.7015:0.1605	.	380	Q08ER8	ZN543_HUMAN	T	380	ENSP00000322545:A380T	ENSP00000322545:A380T	A	+	1	0	ZNF543	62531780	0.000000	0.05858	0.000000	0.03702	0.661000	0.39034	-1.477000	0.02331	-0.214000	0.10078	0.561000	0.74099	GCA	.	.	.	none		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
ZNF335	63925	hgsc.bcm.edu	37	20	44578919	44578919	+	Silent	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:44578919G>C	ENST00000322927.2	-	22	3526	c.3426C>G	c.(3424-3426)acC>acG	p.T1142T	ZNF335_ENST00000426788.1_Silent_p.T987T	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1142					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TTGGGGTCTGGGTAGGGGCCC	0.612																																					p.T1142T		Atlas-SNP	.											.	ZNF335	115	.	0			c.C3426G						PASS	.						90.0	93.0	92.0					20																	44578919		2203	4300	6503	SO:0001819	synonymous_variant	63925	exon22			GGTCTGGGTAGGG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3426C>G	chr20.hg19:g.44578919G>C		133.0	0.0	.		97.0	30.0	.	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	hg19	CCDS13389.1																																																																																			.	.	.	none		0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
PARD6B	84612	hgsc.bcm.edu	37	20	49366295	49366295	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:49366295A>G	ENST00000371610.2	+	3	632	c.389A>G	c.(388-390)cAt>cGt	p.H130R	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	130	Interaction with PARD3 and CDC42. {ECO:0000250}.				axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.H130R(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						AAAAAGCCACATATAGTCATT	0.403																																					p.H130R		Atlas-SNP	.											PARD6B,NS,carcinoma,0,1	PARD6B	31	.	1	Substitution - Missense(1)	kidney(1)	c.A389G						PASS	.						76.0	74.0	75.0					20																	49366295		2203	4300	6503	SO:0001583	missense	84612	exon3			AGCCACATATAGT	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"""par-6 (partitioning defective 6, C.elegans) homolog beta"", ""par-6 partitioning defective 6 homolog beta (C. elegans)"""			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.389A>G	chr20.hg19:g.49366295A>G	ENSP00000360672:p.His130Arg	77.0	0.0	.		48.0	16.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597328	0.28445	.	.	ENSG00000124171	ENST00000371610	T	0.41400	1.0	5.6	5.6	0.85130	.	0.151580	0.64402	D	0.000014	T	0.36991	0.0987	L	0.43152	1.355	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.11421	-1.0588	10	0.25106	T	0.35	-32.4385	15.7847	0.78294	1.0:0.0:0.0:0.0	.	130	Q9BYG5	PAR6B_HUMAN	R	130	ENSP00000360672:H130R	ENSP00000360672:H130R	H	+	2	0	PARD6B	48799702	0.992000	0.36948	0.650000	0.29550	0.857000	0.48899	3.467000	0.53078	2.135000	0.66039	0.533000	0.62120	CAT	.	.	.	none		0.403	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521	
GAL3ST1	9514	hgsc.bcm.edu	37	22	30951203	30951203	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr22:30951203C>G	ENST00000402321.1	-	3	1326	c.1009G>C	c.(1009-1011)Gcc>Ccc	p.A337P	GAL3ST1_ENST00000338911.5_Missense_Mutation_p.A337P|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.A337P|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.A337P			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	337					galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						CGCTCGTTGGCATGGCGCAGG	0.721																																					p.A337P		Atlas-SNP	.											.	GAL3ST1	44	.	0			c.G1009C						PASS	.						20.0	22.0	21.0					22																	30951203		2199	4288	6487	SO:0001583	missense	9514	exon4			CGTTGGCATGGCG	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"""Sulfotransferases, membrane-bound"""	24240	protein-coding gene	gene with protein product	"""cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"""	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.1009G>C	chr22.hg19:g.30951203C>G	ENSP00000385735:p.Ala337Pro	23.0	0.0	.		25.0	13.0	.	NM_004861	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	hg19	CCDS13879.