#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CCNL2	81669	hgsc.bcm.edu	37	1	1322749	1322749	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:1322749C>T	ENST00000400809.3	-	11	1430	c.1425G>A	c.(1423-1425)gaG>gaA	p.E475E	CCNL2_ENST00000505849.1_5'UTR|CCNL2_ENST00000408952.5_Silent_p.E253E	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	475					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	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;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		TATCCGCCCGCTCCCGTGACC	0.562																																					p.E475E		Atlas-SNP	.											.	CCNL2	54	.	0			c.G1425A						.						110.0	120.0	117.0					1																	1322749		2203	4296	6499	SO:0001819	synonymous_variant	81669	exon11			CGCCCGCTCCCGT	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"""cyclin S"""	613482	"""cyclin M"""	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.1425G>A	chr1.hg19:g.1322749C>T		56.0	0.0		96.0	31.0	NM_030937	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Silent	SNP	ENST00000400809.3	hg19	CCDS30557.1																																																																																			.	.		0.562	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937	
MMEL1	79258	hgsc.bcm.edu	37	1	2535696	2535696	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:2535696T>C	ENST00000378412.3	-	10	1002	c.841A>G	c.(841-843)Atg>Gtg	p.M281V	MMEL1_ENST00000502556.1_Intron|MMEL1_ENST00000288709.6_Missense_Mutation_p.M272V			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	281						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		ACTGACACCATGAACTGCAGG	0.652																																					p.M281V		Atlas-SNP	.											.	MMEL1	64	.	0			c.A841G						.						63.0	65.0	64.0					1																	2535696		2202	4299	6501	SO:0001583	missense	79258	exon10			ACACCATGAACTG	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.841A>G	chr1.hg19:g.2535696T>C	ENSP00000367668:p.Met281Val	67.0	0.0		126.0	82.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	hg19	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	T	18.27	3.585868	0.66105	.	.	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.75050	-0.9;-0.9	4.43	4.43	0.53597	Peptidase M13 (1);	0.000000	0.85682	D	0.000000	D	0.85639	0.5743	M	0.82823	2.61	0.80722	D	1	D	0.76494	0.999	D	0.69654	0.965	D	0.87970	0.2736	10	0.87932	D	0	-31.6286	13.1682	0.59583	0.0:0.0:0.0:1.0	.	281	Q495T6	MMEL1_HUMAN	V	272;281	ENSP00000288709:M272V;ENSP00000367668:M281V	ENSP00000288709:M272V	M	-	1	0	MMEL1	2525556	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	3.567000	0.53813	1.741000	0.51731	0.397000	0.26171	ATG	.	.		0.652	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
MTOR	2475	hgsc.bcm.edu	37	1	11204794	11204794	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:11204794T>C	ENST00000361445.4	-	34	4859	c.4783A>G	c.(4783-4785)Atg>Gtg	p.M1595V	MTOR-AS1_ENST00000445982.1_RNA|MTOR_ENST00000495435.1_5'UTR|MTOR-AS1_ENST00000420480.1_RNA	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1595	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCGGACAGCATGTGGCAAGAA	0.483																																					p.M1595V		Atlas-SNP	.											.	MTOR	327	.	0			c.A4783G						.						92.0	83.0	86.0					1																	11204794		2203	4300	6503	SO:0001583	missense	2475	exon34			ACAGCATGTGGCA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4783A>G	chr1.hg19:g.11204794T>C	ENSP00000354558:p.Met1595Val	28.0	0.0		42.0	28.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.157965	0.78114	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.71579	-0.58	5.6	5.6	0.85130	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	D	0.85323	0.5670	M	0.93763	3.455	0.80722	D	1	P	0.35542	0.508	P	0.48795	0.59	D	0.87752	0.2592	10	0.72032	D	0.01	-11.5413	15.7961	0.78412	0.0:0.0:0.0:1.0	.	1595	P42345	MTOR_HUMAN	V	1595	ENSP00000354558:M1595V	ENSP00000354558:M1595V	M	-	1	0	MTOR	11127381	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.665000	0.83852	2.131000	0.65755	0.533000	0.62120	ATG	.	.		0.483	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
CELA3A	10136	hgsc.bcm.edu	37	1	22332241	22332241	+	Missense_Mutation	SNP	A	A	G	rs75527968	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:22332241A>G	ENST00000290122.3	+	4	333	c.314A>G	c.(313-315)gAg>gGg	p.E105G	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.E105G	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	105	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ATCAACTCTGAGGAGCTGTTT	0.592											OREG0013211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	5	0.000998403	0.0015	0.0014	5008	,	,		21127	0.0		0.0	False		,,,				2504	0.002				p.E105G		Atlas-SNP	.											.	CELA3A	35	.	0			c.A314G						.						128.0	112.0	118.0					1																	22332241		2197	4300	6497	SO:0001583	missense	10136	exon4			ACTCTGAGGAGCT	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.314A>G	chr1.hg19:g.22332241A>G	ENSP00000290122:p.Glu105Gly	70.0	0.0	755	133.0	9.0	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	hg19	CCDS220.1	.	.	.	.	.	.	.	.	.	.	A	5.149	0.213076	0.09757	.	.	ENSG00000142789	ENST00000290122;ENST00000374663;ENST00000374661	T;D	0.93547	2.21;-3.24	3.88	-0.633	0.11519	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.86560	0.5962	L	0.38953	1.18	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.16289	0.015;0.005	T	0.71262	-0.4645	9	0.18710	T	0.47	-3.7117	6.9051	0.24305	0.575:0.0:0.425:0.0	.	105;105	B1AQ52;P09093	.;CEL3A_HUMAN	G	105;105;121	ENSP00000290122:E105G;ENSP00000363795:E105G	ENSP00000290122:E105G	E	+	2	0	CELA3A	22204828	0.000000	0.05858	0.003000	0.11579	0.017000	0.09413	-1.034000	0.03567	0.009000	0.14813	-1.727000	0.00703	GAG	.	A|0.500;G|0.500		0.592	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
CELA3A	10136	hgsc.bcm.edu	37	1	22332245	22332245	+	Missense_Mutation	SNP	G	G	C	rs74958230	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:22332245G>C	ENST00000290122.3	+	4	337	c.318G>C	c.(316-318)gaG>gaC	p.E106D	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.E106D	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	106	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			Missing (in Ref. 1; AAA66350). {ECO:0000305}.	cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ACTCTGAGGAGCTGTTTGTGC	0.592													c|||	222	0.0443291	0.0325	0.0749	5008	,	,		19649	0.0357		0.0626	False		,,,				2504	0.0286				p.E106D		Atlas-SNP	.											.	CELA3A	35	.	0			c.G318C						.						130.0	113.0	119.0					1																	22332245		2197	4300	6497	SO:0001583	missense	10136	exon4			TGAGGAGCTGTTT	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.318G>C	chr1.hg19:g.22332245G>C	ENSP00000290122:p.Glu106Asp	69.0	0.0		140.0	10.0	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	hg19	CCDS220.1	.	.	.	.	.	.	.	.	.	.	G	8.422	0.846631	0.16963	.	.	ENSG00000142789	ENST00000290122;ENST00000374663;ENST00000374661	T;D	0.93189	2.26;-3.18	3.88	0.792	0.18625	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85487	0.5708	N	0.21545	0.675	0.19300	N	0.999971	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.70371	-0.4890	9	0.22706	T	0.39	-20.2782	7.771	0.29008	0.321:0.5221:0.157:0.0	.	106;106	B1AQ52;P09093	.;CEL3A_HUMAN	D	106;106;122	ENSP00000290122:E106D;ENSP00000363795:E106D	ENSP00000290122:E106D	E	+	3	2	CELA3A	22204832	0.909000	0.30893	0.224000	0.23877	0.007000	0.05969	0.262000	0.18460	-0.019000	0.14055	-0.514000	0.04452	GAG	.	G|0.500;C|0.500		0.592	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
SLC22A15	55356	hgsc.bcm.edu	37	1	116563474	116563474	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:116563474A>G	ENST00000369503.4	+	4	696	c.566A>G	c.(565-567)gAa>gGa	p.E189G	SLC22A15_ENST00000369502.1_Missense_Mutation_p.E189G	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	189					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTGCTTAATGAATGTGTGGGC	0.488											OREG0013699	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E189G		Atlas-SNP	.											.	SLC22A15	65	.	0			c.A566G						.						106.0	104.0	105.0					1																	116563474		1984	4168	6152	SO:0001583	missense	55356	exon4			TTAATGAATGTGT	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"""Solute carriers"""	20301	protein-coding gene	gene with protein product		608275	"""solute carrier family 22 (organic cation transporter), member 15"""			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.566A>G	chr1.hg19:g.116563474A>G	ENSP00000358515:p.Glu189Gly	136.0	0.0	1474	366.0	151.0	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	hg19	CCDS44198.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.919801	0.92249	.	.	ENSG00000163393	ENST00000369503;ENST00000369502	D;T	0.86694	-2.16;0.33	5.84	5.84	0.93424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.95752	0.8618	H	0.98256	4.185	0.58432	D	0.99999	D;D	0.58268	0.974;0.982	D;D	0.70487	0.969;0.959	D	0.97366	0.9973	10	0.87932	D	0	.	16.2254	0.82286	1.0:0.0:0.0:0.0	.	189;189	Q8IZD6;Q8IZD6-2	S22AF_HUMAN;.	G	189	ENSP00000358515:E189G;ENSP00000358514:E189G	ENSP00000358514:E189G	E	+	2	0	SLC22A15	116364997	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.980000	0.88113	2.225000	0.72522	0.528000	0.53228	GAA	.	.		0.488	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420	
MUC1	4582	hgsc.bcm.edu	37	1	155160803	155160803	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:155160803C>T	ENST00000368395.1	-	3	795	c.724G>A	c.(724-726)Gta>Ata	p.V242I	MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000343256.5_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000462215.1_Splice_Site|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000342482.4_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000438413.1_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	1022	42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R.				cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AGAGGAGGTACCGTGCTATGG	0.498			T	IGH@	B-NHL																																p.V251I		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	.	MUC1	94	.	0			c.G751A						.						42.0	48.0	46.0					1																	155160803		2197	4297	6494	SO:0001583	missense	4582	exon4			GAGGTACCGTGCT	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.724G>A	chr1.hg19:g.155160803C>T	ENSP00000357380:p.Val242Ile	143.0	0.0		509.0	90.0	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Missense_Mutation	SNP	ENST00000368395.1	hg19	CCDS55640.1	.	.	.	.	.	.	.	.	.	.	C	5.638	0.302342	0.10678	.	.	ENSG00000185499	ENST00000368395;ENST00000425082	T	0.17213	2.29	3.46	2.53	0.30540	.	1.764090	0.03886	N	0.277917	T	0.03136	0.0092	N	0.14661	0.345	0.09310	N	0.999991	B;B;B	0.28880	0.123;0.226;0.11	B;B;B	0.28709	0.026;0.093;0.039	T	0.31943	-0.9925	10	0.20519	T	0.43	3.0263	4.7736	0.13167	0.0:0.7446:0.0:0.2554	.	1019;328;242	P15941-3;B4DWK6;B1AVQ5	.;.;.	I	242;328	ENSP00000357380:V242I	ENSP00000357380:V242I	V	-	1	0	MUC1	153427427	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	1.455000	0.35190	1.944000	0.56390	0.467000	0.42956	GTA	.	.		0.498	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
FAM189B	10712	hgsc.bcm.edu	37	1	155224577	155224577	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:155224577A>C	ENST00000361361.2	-	1	601	c.92T>G	c.(91-93)cTg>cGg	p.L31R	FAM189B_ENST00000472550.1_5'UTR|FAM189B_ENST00000350210.2_Missense_Mutation_p.L31R|SCAMP3_ENST00000472397.1_5'Flank|FAM189B_ENST00000368368.3_Missense_Mutation_p.L31R	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	31						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						CAGGGCCTGCAGCCAGGGTCG	0.672																																					p.L31R		Atlas-SNP	.											.	FAM189B	51	.	0			c.T92G						.						43.0	39.0	40.0					1																	155224577		2203	4300	6503	SO:0001583	missense	10712	exon1			GCCTGCAGCCAGG	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 2"""	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.92T>G	chr1.hg19:g.155224577A>C	ENSP00000354958:p.Leu31Arg	47.0	0.0		170.0	19.0	NM_001267608	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	hg19	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	A	19.34	3.809219	0.70797	.	.	ENSG00000160767	ENST00000350210;ENST00000333966;ENST00000368368;ENST00000361361;ENST00000491082	T;T;T;T	0.24350	2.16;2.43;2.42;1.86	4.59	4.59	0.56863	.	0.195943	0.35013	N	0.003501	T	0.13200	0.0320	N	0.08118	0	0.32694	N	0.513739	D;D;D;D	0.65815	0.968;0.995;0.994;0.995	P;D;P;P	0.69142	0.724;0.962;0.81;0.884	T	0.07271	-1.0781	10	0.32370	T	0.25	.	6.958	0.24582	0.8987:0.0:0.1013:0.0	.	31;31;31;31	D6RD59;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	R	31	ENSP00000307128:L31R;ENSP00000357352:L31R;ENSP00000354958:L31R;ENSP00000427011:L31R	ENSP00000333944:L31R	L	-	2	0	FAM189B	153491201	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.772000	0.55325	2.057000	0.61298	0.533000	0.62120	CTG	.	.		0.672	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589	