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017684	0.75161	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111	T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.55	5.55	0.83447	.	0.225320	0.47455	D	0.000227	T	0.24547	0.0595	L	0.55990	1.75	0.80722	D	1	P	0.43938	0.822	P	0.48425	0.577	T	0.00557	-1.1672	10	0.30854	T	0.27	-13.5376	12.4548	0.55697	0.0:0.9221:0.0:0.0779	.	337	Q99999	G3ST1_HUMAN	P	337	ENSP00000385825:A337P;ENSP00000385735:A337P;ENSP00000384122:A337P;ENSP00000384388:A337P;ENSP00000343234:A337P;ENSP00000385207:A337P;ENSP00000402587:A337P	ENSP00000343234:A337P	A	-	1	0	GAL3ST1	29281203	0.970000	0.33590	0.958000	0.39756	0.894000	0.52154	2.095000	0.41729	2.615000	0.88500	0.561000	0.74099	GCC	.	.	.	none		0.721	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861	
CARD10	29775	hgsc.bcm.edu	37	22	37914027	37914027	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr22:37914027G>C	ENST00000403299.1	-	3	540	c.324C>G	c.(322-324)ttC>ttG	p.F108L	CARD10_ENST00000251973.5_Missense_Mutation_p.F108L			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	108	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					TGAGCAGCGTGAAGTGTTCGG	0.622																																					p.F108L		Atlas-SNP	.											.	CARD10	55	.	0			c.C324G						PASS	.						94.0	80.0	85.0					22																	37914027		2203	4300	6503	SO:0001583	missense	29775	exon2			CAGCGTGAAGTGT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.324C>G	chr22.hg19:g.37914027G>C	ENSP00000384570:p.Phe108Leu	93.0	0.0	.		60.0	13.0	.	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	hg19	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694688	0.88830	.	.	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.20069	2.1;2.1	4.67	3.64	0.41730	DEATH-like (2);Caspase Recruitment (2);	0.151059	0.46442	D	0.000290	T	0.20007	0.0481	L	0.47716	1.5	0.46774	D	0.99919	P	0.40000	0.698	B	0.38683	0.279	T	0.02713	-1.1120	10	0.66056	D	0.02	-23.0196	11.2943	0.49269	0.0863:0.0:0.9137:0.0	.	108	Q9BWT7	CAR10_HUMAN	L	108	ENSP00000384570:F108L;ENSP00000251973:F108L	ENSP00000251973:F108L	F	-	3	2	CARD10	36243973	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.159000	0.58157	1.061000	0.40601	0.462000	0.41574	TTC	.	.	.	none		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
MT-ND5	4540	hgsc.bcm.edu	37	M	14102	14102	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chrM:14102T>C	ENST00000361567.2	+	1	1766	c.1766T>C	c.(1765-1767)cTc>cCc	p.L589P	MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	589					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACTTTACTTCCTCTCTTTCTT	0.383																																					p.L589P		Atlas-SNP	.											.	.	.	.	0			c.T1766C						PASS	.																																			SO:0001583	missense	0	exon1			ACTTCCTCTCTTT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1766T>C	chrM.hg19:g.14102T>C	ENSP00000354813:p.Leu589Pro	8.0	0.0	.		152.0	74.0	.	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.	.	none		0.383	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
BAI3	577	hgsc.bcm.edu	37	6	69666026	69666027	+	Frame_Shift_Ins	INS	-	-	A	rs141698131		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:69666026_69666027insA	ENST00000370598.1	+	7	2127_2128	c.1306_1307insA	c.(1306-1308)gaafs	p.E436fs		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	436	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)				TGGAGGCTCCGAATGCAGAGGG	0.554																																					p.E436fs		Atlas-INDEL	.											.	BAI3	451	.	0			c.1306_1307insA						PASS	.																																			SO:0001589	frameshift_variant	577	exon7			.	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.1308dupA	chr6.hg19:g.69666028_69666028dupA	ENSP00000359630:p.Glu436fs	37.0	0.0	0		53.0	22.0	0.415094	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Frame_Shift_Ins	INS	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.	.	none		0.554	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
MANSC1	54682	hgsc.bcm.edu	37	12	12483592	12483592	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:12483592delT	ENST00000535902.1	-	4	1228	c.665delA	c.(664-666)aatfs	p.N222fs	MANSC1_ENST00000545735.1_Frame_Shift_Del_p.N141fs|MANSC1_ENST00000396349.3_Frame_Shift_Del_p.N188fs			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	222						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		CGCACTCACATTTTCAGGCAG	0.502																																					p.N222fs		Atlas-INDEL	.											.	MANSC1	38	.	0			c.666delT						PASS	.						101.0	106.0	104.0					12																	12483592		2203	4300	6503	SO:0001589	frameshift_variant	54682	exon4			.	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.665delA	chr12.hg19:g.12483592delT	ENSP00000438205:p.Asn222fs	107.0	0.0	0		109.0	37.0	0.33945	NM_018050	Q8NEC1|Q9NW60	Frame_Shift_Del	DEL	ENST00000535902.1	hg19	CCDS8648.1																																																																																			.	.	.	none		0.502	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
LIX1L	128077	hgsc.bcm.edu	37	1	145497429	145497430	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:145497429_145497430insT	ENST00000369308.3	+	4	708_709	c.634_635insT	c.(634-636)attfs	p.I212fs	RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	212										large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAATACAGGGATTGGTGCCTTC	0.45																																					p.I212fs		Atlas-INDEL	.											.	LIX1L	28	.	0			c.634_635insT						PASS	.																																			SO:0001589	frameshift_variant	128077	exon4			.	AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"""Lix1 homolog (mouse) like"", ""Lix1 homolog (chicken)-like"""			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.636dupT	chr1.hg19:g.145497431_145497431dupT	ENSP00000358314:p.Ile212fs	58.0	0.0	0		44.0	15.0	0.340909	NM_153713	Q6AI36	Frame_Shift_Ins	INS	ENST00000369308.3	hg19	CCDS915.1																																																																																			.	.	.	none		0.450	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713	
ABCB9	23457	hgsc.bcm.edu	37	12	123429030	123429030	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:123429030delA	ENST00000542678.1	-	7	4126	c.1288delT	c.(1288-1290)tacfs	p.Y430fs	ABCB9_ENST00000392439.3_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000280560.8_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000540285.1_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000442833.2_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000541983.1_5'UTR|ABCB9_ENST00000442028.2_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000344275.7_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000346530.5_Intron			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	430	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		TGGCCCCCGTAGTAGAGGATG	0.592																																					p.Y430fs	Ovarian(49;786 1333 9175 38236)	Atlas-INDEL	.											.	ABCB9	50	.	0			c.1289delA						PASS	.						139.0	120.0	127.0					12																	123429030		2203	4300	6503	SO:0001589	frameshift_variant	23457	exon7			.	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1288delT	chr12.hg19:g.123429030delA	ENSP00000440288:p.Tyr430fs	210.0	0.0	0		180.0	58.0	0.322222	NM_001243014	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	hg19	CCDS9241.1																																																																																			.	.	.	none		0.592	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