OR6K6	128371	hgsc.bcm.edu	37	1	158725609	158725609	+	Missense_Mutation	SNP	A	A	G	rs559439148		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:158725609A>G	ENST00000368144.2	+	1	1100	c.1004A>G	c.(1003-1005)cAg>cGg	p.Q335R		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	335						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					TTCCACTATCAGAAGAGGGCT	0.418													A|||	1	0.000199681	0.0	0.0	5008	,	,		19386	0.0		0.0	False		,,,				2504	0.001				p.Q335R		Atlas-SNP	.											.	OR6K6	81	.	0			c.A1004G						.						83.0	87.0	86.0					1																	158725609		2203	4300	6503	SO:0001583	missense	128371	exon1			ACTATCAGAAGAG	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"""GPCR / Class A : Olfactory receptors"""	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.1004A>G	chr1.hg19:g.158725609A>G	ENSP00000357126:p.Gln335Arg	118.0	0.0		301.0	46.0	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	hg19	CCDS30904.1	.	.	.	.	.	.	.	.	.	.	A	7.484	0.649280	0.14516	.	.	ENSG00000180433	ENST00000368144	T	0.35048	1.33	5.26	2.92	0.33932	.	0.634090	0.12974	N	0.423879	T	0.05502	0.0145	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41288	-0.9517	10	0.27082	T	0.32	-1.0501	7.7691	0.28997	0.8182:0.0:0.1818:0.0	.	335	Q8NGW6	OR6K6_HUMAN	R	335	ENSP00000357126:Q335R	ENSP00000357126:Q335R	Q	+	2	0	OR6K6	156992233	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	1.190000	0.32126	0.440000	0.26502	-0.274000	0.10170	CAG	.	.		0.418	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184	
TDRD5	163589	hgsc.bcm.edu	37	1	179621325	179621325	+	Missense_Mutation	SNP	G	G	A	rs375929466		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:179621325G>A	ENST00000367614.1	+	13	2512	c.2153G>A	c.(2152-2154)cGt>cAt	p.R718H	TDRD5_ENST00000444136.1_Missense_Mutation_p.R718H|TDRD5_ENST00000294848.8_Missense_Mutation_p.R718H	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	718					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AGTGAGTTACGTATCTTGGTA	0.348																																					p.R718H		Atlas-SNP	.											.	TDRD5	149	.	0			c.G2153A						.	A	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	825.9+/-416.6	0,1,2202	81.0	79.0	80.0		2153,818,2153,2153,2153	-0.7	0.0	1		80	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	TDRD5	NM_173533.3,NM_001199092.1,NM_001199091.1,NM_001199089.1,NM_001199085.1	29,29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	718/982,273/537,718/982,718/1036,718/1036	179621325	1,13005	2203	4300	6503	SO:0001583	missense	163589	exon13			AGTTACGTATCTT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2153G>A	chr1.hg19:g.179621325G>A	ENSP00000356586:p.Arg718His	106.0	0.0		239.0	23.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513657	0.27123	2.27E-4	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.30182	2.76;2.76;2.92;1.54	4.75	-0.711	0.11230	.	1.820450	0.03225	N	0.178189	T	0.13372	0.0324	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11227	-1.0596	10	0.20519	T	0.43	.	0.2658	0.00225	0.325:0.1442:0.2511:0.2797	.	718;718	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	H	718;718;718;174	ENSP00000356586:R718H;ENSP00000294848:R718H;ENSP00000406052:R718H;ENSP00000410744:R174H	ENSP00000294848:R718H	R	+	2	0	TDRD5	177887948	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-0.429000	0.06982	-0.227000	0.09884	-0.381000	0.06696	CGT	.	.		0.348	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
DENND1B	163486	hgsc.bcm.edu	37	1	197704850	197704850	+	Intron	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:197704850T>C	ENST00000367396.3	-	3	252				DENND1B_ENST00000235453.4_5'UTR|DENND1B_ENST00000400967.2_5'Flank|DENND1B_ENST00000477581.1_5'UTR	NM_144977.4	NP_659414.2	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B						positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|kidney(2)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	22						CAGGAAAGTTTTCCAGTTTCT	0.547																																					p.E53E		Atlas-SNP	.											.	DENND1B	108	.	0			c.A159G						.																																			SO:0001627	intron_variant	163486	exon3			AAAGTTTTCCAGT	BC016588	CCDS41452.2, CCDS72996.1, CCDS72997.1	1q31.3	2012-10-03	2005-08-17	2005-08-17	ENSG00000213047	ENSG00000213047		"""DENN/MADD domain containing"""	28404	protein-coding gene	gene with protein product		613292	"""family with sequence similarity 31, member B"", ""chromosome 1 open reading frame 218"""	FAM31B, C1orf218		12477932	Standard	NM_144977		Approved	MGC27044, FLJ20054	uc021pgu.1	Q6P3S1	OTTHUMG00000035653	ENST00000367396.3:c.83-20646A>G	chr1.hg19:g.197704850T>C		17.0	0.0		40.0	9.0	NM_001195216	B5MD89|D3PFD5|Q5T3B8|Q5T3B9|Q5T3C1|Q5TAI8|Q6B0I8|Q8NDT1|Q8TBE6|Q9H774|Q9NXU2	Silent	SNP	ENST00000367396.3	hg19	CCDS41452.2																																																																																			.	.		0.547	DENND1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086539.1	NM_144977	
PTPRC	5788	hgsc.bcm.edu	37	1	198721876	198721876	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:198721876A>G	ENST00000367376.2	+	31	3649	c.3478A>G	c.(3478-3480)Agt>Ggt	p.S1160G	PTPRC_ENST00000352140.3_Missense_Mutation_p.S1112G|PTPRC_ENST00000348564.6_Missense_Mutation_p.S1001G|PTPRC_ENST00000594404.1_Missense_Mutation_p.S999G|PTPRC_ENST00000442510.2_Missense_Mutation_p.S1162G	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1160	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GCATCACAAGAGTACACCTCT	0.433																																					p.S1162G		Atlas-SNP	.											.	PTPRC	229	.	0			c.A3484G						.						66.0	62.0	63.0					1																	198721876		2203	4299	6502	SO:0001583	missense	5788	exon31			CACAAGAGTACAC	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.3478A>G	chr1.hg19:g.198721876A>G	ENSP00000356346:p.Ser1160Gly	36.0	0.0		89.0	13.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.12	1.543897	0.27563	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	D	0.84298	-1.83	6.02	3.7	0.42460	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.685138	0.13231	N	0.403621	T	0.75064	0.3799	N	0.25332	0.735	0.24376	N	0.994813	B;B;B	0.14805	0.011;0.011;0.011	B;B;B	0.19666	0.026;0.026;0.018	T	0.62558	-0.6829	10	0.35671	T	0.21	.	7.2685	0.26244	0.7741:0.1523:0.0736:0.0	.	1001;1112;1160	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	G	1162;1112;1160;999	ENSP00000193532:S1112G	ENSP00000306782:S999G	S	+	1	0	PTPRC	196988499	0.801000	0.28930	0.250000	0.24296	0.447000	0.32167	1.536000	0.36072	1.078000	0.41014	0.528000	0.53228	AGT	.	.		0.433	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
OPTC	26254	hgsc.bcm.edu	37	1	203468895	203468895	+	Silent	SNP	G	G	T	rs114294638	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:203468895G>T	ENST00000367222.2	+	5	764	c.648G>T	c.(646-648)ctG>ctT	p.L216L		NM_014359.3	NP_055174.1	Q9UBM4	OPT_HUMAN	opticin	216					negative regulation of angiogenesis (GO:0016525)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			breast(1)|cervix(1)|kidney(5)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.109)			TGGAAGCTCTGCCCGTGCTGC	0.567																																					p.L216L		Atlas-SNP	.											.	OPTC	50	.	0			c.G648T						.						177.0	173.0	175.0					1																	203468895		2203	4300	6503	SO:0001819	synonymous_variant	26254	exon5			AGCTCTGCCCGTG	AF161702	CCDS1439.1	1q31	2008-02-05			ENSG00000188770	ENSG00000188770			8158	protein-coding gene	gene with protein product	"""oculoglycan"""	605127				10636917	Standard	NM_014359		Approved		uc001gzu.1	Q9UBM4	OTTHUMG00000036100	ENST00000367222.2:c.648G>T	chr1.hg19:g.203468895G>T		74.0	0.0		188.0	114.0	NM_014359	Q5T2G4	Silent	SNP	ENST00000367222.2	hg19	CCDS1439.1																																																																																			.	G|0.998;A|0.002		0.567	OPTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087964.1	NM_014359	
DNAH14	127602	hgsc.bcm.edu	37	1	225147985	225147985	+	Intron	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:225147985T>C	ENST00000445597.2	+	6	748				DNAH14_ENST00000366849.1_Silent_p.P116P|DNAH14_ENST00000430092.1_Silent_p.P116P|DNAH14_ENST00000439375.2_Silent_p.P116P|DNAH14_ENST00000498360.1_3'UTR|DNAH14_ENST00000366848.1_Silent_p.P116P|DNAH14_ENST00000400952.3_Silent_p.P116P|DNAH14_ENST00000366850.3_Silent_p.P116P			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AAGCCAGGCCTGTGTCCTATG	0.398																																					p.P116P		Atlas-SNP	.											.	DNAH14	300	.	0			c.T348C						.						92.0	87.0	88.0					1																	225147985		1880	4112	5992	SO:0001627	intron_variant	127602	exon4			CAGGCCTGTGTCC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.749-4196T>C	chr1.hg19:g.225147985T>C		79.0	0.0		150.0	37.0	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	hg19																																																																																				.	.		0.398	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
EXO1	9156	hgsc.bcm.edu	37	1	242035389	242035389	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr1:242035389G>A	ENST00000366548.3	+	12	1916	c.1323G>A	c.(1321-1323)aaG>aaA	p.K441K	EXO1_ENST00000348581.5_Silent_p.K441K|EXO1_ENST00000518483.1_Silent_p.K441K	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	441	Interaction with MLH1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			TTACGAAGAAGACCAAGAAAA	0.358								Editing and processing nucleases																													p.K441K		Atlas-SNP	.											EXO1,colon,carcinoma,0,1	EXO1	103	.	0			c.G1323A						.						44.0	45.0	45.0					1																	242035389		2203	4300	6503	SO:0001819	synonymous_variant	9156	exon10			GAAGAAGACCAAG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1323G>A	chr1.hg19:g.242035389G>A		140.0	0.0		376.0	32.0	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Silent	SNP	ENST00000366548.3	hg19	CCDS1620.1																																																																																			.	.		0.358	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
UBXN2A	165324	hgsc.bcm.edu	37	2	24194229	24194229	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:24194229A>T	ENST00000309033.4	+	3	369	c.125A>T	c.(124-126)gAg>gTg	p.E42V	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000404924.1_Missense_Mutation_p.E42V|UBXN2A_ENST00000535786.1_Missense_Mutation_p.E42V	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	42					regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						AGCCTTTTTGAGGAAGCTCAG	0.333																																					p.E42V		Atlas-SNP	.											.	UBXN2A	20	.	0			c.A125T						.						128.0	135.0	133.0					2																	24194229		2203	4300	6503	SO:0001583	missense	165324	exon3			TTTTTGAGGAAGC	BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"""UBX domain containing"""	27265	protein-coding gene	gene with protein product			"""UBX domain containing 4"""	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.125A>T	chr2.hg19:g.24194229A>T	ENSP00000312107:p.Glu42Val	69.0	0.0		106.0	64.0	NM_181713	A8K577|B7ZKP8|Q569G8	Missense_Mutation	SNP	ENST00000309033.4	hg19	CCDS1704.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.948036	0.73787	.	.	ENSG00000173960	ENST00000404924;ENST00000309033;ENST00000535786	T;T;T	0.51574	0.75;0.75;0.7	4.53	4.53	0.55603	.	0.096452	0.64402	D	0.000001	T	0.54951	0.1890	L	0.32530	0.975	0.41646	D	0.989103	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.957	T	0.52533	-0.8563	10	0.33940	T	0.23	-0.4989	12.105	0.53807	1.0:0.0:0.0:0.0	.	42;42	B7ZKP8;P68543	.;UBX2A_HUMAN	V	42	ENSP00000385525:E42V;ENSP00000312107:E42V;ENSP00000440533:E42V	ENSP00000312107:E42V	E	+	2	0	UBXN2A	24047733	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.240000	0.65378	2.011000	0.59026	0.524000	0.50904	GAG	.	.		0.333	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713	
MTIF2	4528	hgsc.bcm.edu	37	2	55473534	55473534	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:55473534C>T	ENST00000263629.4	-	10	1360	c.1045G>A	c.(1045-1047)Gca>Aca	p.A349T	MTIF2_ENST00000394600.3_Missense_Mutation_p.A349T|MTIF2_ENST00000403721.1_Missense_Mutation_p.A349T	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	349					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TTGGGATCTGCTTTCAATTCT	0.378																																					p.A349T		Atlas-SNP	.											.	MTIF2	64	.	0			c.G1045A						.						169.0	155.0	159.0					2																	55473534		2203	4300	6503	SO:0001583	missense	4528	exon10			GATCTGCTTTCAA	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1045G>A	chr2.hg19:g.55473534C>T	ENSP00000263629:p.Ala349Thr	125.0	0.0		256.0	24.0	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	hg19	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553310	0.96501	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823;ENST00000535023	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.33	5.33	0.75918	.	0.110995	0.64402	D	0.000010	T	0.63558	0.2521	M	0.85710	2.77	0.80722	D	1	P	0.38978	0.652	P	0.49829	0.623	T	0.66779	-0.5837	10	0.52906	T	0.07	-15.7217	19.0262	0.92932	0.0:1.0:0.0:0.0	.	349	P46199	IF2M_HUMAN	T	349;349;349;69;349	ENSP00000384481:A349T;ENSP00000263629:A349T;ENSP00000378099:A349T;ENSP00000403492:A69T	ENSP00000263629:A349T	A	-	1	0	MTIF2	55327038	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.268000	0.78473	2.505000	0.84491	0.655000	0.94253	GCA	.	.		0.378	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
C2orf81	388963	hgsc.bcm.edu	37	2	74641896	74641896	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:74641896G>A	ENST00000517883.1	-	1	1814	c.1123C>T	c.(1123-1125)Ctg>Ttg	p.L375L	C2orf81_ENST00000290390.5_Silent_p.L443L			A6NN90	CB081_HUMAN	chromosome 2 open reading frame 81	436										endometrium(3)|kidney(1)	4						GGGAGTGGCAGCTTTGACTCG	0.617																																					p.L443L		Atlas-SNP	.											.	C2orf81	23	.	0			c.C1327T						.						120.0	133.0	129.0					2																	74641896		692	1591	2283	SO:0001819	synonymous_variant	388963	exon4			GTGGCAGCTTTGA	AC005041, CH471053		2p13.1	2012-08-07			ENSG00000159239	ENSG00000159239			34350	protein-coding gene	gene with protein product						15815621	Standard	NM_001145054		Approved	LOC388963, hCG40743	uc010yrq.1	A6NN90	OTTHUMG00000164184	ENST00000517883.1:c.1123C>T	chr2.hg19:g.74641896G>A		48.0	0.0		102.0	19.0	NM_001145054		Silent	SNP	ENST00000517883.1	hg19																																																																																				.	.		0.617	C2orf81-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000377683.1	NM_001145054	
WDR33	55339	hgsc.bcm.edu	37	2	128474768	128474768	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:128474768G>T	ENST00000322313.4	-	17	2988	c.2830C>A	c.(2830-2832)Ccc>Acc	p.P944T		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	944					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TTCAGAGGGGGAATGCGACCT	0.488																																					p.P944T		Atlas-SNP	.											WDR33,scalp,malignant_melanoma,0,1	WDR33	136	.	0			c.C2830A						.						42.0	40.0	41.0					2																	128474768		2203	4300	6503	SO:0001583	missense	55339	exon17			GAGGGGGAATGCG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2830C>A	chr2.hg19:g.128474768G>T	ENSP00000325377:p.Pro944Thr	60.0	0.0		152.0	97.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.564656	0.45694	.	.	ENSG00000136709	ENST00000322313	D	0.89343	-2.5	5.27	5.27	0.74061	.	0.200449	0.35970	N	0.002871	T	0.78451	0.4285	N	0.08118	0	0.80722	D	1	B	0.27498	0.18	B	0.17098	0.017	T	0.78074	-0.2346	10	0.72032	D	0.01	-4.998	14.8293	0.70135	0.0:0.1867:0.8133:0.0	.	944	Q9C0J8	WDR33_HUMAN	T	944	ENSP00000325377:P944T	ENSP00000325377:P944T	P	-	1	0	WDR33	128191238	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.230000	0.58632	2.473000	0.83533	0.563000	0.77884	CCC	.	.		0.488	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
TTN	7273	hgsc.bcm.edu	37	2	179548789	179548789	+	Missense_Mutation	SNP	C	C	T	rs72650032	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:179548789C>T	ENST00000591111.1	-	131	32016	c.31792G>A	c.(31792-31794)Gct>Act	p.A10598T	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A9671T|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A10915T|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				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)			TCTGGGACAGCTCTCTTCGGT	0.363																																					p.A10915T		Atlas-SNP	.											.	TTN	18412	.	0			c.G32743A						.						82.0	81.0	81.0					2																	179548789		1809	4072	5881	SO:0001583	missense	7273	exon133			GGACAGCTCTCTT	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.31792G>A	chr2.hg19:g.179548789C>T	ENSP00000465570:p.Ala10598Thr	91.0	0.0		181.0	115.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.37	2.217774	0.39201	.	.	ENSG00000155657	ENST00000342992	T	0.64438	-0.1	5.58	2.76	0.32466	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.43500	0.1250	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.35798	-0.9774	9	0.87932	D	0	.	9.9864	0.41843	0.0:0.6767:0.1633:0.16	.	10598	Q8WZ42	TITIN_HUMAN	T	9671	ENSP00000343764:A9671T	ENSP00000343764:A9671T	A	-	1	0	TTN	179257034	0.405000	0.25336	0.999000	0.59377	0.829000	0.46940	0.190000	0.17057	0.744000	0.32741	0.563000	0.77884	GCT	.	C|0.998;G|0.002		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179575865	179575865	+	Missense_Mutation	SNP	G	G	C	rs374930292		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:179575865G>C	ENST00000591111.1	-	95	27371	c.27147C>G	c.(27145-27147)agC>agG	p.S9049R	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S8122R|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S9366R|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	13187	Ig-like 73.				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)			GGCCTGCAAGGCTCCGGTCAG	0.428																																					p.S9366R		Atlas-SNP	.											.	TTN	18412	.	0			c.C28098G						.	G	,,,ARG/SER	1,3677		0,1,1838	121.0	121.0	121.0		,,,24366	2.9	1.0	2		121	0,8180		0,0,4090	no	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,110	0,1,5928	CC,CG,GG		0.0,0.0272,0.0084	,,,benign	,,,8122/33424	179575865	1,11857	1839	4090	5929	SO:0001583	missense	7273	exon97			TGCAAGGCTCCGG	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.27147C>G	chr2.hg19:g.179575865G>C	ENSP00000465570:p.Ser9049Arg	70.0	0.0		77.0	13.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.61	1.691391	0.30052	2.72E-4	0.0	ENSG00000155657	ENST00000342992	T	0.46819	0.86	5.76	2.91	0.33838	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.41696	0.1170	L	0.50993	1.605	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.31668	-0.9935	9	0.87932	D	0	.	10.9549	0.47351	0.203:0.0:0.797:0.0	.	9049	Q8WZ42	TITIN_HUMAN	R	8122	ENSP00000343764:S8122R	ENSP00000343764:S8122R	S	-	3	2	TTN	179284110	0.995000	0.38212	0.996000	0.52242	0.989000	0.77384	0.372000	0.20467	0.409000	0.25649	0.655000	0.94253	AGC	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RAPH1	65059	hgsc.bcm.edu	37	2	204326584	204326584	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:204326584G>A	ENST00000319170.5	-	5	1096	c.797C>T	c.(796-798)gCa>gTa	p.A266V	RAPH1_ENST00000308091.4_Missense_Mutation_p.A318V|RAPH1_ENST00000374493.3_Missense_Mutation_p.A318V|RAPH1_ENST00000419464.1_Missense_Mutation_p.A266V|RAPH1_ENST00000439222.1_Missense_Mutation_p.A291V|RAPH1_ENST00000374488.2_Missense_Mutation_p.A291V|RAPH1_ENST00000374489.2_Missense_Mutation_p.A293V|RAPH1_ENST00000453034.1_Missense_Mutation_p.A318V|RAPH1_ENST00000457812.1_Missense_Mutation_p.A266V|RAPH1_ENST00000418114.1_Missense_Mutation_p.A266V|RAPH1_ENST00000423104.1_Missense_Mutation_p.A293V	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	266					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTTCACTTGTGCCTCTTTAAT	0.368																																					p.A318V		Atlas-SNP	.											.	RAPH1	118	.	0			c.C953T						.						132.0	123.0	127.0					2																	204326584		2202	4300	6502	SO:0001583	missense	65059	exon7			ACTTGTGCCTCTT	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.797C>T	chr2.hg19:g.204326584G>A	ENSP00000316543:p.Ala266Val	114.0	0.0		474.0	24.0	NM_203365	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	G	34	5.346929	0.95807	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201	T;T;T;T;T;T;T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95;-0.95	5.65	5.65	0.86999	.	0.000000	0.45606	D	0.000345	D	0.83677	0.5306	L	0.48642	1.525	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.91635	0.999;0.985;0.994	D	0.84257	0.0481	10	0.87932	D	0	-20.7348	19.7068	0.96076	0.0:0.0:1.0:0.0	.	318;318;266	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	V	266;266;318;293;291;318;291;266;293;318;291;266;293	ENSP00000392854:A266V;ENSP00000316543:A266V;ENSP00000363617:A318V;ENSP00000363613:A293V;ENSP00000363612:A291V;ENSP00000311293:A318V;ENSP00000411138:A291V;ENSP00000390578:A266V;ENSP00000397751:A293V;ENSP00000406662:A318V;ENSP00000396711:A266V	ENSP00000311293:A318V	A	-	2	0	RAPH1	204034829	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.924000	0.87555	2.824000	0.97209	0.655000	0.94253	GCA	.	.		0.368	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
SPHKAP	80309	hgsc.bcm.edu	37	2	228884727	228884727	+	Silent	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:228884727A>T	ENST00000392056.3	-	7	889	c.843T>A	c.(841-843)atT>atA	p.I281I	SPHKAP_ENST00000344657.5_Silent_p.I281I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	281						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GTTCTGTTTTAATCAATGGTG	0.443																																					p.I281I		Atlas-SNP	.											.	SPHKAP	750	.	0			c.T843A						.						236.0	251.0	246.0					2																	228884727		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			TGTTTTAATCAAT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.843T>A	chr2.hg19:g.228884727A>T		187.0	0.0		1095.0	145.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.443	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
ITPR1	3708	hgsc.bcm.edu	37	3	4732940	4732940	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:4732940G>A	ENST00000443694.2	+	29	3896	c.3896G>A	c.(3895-3897)cGg>cAg	p.R1299Q	ITPR1_ENST00000354582.6_Missense_Mutation_p.R1314Q|ITPR1_ENST00000423119.2_Missense_Mutation_p.R1305Q|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.R1299Q|ITPR1_ENST00000357086.4_Missense_Mutation_p.R1305Q|ITPR1_ENST00000456211.2_Missense_Mutation_p.R1290Q			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1314					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ACTCACGGTCGGAATGTCCAG	0.408																																					p.R1305Q		Atlas-SNP	.											.	ITPR1	659	.	0			c.G3914A						.						89.0	87.0	88.0					3																	4732940		1917	4149	6066	SO:0001583	missense	3708	exon32			ACGGTCGGAATGT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3896G>A	chr3.hg19:g.4732940G>A	ENSP00000401671:p.Arg1299Gln	106.0	0.0		225.0	68.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351730	0.95830	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.24	5.24	0.73138	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.968;0.979	D	0.98763	1.0725	10	0.56958	D	0.05	.	18.8583	0.92262	0.0:0.0:1.0:0.0	.	1314;1305	Q14643;G5E9P1	ITPR1_HUMAN;.	Q	1314;1299;1314;1305;1305;1290;1299	ENSP00000306253:R1299Q;ENSP00000346595:R1314Q;ENSP00000405934:R1305Q;ENSP00000349597:R1305Q;ENSP00000397885:R1290Q;ENSP00000401671:R1299Q	ENSP00000306253:R1299Q	R	+	2	0	ITPR1	4707940	1.000000	0.71417	0.849000	0.33467	0.941000	0.58515	9.778000	0.99011	2.437000	0.82529	0.655000	0.94253	CGG	.	.		0.408	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
DLEC1	9940	hgsc.bcm.edu	37	3	38135225	38135225	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:38135225C>T	ENST00000308059.6	+	12	1907	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M	DLEC1_ENST00000452631.2_Missense_Mutation_p.T629M|DLEC1_ENST00000346219.3_Missense_Mutation_p.T629M					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CTTCGGTCCACGGCTAGGAAG	0.502																																					p.T629M		Atlas-SNP	.											.	DLEC1	278	.	0			c.C1886T						.						123.0	124.0	123.0					3																	38135225		1909	4135	6044	SO:0001583	missense	9940	exon12			GGTCCACGGCTAG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1886C>T	chr3.hg19:g.38135225C>T	ENSP00000308597:p.Thr629Met	68.0	0.0		189.0	54.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	13.25	2.180990	0.38511	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05996	3.37;3.36;3.6	5.08	3.25	0.37280	.	0.239343	0.42420	D	0.000702	T	0.07548	0.0190	L	0.53249	1.67	0.09310	N	0.999999	D;D;D	0.56521	0.976;0.976;0.976	P;B;P	0.44673	0.457;0.356;0.457	T	0.25745	-1.0123	10	0.34782	T	0.22	-12.8453	6.5019	0.22174	0.0:0.7237:0.0:0.2763	.	629;629;629	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	M	629	ENSP00000308597:T629M;ENSP00000315914:T629M;ENSP00000410427:T629M	ENSP00000308597:T629M	T	+	2	0	DLEC1	38110229	0.020000	0.18652	0.645000	0.29479	0.974000	0.67602	1.115000	0.31209	1.096000	0.41439	0.655000	0.94253	ACG	.	.		0.502	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