KDM6A	7403	hgsc.bcm.edu	37	X	44870257	44870257	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chrX:44870257delT	ENST00000377967.4	+	5	477	c.436delT	c.(436-438)tttfs	p.F146fs	KDM6A_ENST00000536777.1_Frame_Shift_Del_p.F146fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.F146fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.F146fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	146	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0(12)|p.0?(6)|p.?(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TTATAATGCATTTCAGTGGTA	0.323			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																p.A145fs	Colon(129;1273 1667 15230 27352 52914)	Atlas-INDEL	.		Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A	274	.	19	No detectable mRNA/protein(12)|Whole gene deletion(6)|Unknown(1)	haematopoietic_and_lymphoid_tissue(11)|oesophagus(4)|breast(2)|pancreas(2)	c.435delA						PASS	.						117.0	99.0	105.0					X																	44870257		2203	4297	6500	SO:0001589	frameshift_variant	7403	exon5			.	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.436delT	chrX.hg19:g.44870257delT	ENSP00000367203:p.Phe146fs	35.0	0.0	0		20.0	13.0	0.65	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.323	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	
RMDN3	55177	hgsc.bcm.edu	37	15	41037304	41037305	+	Frame_Shift_Ins	INS	-	-	GCACT			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:41037304_41037305insGCACT	ENST00000260385.6	-	4	1744_1745	c.677_678insAGTGC	c.(676-678)gccfs	p.-226fs	RMDN3_ENST00000338376.3_Frame_Shift_Ins_p.-226fs|RMDN3_ENST00000558560.1_Intron			Q96TC7	RMD3_HUMAN	regulator of microtubule dynamics 3						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)	integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CAGCCTCCAGGGCACTGGAGGC	0.599																																					p.A226fs		Atlas-INDEL	.											.	.	.	.	0			c.678_679insAGTGC						PASS	.																																			SO:0001589	frameshift_variant	55177	exon5			.	AK001441	CCDS10063.1	15q15.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000137824	ENSG00000137824			25550	protein-coding gene	gene with protein product		611873	"""family with sequence similarity 82, member A2"""	FAM82C, FAM82A2		12975309	Standard	XM_005254531		Approved	FLJ10579, PTPIP51, RMD3	uc001zmp.1	Q96TC7	OTTHUMG00000130066	ENST00000260385.6:c.673_677dupAGTGC	chr15.hg19:g.41037305_41037309dupGCACT	ENSP00000260385:p.Ala226fs	114.0	0.0	0		61.0	16.0	0.262295	NM_018145	A9UMZ9|B3KRR3|Q6ZWE9|Q96H23|Q96SD6|Q9H6G1|Q9NVQ6	Frame_Shift_Ins	INS	ENST00000260385.6	hg19	CCDS10063.1																																																																																			.	.	.	none		0.599	RMDN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252357.1	NM_018145	
DUOX1	53905	hgsc.bcm.edu	37	15	45453182	45453182	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:45453182delC	ENST00000321429.4	+	30	4257	c.3850delC	c.(3850-3852)cccfs	p.P1284fs	DUOX1_ENST00000561166.1_Frame_Shift_Del_p.P930fs|DUOX1_ENST00000389037.3_Frame_Shift_Del_p.P1284fs|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1284	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GGAGCTGCTGCCCTCAGGTAC	0.617																																					p.L1283fs		Atlas-INDEL	.											.	DUOX1	125	.	0			c.3849delG						PASS	.						81.0	65.0	71.0					15																	45453182		2198	4298	6496	SO:0001589	frameshift_variant	53905	exon29			.	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3850delC	chr15.hg19:g.45453182delC	ENSP00000317997:p.Pro1284fs	67.0	0.0	0		61.0	22.0	0.360656	NM_175940	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Frame_Shift_Del	DEL	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.	.	none		0.617	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
KRT32	3882	hgsc.bcm.edu	37	17	39622089	39622090	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:39622089_39622090insC	ENST00000225899.3	-	3	746_747	c.643_644insG	c.(643-645)gacfs	p.D215fs	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	215	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GGCCTCCAGGTCAGCCTTGCAC	0.604																																					p.D215fs		Atlas-INDEL	.											.	KRT32	57	.	0			c.644_645insG						PASS	.																																			SO:0001589	frameshift_variant	3882	exon3			.	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.644dupG	chr17.hg19:g.39622090_39622090dupC	ENSP00000225899:p.Asp215fs	120.0	0.0	0		146.0	85.0	0.582192	NM_002278		Frame_Shift_Ins	INS	ENST00000225899.3	hg19	CCDS11393.1																																																																																			.	.	.	none		0.604	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