PHLDB2	90102	hgsc.bcm.edu	37	3	111688738	111688738	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:111688738A>T	ENST00000431670.2	+	16	3928	c.3517A>T	c.(3517-3519)Aca>Tca	p.T1173S	PHLDB2_ENST00000393925.3_Missense_Mutation_p.T1173S|PHLDB2_ENST00000481953.1_Missense_Mutation_p.T1130S|PHLDB2_ENST00000412622.1_Missense_Mutation_p.T1130S|PHLDB2_ENST00000393923.3_Missense_Mutation_p.T1157S|PHLDB2_ENST00000495180.1_Missense_Mutation_p.T664S	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	1173	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						GAACAAGCGAACATTCTCTTA	0.378																																					p.T1173S		Atlas-SNP	.											.	PHLDB2	449	.	0			c.A3517T						.						130.0	134.0	132.0					3																	111688738		2203	4300	6503	SO:0001583	missense	90102	exon16			AAGCGAACATTCT		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.3517A>T	chr3.hg19:g.111688738A>T	ENSP00000405405:p.Thr1173Ser	72.0	0.0		123.0	39.0	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	hg19	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049472	0.75846	.	.	ENSG00000144824	ENST00000393923;ENST00000431670;ENST00000412622;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89;-0.89	5.09	3.92	0.45320	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.056069	0.64402	D	0.000001	T	0.72574	0.3477	N	0.12443	0.215	0.50813	D	0.999894	D;P;P;D;D	0.76494	0.999;0.558;0.856;0.991;0.991	D;B;P;D;D	0.83275	0.996;0.262;0.722;0.981;0.952	T	0.74061	-0.3786	10	0.52906	T	0.07	.	10.3965	0.44203	0.8532:0.0:0.0:0.1468	.	285;664;1173;1130;1157	Q658P8;E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;.;PHLB2_HUMAN;.;.	S	1157;1173;1130;1173;1130;664	ENSP00000377500:T1157S;ENSP00000405405:T1173S;ENSP00000405292:T1130S;ENSP00000377502:T1173S;ENSP00000418319:T1130S;ENSP00000420303:T664S	ENSP00000377500:T1157S	T	+	1	0	PHLDB2	113171428	1.000000	0.71417	0.924000	0.36721	0.992000	0.81027	8.718000	0.91430	0.938000	0.37419	0.477000	0.44152	ACA	.	.		0.378	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
BOC	91653	hgsc.bcm.edu	37	3	112969411	112969411	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:112969411C>T	ENST00000495514.1	+	4	811	c.107C>T	c.(106-108)cCt>cTt	p.P36L	BOC_ENST00000355385.3_Missense_Mutation_p.P36L|BOC_ENST00000484034.1_Missense_Mutation_p.P36L|BOC_ENST00000273395.4_Missense_Mutation_p.P36L|BOC_ENST00000485230.1_Missense_Mutation_p.P36L			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	36	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GACGAGGTCCCTCAGGTCACC	0.562																																					p.P36L		Atlas-SNP	.											.	BOC	139	.	0			c.C107T						.						94.0	90.0	92.0					3																	112969411		2203	4300	6503	SO:0001583	missense	91653	exon4			AGGTCCCTCAGGT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.107C>T	chr3.hg19:g.112969411C>T	ENSP00000418663:p.Pro36Leu	47.0	0.0		94.0	7.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	c	18.51	3.638988	0.67130	.	.	ENSG00000144857	ENST00000464546;ENST00000495514;ENST00000485230;ENST00000273395;ENST00000355385;ENST00000484034	D;T;T;T;T;T	0.84223	-1.82;-1.3;-1.3;-1.3;-1.3;-1.3	5.68	5.68	0.88126	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.064498	0.64402	D	0.000007	D	0.89326	0.6683	M	0.75447	2.3	0.58432	D	0.999997	P;B;P;D	0.62365	0.724;0.282;0.529;0.991	B;B;P;P	0.58013	0.274;0.278;0.521;0.831	D	0.88822	0.3299	10	0.46703	T	0.11	.	10.8259	0.46631	0.0:0.8859:0.0:0.1141	.	36;36;36;36	C9J2L7;Q9BWV1-3;Q9BWV1;Q96DN7	.;.;BOC_HUMAN;.	L	36	ENSP00000417362:P36L;ENSP00000418663:P36L;ENSP00000420154:P36L;ENSP00000273395:P36L;ENSP00000347546:P36L;ENSP00000417337:P36L	ENSP00000273395:P36L	P	+	2	0	BOC	114452101	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	5.579000	0.67457	2.672000	0.90937	0.651000	0.88453	CCT	.	.		0.562	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
POLQ	10721	hgsc.bcm.edu	37	3	121207657	121207657	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:121207657G>A	ENST00000264233.5	-	16	4249	c.4121C>T	c.(4120-4122)cCt>cTt	p.P1374L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1374					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AGCAGGAAAAGGAATGTGACA	0.443								DNA polymerases (catalytic subunits)																													p.P1374L	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C4121T						.						175.0	161.0	166.0					3																	121207657		2203	4300	6503	SO:0001583	missense	10721	exon16			GGAAAAGGAATGT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4121C>T	chr3.hg19:g.121207657G>A	ENSP00000264233:p.Pro1374Leu	144.0	0.0		405.0	46.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.452007	0.26074	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.45668	0.89	5.16	-0.725	0.11174	.	1.325950	0.05226	N	0.509359	T	0.20373	0.0490	N	0.08118	0	0.09310	N	1	B;B	0.23442	0.085;0.0	B;B	0.19666	0.026;0.0	T	0.17899	-1.0354	10	0.14252	T	0.57	.	5.9899	0.19454	0.5432:0.0:0.29:0.1668	.	1374;546	O75417;O75417-2	DPOLQ_HUMAN;.	L	997;1374;1510	ENSP00000264233:P1374L	ENSP00000264233:P1374L	P	-	2	0	POLQ	122690347	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.091000	0.11146	-0.048000	0.13401	0.655000	0.94253	CCT	.	.		0.443	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
TMCC1	23023	hgsc.bcm.edu	37	3	129389440	129389440	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:129389440G>T	ENST00000393238.3	-	4	1584	c.1244C>A	c.(1243-1245)cCa>cAa	p.P415Q	TMCC1_ENST00000426664.2_Missense_Mutation_p.P301Q|TMCC1_ENST00000432054.2_Missense_Mutation_p.P91Q|TMCC1_ENST00000329333.5_Missense_Mutation_p.P236Q	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	415						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						ACCATATTTTGGGCTAGACTG	0.507																																					p.P415Q		Atlas-SNP	.											.	TMCC1	105	.	0			c.C1244A						.						101.0	95.0	97.0					3																	129389440		2203	4300	6503	SO:0001583	missense	23023	exon4			TATTTTGGGCTAG	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"""Transmembrane and coiled-coil domain containing"""	29116	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 1"""			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.1244C>A	chr3.hg19:g.129389440G>T	ENSP00000376930:p.Pro415Gln	119.0	0.0		269.0	32.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934937	0.73442	.	.	ENSG00000172765	ENST00000432054;ENST00000393238;ENST00000426664;ENST00000329333	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	5.21	5.21	0.72293	.	0.093329	0.85682	D	0.000000	T	0.68650	0.3024	M	0.81497	2.545	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.72625	0.978;0.967	T	0.64723	-0.6340	10	0.12430	T	0.62	-16.0998	19.1112	0.93317	0.0:0.0:1.0:0.0	.	236;415	B4DE04;O94876	.;TMCC1_HUMAN	Q	91;415;301;236	ENSP00000404711:P91Q;ENSP00000376930:P415Q;ENSP00000389892:P301Q;ENSP00000327349:P236Q	ENSP00000327349:P236Q	P	-	2	0	TMCC1	130872130	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.301000	0.96167	2.581000	0.87130	0.591000	0.81541	CCA	.	.		0.507	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008	
CLSTN2	64084	hgsc.bcm.edu	37	3	140140017	140140017	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:140140017G>C	ENST00000458420.3	+	5	878	c.688G>C	c.(688-690)Gag>Cag	p.E230Q		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	230	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						ACACCAGTATGAGATCCTGGT	0.512										HNSCC(16;0.037)																											p.E230Q	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G688C						.						164.0	151.0	155.0					3																	140140017		2203	4300	6503	SO:0001583	missense	64084	exon5			CAGTATGAGATCC	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.688G>C	chr3.hg19:g.140140017G>C	ENSP00000402460:p.Glu230Gln	47.0	0.0		87.0	8.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012485	0.35511	.	.	ENSG00000158258	ENST00000458420	T	0.54675	0.56	5.7	5.7	0.88788	Cadherin (5);Cadherin-like (1);	0.260319	0.37809	N	0.001938	T	0.48241	0.1489	L	0.49126	1.545	0.42028	D	0.99101	B	0.17268	0.021	B	0.19391	0.025	T	0.40942	-0.9536	10	0.14252	T	0.57	-4.5927	17.3368	0.87283	0.0:0.0:1.0:0.0	.	230	Q9H4D0	CSTN2_HUMAN	Q	230	ENSP00000402460:E230Q	ENSP00000402460:E230Q	E	+	1	0	CLSTN2	141622707	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.532000	0.45659	2.679000	0.91253	0.655000	0.94253	GAG	.	.		0.512	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
ATR	545	hgsc.bcm.edu	37	3	142215986	142215986	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:142215986C>T	ENST00000350721.4	-	33	5728	c.5607G>A	c.(5605-5607)caG>caA	p.Q1869Q	ATR_ENST00000383101.3_Silent_p.Q1805Q	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1869	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTGGAGAATGCTGGAAAAGTG	0.413								Other conserved DNA damage response genes																													p.Q1869Q		Atlas-SNP	.											.	ATR	285	.	0			c.G5607A						.						112.0	120.0	118.0					3																	142215986		2203	4300	6503	SO:0001819	synonymous_variant	545	exon33			AGAATGCTGGAAA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5607G>A	chr3.hg19:g.142215986C>T		43.0	0.0		96.0	42.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.413	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
MED12L	116931	hgsc.bcm.edu	37	3	150873991	150873991	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:150873991C>T	ENST00000474524.1	+	5	638	c.600C>T	c.(598-600)gcC>gcT	p.A200A	MED12L_ENST00000273432.4_Silent_p.A200A|MED12L_ENST00000422248.2_Silent_p.A200A|MED12L_ENST00000309237.4_Silent_p.A200A	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	200						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGCAGTTGGCCAAGATTTCTG	0.458																																					p.A200A		Atlas-SNP	.											.	MED12L	271	.	0			c.C600T						.						104.0	100.0	101.0					3																	150873991		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GTTGGCCAAGATT	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.600C>T	chr3.hg19:g.150873991C>T		41.0	0.0		87.0	27.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.		0.458	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
EHHADH	1962	hgsc.bcm.edu	37	3	184910999	184910999	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:184910999A>C	ENST00000231887.3	-	7	1262	c.1187T>G	c.(1186-1188)cTc>cGc	p.L396R	EHHADH_ENST00000456310.1_Missense_Mutation_p.L300R|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	396	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CACAGCTGAGAGTTCAGCAAA	0.443																																					p.L396R		Atlas-SNP	.											.	EHHADH	73	.	0			c.T1187G						.						183.0	173.0	176.0					3																	184910999		2203	4300	6503	SO:0001583	missense	1962	exon7			GCTGAGAGTTCAG	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1187T>G	chr3.hg19:g.184910999A>C	ENSP00000231887:p.Leu396Arg	98.0	0.0		169.0	64.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.055404	0.75960	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	D;D	0.81821	-1.54;-1.54	6.08	6.08	0.98989	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.93190	0.7831	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95085	0.8217	10	0.87932	D	0	-11.8271	16.6512	0.85203	1.0:0.0:0.0:0.0	.	396	Q08426	ECHP_HUMAN	R	396;396;300	ENSP00000231887:L396R;ENSP00000387746:L300R	ENSP00000231887:L396R	L	-	2	0	EHHADH	186393693	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.818000	0.91991	2.333000	0.79357	0.482000	0.46254	CTC	.	.		0.443	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
MUC4	4585	hgsc.bcm.edu	37	3	195515393	195515393	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:195515393C>T	ENST00000463781.3	-	2	3517	c.3058G>A	c.(3058-3060)Ggt>Agt	p.G1020S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1020S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	455	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGGTGTGACCTGTGGATACT	0.567																																					p.G1020S		Atlas-SNP	.											.	MUC4	1505	.	4	Deletion - In frame(4)	stomach(4)	c.G3058A						.						46.0	25.0	31.0					3																	195515393		692	1589	2281	SO:0001583	missense	4585	exon2			TGTGACCTGTGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3058G>A	chr3.hg19:g.195515393C>T	ENSP00000417498:p.Gly1020Ser	78.0	0.0		243.0	15.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	hg19	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	9.185	1.024626	0.19433	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.56611	0.45;0.47	0.573	0.573	0.17363	.	.	.	.	.	T	0.27663	0.0680	N	0.19112	0.55	0.09310	N	1	P	0.51933	0.949	B	0.34138	0.176	T	0.11470	-1.0586	8	.	.	.	.	7.0509	0.25073	0.0:0.9999:0.0:1.0E-4	.	1020	E7ESK3	.	S	1020	ENSP00000417498:G1020S;ENSP00000420243:G1020S	.	G	-	1	0	MUC4	196999788	.	.	0.001000	0.08648	0.051000	0.14879	.	.	0.598000	0.29829	0.064000	0.15345	GGT	.	.		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LYAR	55646	hgsc.bcm.edu	37	4	4275388	4275388	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:4275388C>T	ENST00000343470.4	-	8	1081	c.841G>A	c.(841-843)Gat>Aat	p.D281N	LYAR_ENST00000452476.1_Missense_Mutation_p.D281N	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	281	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTCTTAGAATCTGTTTCAACT	0.403																																					p.D281N		Atlas-SNP	.											.	LYAR	36	.	0			c.G841A						.						78.0	80.0	79.0					4																	4275388		2203	4300	6503	SO:0001583	missense	55646	exon8			TAGAATCTGTTTC	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"""Zinc fingers, C2HC-type containing"""	26021	protein-coding gene	gene with protein product			"""Ly1 antibody reactive homolog (mouse)"""			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.841G>A	chr4.hg19:g.4275388C>T	ENSP00000345917:p.Asp281Asn	76.0	0.0		149.0	40.0	NM_017816	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	hg19	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.862908	0.32884	.	.	ENSG00000145220	ENST00000343470;ENST00000452476	T;T	0.32515	1.45;1.45	5.24	1.32	0.21799	.	1.811300	0.01927	N	0.040948	T	0.19604	0.0471	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.12630	-1.0540	10	0.23302	T	0.38	-3.6287	3.4773	0.07589	0.176:0.5217:0.0:0.3022	.	281	Q9NX58	LYAR_HUMAN	N	281	ENSP00000345917:D281N;ENSP00000397367:D281N	ENSP00000345917:D281N	D	-	1	0	LYAR	4326289	0.000000	0.05858	0.000000	0.03702	0.581000	0.36288	0.130000	0.15850	0.245000	0.21373	-0.366000	0.07423	GAT	.	.		0.403	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816	
STK32B	55351	hgsc.bcm.edu	37	4	5170120	5170120	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:5170120T>A	ENST00000282908.5	+	3	625	c.203T>A	c.(202-204)gTt>gAt	p.V68D	STK32B_ENST00000510398.1_Missense_Mutation_p.V21D|STK32B_ENST00000512636.1_Missense_Mutation_p.V21D	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GTTCGGAATGTTTTCCGGGAG	0.532																																					p.V68D		Atlas-SNP	.											.	STK32B	87	.	0			c.T203A						.						105.0	94.0	98.0					4																	5170120		2203	4300	6503	SO:0001583	missense	55351	exon3			GGAATGTTTTCCG	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.203T>A	chr4.hg19:g.5170120T>A	ENSP00000282908:p.Val68Asp	56.0	0.0		176.0	34.0	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561482	0.65538	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.26518	1.73;1.73;1.73	5.03	5.03	0.67393	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38778	U	0.001569	T	0.58119	0.2100	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68062	-0.5508	10	0.87932	D	0	.	13.9602	0.64175	0.0:0.0:0.0:1.0	.	68	Q9NY57	ST32B_HUMAN	D	68;21;21	ENSP00000282908:V68D;ENSP00000423209:V21D;ENSP00000420984:V21D	ENSP00000282908:V68D	V	+	2	0	STK32B	5221021	1.000000	0.71417	0.988000	0.46212	0.331000	0.28603	7.552000	0.82192	1.890000	0.54733	0.533000	0.62120	GTT	.	.		0.532	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
PROM1	8842	hgsc.bcm.edu	37	4	16035130	16035130	+	Silent	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:16035130A>G	ENST00000510224.1	-	5	554	c.306T>C	c.(304-306)atT>atC	p.I102I	PROM1_ENST00000505450.1_Silent_p.I93I|PROM1_ENST00000543373.1_Silent_p.I93I|PROM1_ENST00000540805.1_Silent_p.I102I|PROM1_ENST00000539194.1_Silent_p.I102I|PROM1_ENST00000502943.1_5'UTR|PROM1_ENST00000447510.2_Silent_p.I102I|PROM1_ENST00000508167.1_Silent_p.I93I			O43490	PROM1_HUMAN	prominin 1	102					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						CATAGTAGACAATCTGCAATT	0.343																																					p.I102I		Atlas-SNP	.											.	PROM1	91	.	0			c.T306C						.						36.0	33.0	34.0					4																	16035130		1866	4111	5977	SO:0001819	synonymous_variant	8842	exon4			GTAGACAATCTGC	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.306T>C	chr4.hg19:g.16035130A>G		75.0	0.0		172.0	46.0	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Silent	SNP	ENST00000510224.1	hg19	CCDS47029.1																																																																																			.	.		0.343	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	
FRAS1	80144	hgsc.bcm.edu	37	4	79428611	79428611	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:79428611C>T	ENST00000264895.6	+	62	9793	c.9353C>T	c.(9352-9354)tCc>tTc	p.S3118F		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3114	Calx-beta 5.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GAGATCCTGTCCAATGAAGAC	0.473																																					p.S3118F		Atlas-SNP	.											.	FRAS1	779	.	0			c.C9353T						.						110.0	103.0	105.0					4																	79428611		1984	4165	6149	SO:0001583	missense	80144	exon62			TCCTGTCCAATGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9353C>T	chr4.hg19:g.79428611C>T	ENSP00000264895:p.Ser3118Phe	99.0	0.0		179.0	51.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.198610	0.38806	.	.	ENSG00000138759	ENST00000264895	T	0.28255	1.62	5.25	5.25	0.73442	.	0.126361	0.56097	D	0.000037	T	0.35711	0.0941	N	0.21097	0.63	0.80722	D	1	D;D	0.59767	0.983;0.986	P;P	0.58331	0.776;0.837	T	0.03335	-1.1047	10	0.10377	T	0.69	.	19.1854	0.93641	0.0:1.0:0.0:0.0	.	3117;3118	Q86XX4-2;E9PHH6	.;.	F	3118	ENSP00000264895:S3118F	ENSP00000264895:S3118F	S	+	2	0	FRAS1	79647635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.648000	0.83479	2.612000	0.88384	0.591000	0.81541	TCC	.	.		0.473	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ABCG2	9429	hgsc.bcm.edu	37	4	89039357	89039357	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:89039357T>C	ENST00000237612.3	-	7	1290	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	ABCG2_ENST00000515655.1_Missense_Mutation_p.I249V	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	249	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	AACTTGAAGATGGAATATCGA	0.423																																					p.I249V		Atlas-SNP	.											.	ABCG2	151	.	0			c.A745G						.						139.0	125.0	129.0					4																	89039357		2203	4300	6503	SO:0001583	missense	9429	exon7			TGAAGATGGAATA	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.745A>G	chr4.hg19:g.89039357T>C	ENSP00000237612:p.Ile249Val	80.0	0.0		109.0	34.0	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	hg19	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.275027	0.80580	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.43688	0.94;0.94	5.45	4.25	0.50352	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	T	0.44685	0.1305	N	0.21508	0.67	0.50467	D	0.999873	D;D;D	0.62365	0.991;0.969;0.969	D;P;P	0.63877	0.919;0.589;0.589	T	0.21348	-1.0248	10	0.26408	T	0.33	-36.5828	11.6976	0.51553	0.1328:0.0:0.0:0.8672	.	249;249;249	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	V	249	ENSP00000426917:I249V;ENSP00000237612:I249V	ENSP00000237612:I249V	I	-	1	0	ABCG2	89258381	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	0.981000	0.38548	0.533000	0.62120	ATC	.	.		0.423	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
SMARCA5	8467	hgsc.bcm.edu	37	4	144467138	144467138	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:144467138A>G	ENST00000283131.3	+	19	2920	c.2458A>G	c.(2458-2460)Att>Gtt	p.I820V		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	820					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					ACAGCTTAAAATTGATGAAGC	0.348																																					p.I820V		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A2458G						.						86.0	90.0	88.0					4																	144467138		2203	4300	6503	SO:0001583	missense	8467	exon19			CTTAAAATTGATG	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2458A>G	chr4.hg19:g.144467138A>G	ENSP00000283131:p.Ile820Val	102.0	0.0		243.0	84.0	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	hg19	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354537	0.61293	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91464	-2.85	5.3	5.3	0.74995	ATPase, nucleosome remodelling ISWI, HAND domain (2);	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	L	0.56769	1.78	0.58432	D	0.999999	B	0.20368	0.044	B	0.22152	0.038	D	0.85626	0.1267	10	0.37606	T	0.19	-19.4602	15.5566	0.76200	1.0:0.0:0.0:0.0	.	820	O60264	SMCA5_HUMAN	V	820;763;763	ENSP00000283131:I820V	ENSP00000283131:I820V	I	+	1	0	SMARCA5	144686588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.680000	0.91225	2.136000	0.66102	0.533000	0.62120	ATT	.	.		0.348	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
ZNF827	152485	hgsc.bcm.edu	37	4	146686272	146686272	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:146686272A>T	ENST00000508784.1	-	13	3325	c.3098T>A	c.(3097-3099)aTg>aAg	p.M1033K	ZNF827_ENST00000379448.4_Missense_Mutation_p.M1033K|ZNF827_ENST00000513320.1_Missense_Mutation_p.M683K			Q17R98	ZN827_HUMAN	zinc finger protein 827	1033					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					ACGCTCAAACATGTTCTTCGT	0.522																																					p.M1033K		Atlas-SNP	.											.	ZNF827	102	.	0			c.T3098A						.						87.0	79.0	82.0					4																	146686272		2203	4300	6503	SO:0001583	missense	152485	exon13			TCAAACATGTTCT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"""Zinc fingers, C2H2-type"""	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.3098T>A	chr4.hg19:g.146686272A>T	ENSP00000421863:p.Met1033Lys	62.0	0.0		104.0	20.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.3|20.3	3.969817|3.969817	0.74246|0.74246	.|.	.|.	ENSG00000151612|ENSG00000151612	ENST00000511659|ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	.|T;T;T	.|0.59772	.|0.24;0.24;0.24	4.83|4.83	4.83|4.83	0.62350|0.62350	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52354|0.52354	0.1729|0.1729	N|N	0.03177|0.03177	-0.4|-0.4	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D;P	.|0.54772	.|0.96;0.968;0.96;0.932	.|D;D;D;P	.|0.70487	.|0.948;0.969;0.948;0.888	T|T	0.57539|0.57539	-0.7794|-0.7794	5|10	.|0.23891	.|T	.|0.37	-18.7384|-18.7384	14.7219|14.7219	0.69314|0.69314	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|683;1033;1033;683	.|G5E9Z1;Q17R98;Q17R98-2;E7ESI8	.|.;ZN827_HUMAN;.;.	S|K	134|1033;683;1033;1032;683	.|ENSP00000421863:M1033K;ENSP00000423130:M683K;ENSP00000368761:M1033K	.|ENSP00000281318:M1032K	C|M	-|-	1|2	0|0	ZNF827|ZNF827	146905722|146905722	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.910000|8.910000	0.92685|0.92685	1.920000|1.920000	0.55613|0.55613	0.533000|0.533000	0.62120|0.62120	TGT|ATG	.	.		0.522	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835	
DCHS2	54798	hgsc.bcm.edu	37	4	155278437	155278437	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr4:155278437T>C	ENST00000357232.4	-	6	733	c.734A>G	c.(733-735)aAc>aGc	p.N245S	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	245	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tgctgaaaagttgacagcact	0.433																																					p.N245S		Atlas-SNP	.											.	DCHS2	594	.	0			c.A734G						.						117.0	122.0	120.0					4																	155278437		2203	4300	6503	SO:0001583	missense	54798	exon6			GAAAAGTTGACAG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.734A>G	chr4.hg19:g.155278437T>C	ENSP00000349768:p.Asn245Ser	46.0	0.0		60.0	19.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.575094	0.00131	.	.	ENSG00000197410	ENST00000357232	T	0.55413	0.52	0.772	-0.951	0.10369	Cadherin (1);	.	.	.	.	T	0.28034	0.0691	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.21415	-1.0246	9	0.09338	T	0.73	.	3.0531	0.06175	0.0:0.3566:0.0:0.6434	.	245	Q6V1P9	PCD23_HUMAN	S	245	ENSP00000349768:N245S	ENSP00000349768:N245S	N	-	2	0	DCHS2	155497887	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-1.189000	0.03061	-0.333000	0.08476	-0.495000	0.04643	AAC	.	.		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	181677	181677	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:181677T>C	ENST00000283426.6	+	17	3433	c.3383T>C	c.(3382-3384)tTc>tCc	p.F1128S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1128							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AACCAGCCATTCATGGATGTC	0.527																																					p.F1128S		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.T3383C						.						97.0	96.0	96.0					5																	181677		2203	4300	6503	SO:0001583	missense	153478	exon17			AGCCATTCATGGA	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3383T>C	chr5.hg19:g.181677T>C	ENSP00000283426:p.Phe1128Ser	49.0	0.0		99.0	25.0	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.879233	0.33162	.	.	ENSG00000153404	ENST00000283426	T	0.35789	1.29	3.64	2.45	0.29901	Pleckstrin homology-type (1);	.	.	.	.	T	0.54549	0.1865	M	0.83223	2.63	0.34532	D	0.709334	D	0.89917	1.0	D	0.72625	0.978	T	0.60994	-0.7152	9	0.20519	T	0.43	.	7.071	0.25179	0.0:0.1158:0.0:0.8842	.	1128	Q96PX9	PKH4B_HUMAN	S	1128	ENSP00000283426:F1128S	ENSP00000283426:F1128S	F	+	2	0	PLEKHG4B	234677	1.000000	0.71417	0.005000	0.12908	0.045000	0.14185	4.841000	0.62824	0.301000	0.22738	0.377000	0.23210	TTC	.	.		0.527	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