EXOC3L2	90332	hgsc.bcm.edu	37	19	45720794	45720794	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:45720794delG	ENST00000252482.3	-	7	838	c.811delC	c.(811-813)cggfs	p.R272fs	EXOC3L2_ENST00000413988.1_Frame_Shift_Del_p.R272fs			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	272					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		ACCAGCCGCCGGAACAGCCTC	0.701																																					p.R271fs		Atlas-INDEL	.											.	EXOC3L2	30	.	0			c.812delG						PASS	.						9.0	12.0	11.0					19																	45720794		2147	4221	6368	SO:0001589	frameshift_variant	90332	exon8			.	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.811delC	chr19.hg19:g.45720794delG	ENSP00000252482:p.Arg272fs	28.0	0.0	0		19.0	10.0	0.526316	NM_138568	Q8N9W2|Q96GV2	Frame_Shift_Del	DEL	ENST00000252482.3	hg19	CCDS12657.1																																																																																			.	.	.	none		0.701	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
ABL2	27	hgsc.bcm.edu	37	1	179087902	179087902	+	Intron	DEL	A	A	-			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:179087902delA	ENST00000502732.1	-	7	1249				ABL2_ENST00000512653.1_Intron|ABL2_ENST00000507173.1_Intron|ABL2_ENST00000392043.3_Intron|ABL2_ENST00000511413.1_Intron|ABL2_ENST00000367623.4_Intron|ABL2_ENST00000344730.3_Intron|ABL2_ENST00000408940.3_Intron|ABL2_ENST00000504405.1_Intron	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase						actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	ACACACACCTAAAAGTTGAAC	0.398			T	ETV6	AML																																.		Atlas-INDEL	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.1046-2T>-						PASS	.						125.0	116.0	119.0					1																	179087902		2203	4300	6503	SO:0001627	intron_variant	27	exon8			.	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"""SH2 domain containing"""	77	protein-coding gene	gene with protein product	"""Abelson-related gene"""	164690	"""v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)"", ""v-abl Abelson murine leukemia viral oncogene homolog 2"", ""c-abl oncogene 2, non-receptor tyrosine kinase"""	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1046-3T>-	chr1.hg19:g.179087902delA		182.0	0.0	0		98.0	37.0	0.377551	NM_001168237	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Splice_Site	DEL	ENST00000502732.1	hg19	CCDS30947.1																																																																																			.	.	.	none		0.398	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158	
ITGB4	3691	hgsc.bcm.edu	37	17	73752854	73752855	+	In_Frame_Ins	INS	-	-	GCTGCA	rs370378040		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:73752854_73752855insGCTGCA	ENST00000200181.3	+	37	5154_5155	c.4967_4968insGCTGCA	c.(4966-4971)tcgctg>tcGCTGCAgctg	p.1659_1660insQL	ITGB4_ENST00000449880.2_In_Frame_Ins_p.1642_1643insQL|ITGB4_ENST00000579662.1_In_Frame_Ins_p.1589_1590insQL|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000339591.3_In_Frame_Ins_p.1642_1643insQL|ITGB4_ENST00000450894.3_In_Frame_Ins_p.1589_1590insQL	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1659	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGCCCAGACTCGCTGCAGCTGA	0.658																																					p.S1656delinsSLQ		Atlas-INDEL	.											.	ITGB4	165	.	0			c.4967_4968insGCTGCA						PASS	.																																			SO:0001652	inframe_insertion	3691	exon37			.		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4968_4973dupGCTGCA	chr17.hg19:g.73752855_73752860dupGCTGCA	ENSP00000200181:p.Gln1658_Leu1659dup	166.0	0.0	0		137.0	35.0	0.255474	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	In_Frame_Ins	INS	ENST00000200181.3	hg19	CCDS11727.1																																																																																			.	.	.	none		0.658	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