DDX4	54514	hgsc.bcm.edu	37	5	55083699	55083699	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:55083699C>T	ENST00000505374.1	+	15	1135	c.1043C>T	c.(1042-1044)gCt>gTt	p.A348V	DDX4_ENST00000353507.5_Missense_Mutation_p.A314V|DDX4_ENST00000511853.1_Missense_Mutation_p.A199V|DDX4_ENST00000354991.5_Missense_Mutation_p.A314V|DDX4_ENST00000514278.2_Missense_Mutation_p.A328V	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	348	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				CCAATTTTGGCTCATATGATG	0.393																																					p.A348V		Atlas-SNP	.											.	DDX4	194	.	0			c.C1043T						.						100.0	101.0	101.0					5																	55083699		2203	4300	6503	SO:0001583	missense	54514	exon15			TTTTGGCTCATAT	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"""DEAD-boxes"""	18700	protein-coding gene	gene with protein product		605281	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"""			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1043C>T	chr5.hg19:g.55083699C>T	ENSP00000424838:p.Ala348Val	81.0	0.0		128.0	30.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	hg19	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156592	0.78114	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000354991;ENST00000511853	T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41;2.41	5.83	5.83	0.93111	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.175936	0.51477	D	0.000096	T	0.27524	0.0676	L	0.28344	0.845	0.35409	D	0.792272	B;D;P;D	0.76494	0.126;0.974;0.864;0.999	B;P;P;D	0.74023	0.113;0.777;0.713;0.982	T	0.18903	-1.0322	10	0.56958	D	0.05	-17.2683	12.0012	0.53232	0.1349:0.7351:0.13:0.0	.	328;199;314;348	D6RDK4;E9PCD8;Q9NQI0-2;Q9NQI0	.;.;.;DDX4_HUMAN	V	314;328;348;328;314;199	ENSP00000334167:A314V;ENSP00000425359:A328V;ENSP00000424838:A348V;ENSP00000427167:A328V;ENSP00000347087:A314V;ENSP00000423123:A199V	ENSP00000334167:A314V	A	+	2	0	DDX4	55119456	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.937000	0.48979	2.756000	0.94617	0.655000	0.94253	GCT	.	.		0.393	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415	
SRFBP1	153443	hgsc.bcm.edu	37	5	121358098	121358098	+	Silent	SNP	C	C	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:121358098C>G	ENST00000339397.4	+	7	1173	c.1101C>G	c.(1099-1101)tcC>tcG	p.S367S	SRFBP1_ENST00000504881.1_3'UTR	NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AAACAAGATCCCTAGGTATGT	0.303																																					p.S367S		Atlas-SNP	.											.	SRFBP1	47	.	0			c.C1101G						.						64.0	59.0	60.0					5																	121358098		1813	4069	5882	SO:0001819	synonymous_variant	153443	exon7			AAGATCCCTAGGT	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.1101C>G	chr5.hg19:g.121358098C>G		93.0	0.0		110.0	35.0	NM_152546		Silent	SNP	ENST00000339397.4	hg19	CCDS43354.1																																																																																			.	.		0.303	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188279	140188279	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:140188279G>A	ENST00000530339.1	+	1	1507	c.1507G>A	c.(1507-1509)Gcg>Acg	p.A503T	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.A503T|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.A503T|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	503	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGGGAGCGCGCGCTGTCGAG	0.662																																					p.A503T		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1507A						.						54.0	55.0	55.0					5																	140188279		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGCGCGCGCTGT	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1507G>A	chr5.hg19:g.140188279G>A	ENSP00000435300:p.Ala503Thr	40.0	0.0		112.0	36.0	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	hg19	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	10.70	1.422976	0.25639	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.52983	0.7;0.64;0.68	4.18	-1.28	0.09318	Cadherin (4);Cadherin-like (1);	0.515141	0.14366	U	0.324099	T	0.23094	0.0558	N	0.10874	0.06	0.09310	N	1	B;P;B	0.35033	0.362;0.481;0.416	B;B;B	0.37550	0.072;0.253;0.113	T	0.14811	-1.0459	10	0.62326	D	0.03	.	1.7485	0.02967	0.1824:0.4049:0.1981:0.2145	.	503;503;503	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	T	503	ENSP00000423470:A503T;ENSP00000349344:A503T;ENSP00000435300:A503T	ENSP00000349344:A503T	A	+	1	0	PCDHA4	140168463	0.000000	0.05858	0.470000	0.27216	0.651000	0.38670	-0.431000	0.06965	-0.017000	0.14103	0.580000	0.79431	GCG	.	.		0.662	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140723657	140723657	+	Silent	SNP	C	C	T	rs200693710		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:140723657C>T	ENST00000253812.6	+	1	57	c.57C>T	c.(55-57)ctC>ctT	p.L19L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	19					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGCGCGCTCCTGGGGACGC	0.542											OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L19L		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.C57T						.						124.0	137.0	133.0					5																	140723657		2077	4234	6311	SO:0001819	synonymous_variant	56112	exon1			CGCGCTCCTGGGG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.57C>T	chr5.hg19:g.140723657C>T		47.0	0.0	1658	61.0	17.0	NM_032011	Q9Y5D4	Silent	SNP	ENST00000253812.6	hg19	CCDS47290.1																																																																																			.	C|1.000;G|0.000		0.542	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
FAT2	2196	hgsc.bcm.edu	37	5	150922777	150922777	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:150922777G>A	ENST00000261800.5	-	9	7923	c.7911C>T	c.(7909-7911)aaC>aaT	p.N2637N		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2637	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGTGACTGGGTTAATTTCAA	0.478																																					p.N2637N		Atlas-SNP	.											.	FAT2	465	.	0			c.C7911T						.						142.0	139.0	140.0					5																	150922777		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon9			GACTGGGTTAATT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7911C>T	chr5.hg19:g.150922777G>A		49.0	0.0		53.0	18.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.478	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
DOCK2	1794	hgsc.bcm.edu	37	5	169484584	169484584	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:169484584T>C	ENST00000256935.8	+	44	4461	c.4381T>C	c.(4381-4383)Tcc>Ccc	p.S1461P	DOCK2_ENST00000520908.1_Splice_Site_p.S953P|DOCK2_ENST00000540750.1_Splice_Site_p.S522P|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1461	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCACGGACAGTCCATGTGGAT	0.567																																					p.S1461P		Atlas-SNP	.											.	DOCK2	389	.	0			c.T4381C						.						106.0	88.0	94.0					5																	169484584		2203	4300	6503	SO:0001630	splice_region_variant	1794	exon44			GGACAGTCCATGT	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4381-1T>C	chr5.hg19:g.169484584T>C		70.0	0.0		101.0	17.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943045	0.73672	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.18810	2.19;2.19;2.19	5.47	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.44456	0.1294	M	0.73598	2.24	0.43025	D	0.994583	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.91635	0.999;0.968;0.996	T	0.34700	-0.9818	10	0.48119	T	0.1	.	11.4863	0.50356	0.1348:0.0:0.0:0.8652	.	953;17;1461	E7ERW7;B3KY14;Q92608	.;.;DOCK2_HUMAN	P	1461;953;522	ENSP00000256935:S1461P;ENSP00000429283:S953P;ENSP00000438827:S522P	ENSP00000256935:S1461P	S	+	1	0	DOCK2	169417162	1.000000	0.71417	0.961000	0.40146	0.906000	0.53458	2.048000	0.41278	0.845000	0.35118	0.533000	0.62120	TCC	.	.		0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	Missense_Mutation
HNRNPH1	3187	hgsc.bcm.edu	37	5	179043886	179043886	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr5:179043886C>T	ENST00000356731.5	-	10	2726	c.1191G>A	c.(1189-1191)atG>atA	p.M397I	HNRNPH1_ENST00000511300.2_Intron|HNRNPH1_ENST00000393432.4_Missense_Mutation_p.M397I|HNRNPH1_ENST00000329433.6_Missense_Mutation_p.M397I|HNRNPH1_ENST00000510411.1_Intron|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000442819.2_Missense_Mutation_p.M397I			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	397	2 X 16 AA Gly-rich approximate repeats.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						CCATGCCTCCCATCATTTGGC	0.338																																					p.M397I		Atlas-SNP	.											.	HNRNPH1	62	.	0			c.G1191A						.						103.0	101.0	102.0					5																	179043886		2203	4300	6503	SO:0001583	missense	3187	exon11			GCCTCCCATCATT	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"""RNA binding motif (RRM) containing"""	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.1191G>A	chr5.hg19:g.179043886C>T	ENSP00000349168:p.Met397Ile	134.0	0.0		290.0	12.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Missense_Mutation	SNP	ENST00000356731.5	hg19	CCDS4446.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	13.68|13.68|13.68	2.310259|2.310259|2.310259	0.40895|0.40895|0.40895	.|.|.	.|.|.	ENSG00000169045|ENSG00000169045|ENSG00000169045	ENST00000523449;ENST00000523136|ENST00000393432;ENST00000442819;ENST00000356731;ENST00000329433;ENST00000523921|ENST00000521173	.|T;T;T;T;T|.	.|0.12361|.	.|2.69;2.69;2.69;2.69;2.69|.	5.84|5.84|5.84	4.97|4.97|4.97	0.65823|0.65823|0.65823	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|.	0.67126|0.67126|.	0.2860|0.2860|.	L|L|L	0.47190|0.47190|0.47190	1.495|1.495|1.495	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B|.	.|0.09022|.	.|0.002|.	.|B|.	.|0.08055|.	.|0.003|.	T|T|.	0.64786|0.64786|.	-0.6325|-0.6325|.	5|10|.	.|0.36615|.	.|T|.	.|0.2|.	-0.6785|-0.6785|-0.6785	16.5635|16.5635|16.5635	0.84573|0.84573|0.84573	0.1317:0.8683:0.0:0.0|0.1317:0.8683:0.0:0.0|0.1317:0.8683:0.0:0.0	.|.|.	.|397|.	.|P31943|.	.|HNRH1_HUMAN|.	R|I|X	65;14|397;397;397;397;191|272	.|ENSP00000377082:M397I;ENSP00000397797:M397I;ENSP00000349168:M397I;ENSP00000327539:M397I;ENSP00000429270:M191I|.	.|ENSP00000327539:M397I|.	G|M|W	-|-|-	1|3|2	0|0|0	HNRNPH1|HNRNPH1|HNRNPH1	178976492|178976492|178976492	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	2.357000|2.357000|2.357000	0.44125|0.44125|0.44125	1.478000|1.478000|1.478000	0.48253|0.48253|0.48253	-0.127000|-0.127000|-0.127000	0.14921|0.14921|0.14921	GGG|ATG|TGG	.	.		0.338	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520	
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839822	27839822	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr6:27839822A>G	ENST00000328488.2	-	1	277	c.272T>C	c.(271-273)aTg>aCg	p.M91T		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	91					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CTGCAGCGCCATCACCGCCGA	0.567																																					p.M91T		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.T272C						.						82.0	88.0	86.0					6																	27839822		2203	4300	6503	SO:0001583	missense	8354	exon1			AGCGCCATCACCG	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"""Histones / Replication-dependent"""	4771	protein-coding gene	gene with protein product		602814	"""H3 histone family, member F"", ""histone 1, H3i"""	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.272T>C	chr6.hg19:g.27839822A>G	ENSP00000329554:p.Met91Thr	65.0	0.0		180.0	85.0	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000328488.2	hg19	CCDS4636.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.582648	0.28180	.	.	ENSG00000182572	ENST00000328488	T	0.66995	-0.24	4.12	4.12	0.48240	.	.	.	.	.	T	0.64182	0.2575	.	.	.	0.41515	D	0.988361	.	.	.	.	.	.	T	0.65105	-0.6249	6	0.39692	T	0.17	.	13.3331	0.60500	1.0:0.0:0.0:0.0	.	.	.	.	T	91	ENSP00000329554:M91T	ENSP00000329554:M91T	M	-	2	0	HIST1H3I	27947801	1.000000	0.71417	0.995000	0.50966	0.668000	0.39293	4.395000	0.59678	2.086000	0.62901	0.528000	0.53228	ATG	.	.		0.567	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533	
OR2B6	26212	hgsc.bcm.edu	37	6	27925139	27925139	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr6:27925139G>A	ENST00000244623.1	+	1	121	c.121G>A	c.(121-123)Ggc>Agc	p.G41S		NM_012367.1	NP_036499.1	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B, member 6	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GACCATCTTTGGCAATCTGAC	0.428																																					p.G41S		Atlas-SNP	.											.	OR2B6	48	.	0			c.G121A						.						187.0	175.0	179.0					6																	27925139		2203	4300	6503	SO:0001583	missense	26212	exon1			ATCTTTGGCAATC	U86275	CCDS4642.1	6p22.1	2012-08-09			ENSG00000124657	ENSG00000124657		"""GPCR / Class A : Olfactory receptors"""	8241	protein-coding gene	gene with protein product				OR2B6P, OR2B1, OR2B1P, OR2B5		9500546	Standard	NM_012367		Approved	OR6-31, dJ408B20.2, OR5-40, OR5-41	uc011dkx.2	P58173	OTTHUMG00000014497	ENST00000244623.1:c.121G>A	chr6.hg19:g.27925139G>A	ENSP00000244623:p.Gly41Ser	147.0	0.0		385.0	16.0	NM_012367	O43883|Q6IF89|Q9H5B0	Missense_Mutation	SNP	ENST00000244623.1	hg19	CCDS4642.1	.	.	.	.	.	.	.	.	.	.	g	13.19	2.164266	0.38217	.	.	ENSG00000124657	ENST00000244623	T	0.04275	3.66	3.78	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34088	U	0.004270	T	0.05868	0.0153	M	0.88105	2.93	0.29422	N	0.860477	B	0.26081	0.141	B	0.37508	0.252	T	0.05649	-1.0872	10	0.72032	D	0.01	.	9.8937	0.41304	0.1074:0.0:0.8926:0.0	.	41	P58173	OR2B6_HUMAN	S	41	ENSP00000244623:G41S	ENSP00000244623:G41S	G	+	1	0	OR2B6	28033118	0.036000	0.19791	0.995000	0.50966	0.669000	0.39330	1.997000	0.40786	0.864000	0.35578	-0.244000	0.11960	GGC	.	.		0.428	OR2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040165.1		
PPT2	9374	hgsc.bcm.edu	37	6	32123651	32123651	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr6:32123651C>T	ENST00000324816.6	+	5	1005	c.437C>T	c.(436-438)aCg>aTg	p.T146M	PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2_ENST00000375143.2_Missense_Mutation_p.T146M|PPT2_ENST00000445576.2_Missense_Mutation_p.T146M|PPT2_ENST00000375137.2_Missense_Mutation_p.T146M|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000395523.1_Missense_Mutation_p.T146M|PPT2_ENST00000361568.2_Missense_Mutation_p.T152M|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000437001.2_Missense_Mutation_p.T23M|PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.T146M			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	146					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						TTGCCAGACACGGACTACTTG	0.527																																					p.T152M		Atlas-SNP	.											.	PPT2	19	.	0			c.C455T						.						159.0	130.0	140.0					6																	32123651		1511	2709	4220	SO:0001583	missense	9374	exon5			CAGACACGGACTA	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.437C>T	chr6.hg19:g.32123651C>T	ENSP00000320528:p.Thr146Met	95.0	0.0		351.0	73.0	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	hg19	CCDS4742.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.780951	0.90282	.	.	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000437001;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118	T;D;D;D;D;D;D;D;D	0.96232	-0.25;-3.95;-3.95;-3.95;-3.95;-3.38;-3.95;-3.95;-3.38	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.97666	0.9235	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.985;0.992;0.992	D	0.98139	1.0435	10	0.62326	D	0.03	-4.8314	16.689	0.85316	0.0:1.0:0.0:0.0	.	146;146;152	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	M	146;152;146;146;146;23;146;146;68;146	ENSP00000398847:T146M;ENSP00000354608:T152M;ENSP00000378894:T146M;ENSP00000412381:T146M;ENSP00000320528:T146M;ENSP00000415350:T23M;ENSP00000364279:T146M;ENSP00000364285:T146M;ENSP00000409877:T68M	ENSP00000320528:T146M	T	+	2	0	PPT2	32231629	1.000000	0.71417	0.995000	0.50966	0.949000	0.60115	6.997000	0.76270	2.527000	0.85204	0.557000	0.71058	ACG	.	.		0.527	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717	
BZW2	28969	hgsc.bcm.edu	37	7	16720997	16720997	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:16720997G>T	ENST00000433922.2	+	4	485	c.307G>T	c.(307-309)Gaa>Taa	p.E103*	BZW2_ENST00000405202.1_Nonsense_Mutation_p.E27*|BZW2_ENST00000258761.3_Nonsense_Mutation_p.E103*|BZW2_ENST00000452975.2_Nonsense_Mutation_p.E103*|BZW2_ENST00000432311.1_3'UTR	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	103					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	membrane (GO:0016020)		p.E103K(1)		cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		TTCAGCAAATGAAGATCATGA	0.428																																					p.E103X		Atlas-SNP	.											BZW2,NS,carcinoma,0,1	BZW2	35	.	1	Substitution - Missense(1)	cervix(1)	c.G307T						.						137.0	121.0	126.0					7																	16720997		2203	4300	6503	SO:0001587	stop_gained	28969	exon4			GCAAATGAAGATC	AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261			18808	protein-coding gene	gene with protein product						11042152	Standard	NM_001159767		Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.307G>T	chr7.hg19:g.16720997G>T	ENSP00000397249:p.Glu103*	57.0	0.0		107.0	19.0	NM_014038	A4D123|Q3B779|Q96JW5|Q9H3F7	Nonsense_Mutation	SNP	ENST00000433922.2	hg19	CCDS5362.1	.	.	.	.	.	.	.	.	.	.	G	39	7.514962	0.98332	.	.	ENSG00000136261	ENST00000415365;ENST00000258761;ENST00000433922;ENST00000452975;ENST00000405202;ENST00000446596;ENST00000438834;ENST00000430000	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-12.2543	20.2527	0.98410	0.0:0.0:1.0:0.0	.	.	.	.	X	103;103;103;103;27;103;103;103	.	ENSP00000258761:E103X	E	+	1	0	BZW2	16687522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.810000	0.99221	2.788000	0.95919	0.557000	0.71058	GAA	.	.		0.428	BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2	NM_014038	
CBX3	11335	hgsc.bcm.edu	37	7	26248077	26248077	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:26248077A>G	ENST00000337620.4	+	4	660	c.232A>G	c.(232-234)Aac>Gac	p.N78D	CBX3_ENST00000497498.1_3'UTR|CBX3_ENST00000409747.1_Intron|CBX3_ENST00000396386.2_Missense_Mutation_p.N78D	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	78	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						AGCGTTTCTTAACTCTCAGAA	0.328																																					p.N78D		Atlas-SNP	.											.	CBX3	25	.	0			c.A232G						.						53.0	60.0	58.0					7																	26248077		2202	4300	6502	SO:0001583	missense	11335	exon4			TTTCTTAACTCTC	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"""HP1 gamma homolog (Drosophila)"""	604477	"""chromobox homolog 3 (Drosophila HP1 gamma)"""			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.232A>G	chr7.hg19:g.26248077A>G	ENSP00000336687:p.Asn78Asp	116.0	0.0		248.0	102.0	NM_016587	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Missense_Mutation	SNP	ENST00000337620.4	hg19	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.087128	0.55968	.	.	ENSG00000122565	ENST00000337620;ENST00000396386	T;T	0.70749	-0.51;-0.51	5.35	5.35	0.76521	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.091219	0.85682	D	0.000000	T	0.52354	0.1729	N	0.10629	0.01	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.48317	-0.9046	10	0.31617	T	0.26	.	15.6276	0.76874	1.0:0.0:0.0:0.0	.	78	Q13185	CBX3_HUMAN	D	78	ENSP00000336687:N78D;ENSP00000379670:N78D	ENSP00000336687:N78D	N	+	1	0	CBX3	26214602	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.135000	0.57997	2.150000	0.67090	0.533000	0.62120	AAC	.	.		0.328	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	
NYAP1	222950	hgsc.bcm.edu	37	7	100085893	100085893	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:100085893C>T	ENST00000300179.2	+	4	708	c.549C>T	c.(547-549)ggC>ggT	p.G183G	NYAP1_ENST00000423930.1_Silent_p.G183G|NYAP1_ENST00000454988.1_Silent_p.G126G	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	183	Involved in CYFIP1- and NCKAP1-binding. {ECO:0000250}.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GCCCCCCAGGCCCCTCTCCTC	0.652																																					p.G183G		Atlas-SNP	.											.	.	.	.	0			c.C549T						.						59.0	68.0	65.0					7																	100085893		2203	4300	6503	SO:0001819	synonymous_variant	222950	exon4			CCCAGGCCCCTCT	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"""chromosome 7 open reading frame 51"", ""KIAA1486-like"""	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.549C>T	chr7.hg19:g.100085893C>T		50.0	0.0		67.0	23.0	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	.		0.652	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564	
SLC12A9	56996	hgsc.bcm.edu	37	7	100452001	100452001	+	Splice_Site	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:100452001G>T	ENST00000354161.3	+	2	306		c.e2+1		SLC12A9_ENST00000428758.1_Splice_Site|SLC12A9_ENST00000540482.1_Splice_Site|SLC12A9_ENST00000415287.1_Splice_Site|SLC12A9_ENST00000275729.3_Splice_Site|RP11-126L15.4_ENST00000412754.1_RNA	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTGAGGATTGGTGAGTGGGTC	0.577																																					.		Atlas-SNP	.											.	SLC12A9	81	.	0			c.181+1G>T						.						120.0	119.0	120.0					7																	100452001		2203	4300	6503	SO:0001630	splice_region_variant	56996	exon2			GGATTGGTGAGTG	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.181+1G>T	chr7.hg19:g.100452001G>T		158.0	0.0		499.0	133.0	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Splice_Site	SNP	ENST00000354161.3	hg19	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655266	0.67472	.	.	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161;ENST00000416675;ENST00000434158	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7812	0.69769	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A9	100289937	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.406000	0.80017	2.340000	0.79590	0.407000	0.27541	.	.	.		0.577	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	Intron
MUC17	140453	hgsc.bcm.edu	37	7	100678400	100678400	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:100678400G>T	ENST00000306151.4	+	3	3767	c.3703G>T	c.(3703-3705)Gag>Tag	p.E1235*		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1235	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GGCCAGTTCTGAGGCTAGCAC	0.517																																					p.E1235X		Atlas-SNP	.											.	MUC17	804	.	0			c.G3703T						.						304.0	291.0	296.0					7																	100678400		2203	4300	6503	SO:0001587	stop_gained	140453	exon3			AGTTCTGAGGCTA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3703G>T	chr7.hg19:g.100678400G>T	ENSP00000302716:p.Glu1235*	67.0	0.0		102.0	21.0	NM_001040105	O14761|Q685J2|Q8TDH7	Nonsense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	38	6.641995	0.97726	.	.	ENSG00000169876	ENST00000306151	.	.	.	0.471	0.471	0.16752	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	.	.	.	.	.	.	.	X	1235	.	ENSP00000302716:E1235X	E	+	1	0	MUC17	100465120	0.000000	0.05858	0.005000	0.12908	0.037000	0.13140	0.216000	0.17585	0.558000	0.29135	0.134000	0.15878	GAG	.	.		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GPR22	2845	hgsc.bcm.edu	37	7	107115448	107115448	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr7:107115448T>C	ENST00000304402.4	+	3	2286	c.943T>C	c.(943-945)Tct>Cct	p.S315P	COG5_ENST00000475638.2_Intron|COG5_ENST00000393603.2_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000297135.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	315					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						CTTCAGGATGTCTTTATTGAT	0.383																																					p.S315P		Atlas-SNP	.											.	GPR22	43	.	0			c.T943C						.						118.0	120.0	119.0					7																	107115448		2203	4300	6503	SO:0001583	missense	2845	exon3			AGGATGTCTTTAT	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"""GPCR / Class A : Orphans"""	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.943T>C	chr7.hg19:g.107115448T>C	ENSP00000302676:p.Ser315Pro	153.0	0.0		330.0	109.0	NM_005295	O14554	Missense_Mutation	SNP	ENST00000304402.4	hg19	CCDS5744.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.514345	0.64522	.	.	ENSG00000172209	ENST00000304402	T	0.37915	1.17	5.66	5.66	0.87406	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	M	0.65498	2.005	0.80722	D	1	D	0.63880	0.993	D	0.79108	0.992	T	0.62900	-0.6756	10	0.87932	D	0	-9.5576	15.8804	0.79201	0.0:0.0:0.0:1.0	.	315	Q99680	GPR22_HUMAN	P	315	ENSP00000302676:S315P	ENSP00000302676:S315P	S	+	1	0	GPR22	106902684	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.040000	0.89188	2.160000	0.67779	0.477000	0.44152	TCT	.	.		0.383	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1		
SGCZ	137868	hgsc.bcm.edu	37	8	13948074	13948074	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:13948074A>T	ENST00000382080.1	-	8	1532	c.817T>A	c.(817-819)Tcc>Acc	p.S273T	SGCZ_ENST00000421524.2_Missense_Mutation_p.S226T	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	260					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		GAACTTGAGGAGCTGGGTGAA	0.433																																					p.S273T		Atlas-SNP	.											.	SGCZ	96	.	0			c.T817A						.						130.0	121.0	124.0					8																	13948074		2203	4300	6503	SO:0001583	missense	137868	exon8			TTGAGGAGCTGGG	AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.817T>A	chr8.hg19:g.13948074A>T	ENSP00000371512:p.Ser273Thr	52.0	0.0		60.0	26.0	NM_139167	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	hg19	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	A	8.987	0.976707	0.18812	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	T;T	0.11385	2.78;2.78	5.5	4.33	0.51752	.	0.385763	0.30177	N	0.010225	T	0.06005	0.0156	N	0.20807	0.61	0.31984	N	0.605484	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.001	T	0.27262	-1.0079	10	0.10377	T	0.69	.	7.1543	0.25628	0.7793:0.146:0.0747:0.0	.	226;273	Q08AT0;Q96LD1-2	.;.	T	273;226	ENSP00000371512:S273T;ENSP00000405224:S226T	ENSP00000371512:S273T	S	-	1	0	SGCZ	13992445	0.999000	0.42202	0.998000	0.56505	0.997000	0.91878	2.276000	0.43408	1.028000	0.39785	0.533000	0.62120	TCC	.	.		0.433	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167	
UBR5	51366	hgsc.bcm.edu	37	8	103293516	103293516	+	Splice_Site	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:103293516C>T	ENST00000520539.1	-	41	6534		c.e41+1		UBR5_ENST00000220959.4_Splice_Site|UBR5_ENST00000521922.1_Splice_Site	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5						cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AGAATGGATACCTTTTGCGTT	0.368																																					.	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.5927+1G>A						.						95.0	75.0	82.0					8																	103293516		2203	4300	6503	SO:0001630	splice_region_variant	51366	exon42			TGGATACCTTTTG	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.5927+1G>A	chr8.hg19:g.103293516C>T		146.0	0.0		727.0	219.0	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Splice_Site	SNP	ENST00000520539.1	hg19	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.547843	0.86022	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.692	0.88271	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBR5	103362692	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.772000	0.85439	2.152000	0.67230	0.563000	0.77884	.	.	.		0.368	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	Intron
ZFPM2	23414	hgsc.bcm.edu	37	8	106331179	106331179	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:106331179C>T	ENST00000407775.2	+	1	260	c.10C>T	c.(10-12)Cga>Tga	p.R4*	ZFPM2_ENST00000520492.1_5'Flank	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	4					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GATGTCCCGGCGAAAGCAAAG	0.741																																					p.R4X		Atlas-SNP	.											ZFPM2,colon,carcinoma,0,1	ZFPM2	219	.	0			c.C10T						.						4.0	5.0	5.0					8																	106331179		1410	3262	4672	SO:0001587	stop_gained	23414	exon1			TCCCGGCGAAAGC	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.10C>T	chr8.hg19:g.106331179C>T	ENSP00000384179:p.Arg4*	37.0	0.0		205.0	30.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Nonsense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	40	7.932149	0.98568	.	.	ENSG00000169946	ENST00000407775	.	.	.	3.5	2.46	0.29980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6804	0.28509	0.5355:0.4645:0.0:0.0	.	.	.	.	X	4	.	ENSP00000384179:R4X	R	+	1	2	ZFPM2	106400355	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.329000	0.52060	1.491000	0.48482	0.460000	0.39030	CGA	.	.		0.741	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
ANGPT1	284	hgsc.bcm.edu	37	8	108297062	108297062	+	Silent	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:108297062G>T	ENST00000520734.1	-	6	738	c.453C>A	c.(451-453)ccC>ccA	p.P151P	ANGPT1_ENST00000520052.1_Silent_p.P150P|ANGPT1_ENST00000518386.1_Intron			Q15389	ANGP1_HUMAN	angiopoietin 1	351					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			ATTCACCGGAGGGATTTCCAA	0.378																																					p.P351P		Atlas-SNP	.											.	ANGPT1	111	.	0			c.C1053A						.						56.0	53.0	54.0					8																	108297062		2203	4300	6503	SO:0001819	synonymous_variant	284	exon7			ACCGGAGGGATTT	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"""Fibrinogen C domain containing"""	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.453C>A	chr8.hg19:g.108297062G>T		76.0	0.0		278.0	40.0	NM_001146	Q5HYA0	Silent	SNP	ENST00000520734.1	hg19																																																																																				.	.		0.378	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290	
ADCY8	114	hgsc.bcm.edu	37	8	131797673	131797673	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:131797673C>T	ENST00000286355.5	-	16	5201	c.3109G>A	c.(3109-3111)Ggc>Agc	p.G1037S	ADCY8_ENST00000377928.3_Missense_Mutation_p.G906S	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1037					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TAGGTGCTGCCAATGGTCTTA	0.483										HNSCC(32;0.087)																											p.G1037S		Atlas-SNP	.											.	ADCY8	291	.	0			c.G3109A						.						112.0	99.0	103.0					8																	131797673		2203	4300	6503	SO:0001583	missense	114	exon16			TGCTGCCAATGGT	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3109G>A	chr8.hg19:g.131797673C>T	ENSP00000286355:p.Gly1037Ser	51.0	0.0		109.0	9.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	C	36	5.714181	0.96830	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	D;D	0.97811	-4.55;-4.55	5.07	5.07	0.68467	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.98654	0.9549	M	0.79926	2.475	0.50632	D	0.99988	D;D	0.69078	0.997;0.997	D;D	0.75484	0.972;0.986	D	0.99572	1.0971	10	0.62326	D	0.03	.	17.8033	0.88595	0.0:1.0:0.0:0.0	.	906;1037	E7EVL1;P40145	.;ADCY8_HUMAN	S	1037;906	ENSP00000286355:G1037S;ENSP00000367161:G906S	ENSP00000286355:G1037S	G	-	1	0	ADCY8	131866855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.770000	0.85390	2.535000	0.85469	0.591000	0.81541	GGC	.	.		0.483	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
TG	7038	hgsc.bcm.edu	37	8	133961019	133961019	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr8:133961019A>G	ENST00000220616.4	+	27	5273		c.e27-1		TG_ENST00000377869.1_Splice_Site|TG_ENST00000542445.1_Splice_Site	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin						hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TGTGATTCTCAGGTGCCATCA	0.498																																					.		Atlas-SNP	.											.	TG	416	.	0			c.5234-2A>G						.						189.0	173.0	179.0					8																	133961019		2203	4300	6503	SO:0001630	splice_region_variant	7038	exon27			ATTCTCAGGTGCC	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5234-1A>G	chr8.hg19:g.133961019A>G		90.0	0.0		266.0	63.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Splice_Site	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296961	0.23650	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000519178;ENST00000542445	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4081	0.55451	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TG	134030201	0.998000	0.40836	0.751000	0.31187	0.003000	0.03518	4.592000	0.61027	2.246000	0.74042	0.533000	0.62120	.	.	.		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	Intron
DMRT2	10655	hgsc.bcm.edu	37	9	1056606	1056606	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:1056606G>T	ENST00000358146.2	+	3	1019	c.1019G>T	c.(1018-1020)aGa>aTa	p.R340I	DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.R340I|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000382251.3_Missense_Mutation_p.R340I			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	340					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		TTGTCCTCAAGATTTTTAGTT	0.478																																					p.R340I		Atlas-SNP	.											.	DMRT2	70	.	0			c.G1019T						.						100.0	105.0	103.0					9																	1056606		2203	4300	6503	SO:0001583	missense	10655	exon4			CCTCAAGATTTTT	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"""terra-like protein"""	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.1019G>T	chr9.hg19:g.1056606G>T	ENSP00000350865:p.Arg340Ile	66.0	0.0		89.0	22.0	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	hg19	CCDS6444.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725832	0.69074	.	.	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.27557	1.66;1.66;1.66	5.62	5.62	0.85841	.	0.240668	0.40908	D	0.000985	T	0.53077	0.1774	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.67145	0.994;0.996	P;D	0.66497	0.88;0.944	T	0.52366	-0.8585	10	0.72032	D	0.01	-15.4915	19.2806	0.94051	0.0:0.0:1.0:0.0	.	340;184	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	I	340	ENSP00000371686:R340I;ENSP00000305785:R340I;ENSP00000350865:R340I	ENSP00000305785:R340I	R	+	2	0	DMRT2	1046606	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	9.153000	0.94687	2.665000	0.90641	0.650000	0.86243	AGA	.	.		0.478	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
IFNA4	3441	hgsc.bcm.edu	37	9	21187344	21187344	+	Missense_Mutation	SNP	C	C	G	rs142712065	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:21187344C>G	ENST00000421715.1	-	1	254	c.187G>C	c.(187-189)Gag>Cag	p.E63Q		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	63					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		AACTCCTCCTCGGGGAATCCG	0.517																																					p.E63Q	NSCLC(154;890 1986 23660 27800 51138)	Atlas-SNP	.											.	IFNA4	34	.	0			c.G187C						.						114.0	114.0	114.0					9																	21187344		2203	4300	6503	SO:0001583	missense	3441	exon1			CCTCCTCGGGGAA		CCDS6498.1	9p22	2010-08-24			ENSG00000236637	ENSG00000236637		"""Interferons"""	5425	protein-coding gene	gene with protein product		147564				1385305	Standard	NM_021068		Approved	MGC142200, IFN-alpha4a	uc003zon.2	P05014	OTTHUMG00000019660	ENST00000421715.1:c.187G>C	chr9.hg19:g.21187344C>G	ENSP00000412897:p.Glu63Gln	135.0	0.0		326.0	103.0	NM_021068	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	hg19	CCDS6498.1	.	.	.	.	.	.	.	.	.	.	-	0.010	-1.794798	0.00617	.	.	ENSG00000236637	ENST00000421715	T	0.03242	4.0	2.96	-2.48	0.06423	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.591514	0.17433	N	0.174416	T	0.00552	0.0018	N	0.00084	-2.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39502	-0.9611	10	0.02654	T	1	.	2.3247	0.04220	0.1004:0.2772:0.342:0.2804	.	63	P05014	IFNA4_HUMAN	Q	63	ENSP00000412897:E63Q	ENSP00000412897:E63Q	E	-	1	0	IFNA4	21177344	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.618000	0.02049	-0.623000	0.05618	-0.332000	0.08345	GAG	.	.		0.517	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068	
SPATA31C2	645961	hgsc.bcm.edu	37	9	90746873	90746873	+	IGR	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:90746873G>A								U6 (133623 upstream) : U3 (242310 downstream)																							GACTGGGAAAGAGGATTGAAG	0.532																																					p.S360F		Atlas-SNP	.											.	.	.	.	0			c.C1079T						.						14.0	17.0	16.0					9																	90746873		691	1590	2281	SO:0001628	intergenic_variant	645961	exon4			GGGAAAGAGGATT																													chr9.hg19:g.90746873G>A		81.0	0.0		139.0	37.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.532								
ZNF189	7743	hgsc.bcm.edu	37	9	104171115	104171115	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:104171115G>A	ENST00000339664.2	+	3	1194	c.1065G>A	c.(1063-1065)cgG>cgA	p.R355R	ZNF189_ENST00000259395.4_Silent_p.R313R|ZNF189_ENST00000374861.3_Silent_p.R341R	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	355					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				GTTTCAGTCGGAGCTCATTCC	0.408																																					p.R355R		Atlas-SNP	.											.	ZNF189	79	.	0			c.G1065A						.						83.0	89.0	87.0					9																	104171115		2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			CAGTCGGAGCTCA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1065G>A	chr9.hg19:g.104171115G>A		52.0	0.0		81.0	19.0	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	hg19	CCDS6754.1																																																																																			.	.		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
CYLC2	1539	hgsc.bcm.edu	37	9	105767037	105767037	+	Silent	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:105767037T>C	ENST00000374798.3	+	4	311	c.241T>C	c.(241-243)Tta>Cta	p.L81L	CYLC2_ENST00000487798.1_Silent_p.L81L	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	81	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				GTACCGTTCTTTAATGAGAAT	0.403																																					p.L81L		Atlas-SNP	.											.	CYLC2	109	.	0			c.T241C						.						86.0	83.0	84.0					9																	105767037		2203	4300	6503	SO:0001819	synonymous_variant	1539	exon4			CGTTCTTTAATGA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.241T>C	chr9.hg19:g.105767037T>C		76.0	0.0		128.0	35.0	NM_001340	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.403	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340	
OR13C9	286362	hgsc.bcm.edu	37	9	107379994	107379994	+	Silent	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:107379994T>C	ENST00000259362.1	-	1	491	c.492A>G	c.(490-492)gtA>gtG	p.V164V		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAGGCAATTGTACTACAAATG	0.438																																					p.V164V		Atlas-SNP	.											.	OR13C9	42	.	0			c.A492G						.						121.0	104.0	110.0					9																	107379994		2203	4300	6503	SO:0001819	synonymous_variant	286362	exon1			CAATTGTACTACA		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.492A>G	chr9.hg19:g.107379994T>C		105.0	0.0		206.0	67.0	NM_001001956	Q6IFL2	Silent	SNP	ENST00000259362.1	hg19	CCDS35093.1																																																																																			.	.		0.438	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
SUSD1	64420	hgsc.bcm.edu	37	9	114820918	114820918	+	Silent	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr9:114820918A>T	ENST00000374270.3	-	14	2071	c.1899T>A	c.(1897-1899)tcT>tcA	p.S633S	SUSD1_ENST00000374263.3_Silent_p.S633S|SUSD1_ENST00000374264.2_Silent_p.S633S	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	633						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CAGAATCACAAGAAAATGTGC	0.483																																					p.S633S		Atlas-SNP	.											.	SUSD1	51	.	0			c.T1899A						.						96.0	100.0	99.0					9																	114820918		2203	4300	6503	SO:0001819	synonymous_variant	64420	exon14			ATCACAAGAAAAT	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1899T>A	chr9.hg19:g.114820918A>T		55.0	0.0		97.0	28.0	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	hg19	CCDS6783.1	.	.	.	.	.	.	.	.	.	.	A	3.405	-0.121499	0.06838	.	.	ENSG00000106868	ENST00000355396	.	.	.	5.44	1.18	0.20946	.	.	.	.	.	T	0.55641	0.1933	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47787	-0.9090	4	.	.	.	-0.135	8.3921	0.32535	0.6833:0.2432:0.0735:0.0	.	.	.	.	M	617	.	.	L	-	1	2	SUSD1	113860739	0.668000	0.27493	0.998000	0.56505	0.165000	0.22458	0.976000	0.29462	0.327000	0.23409	0.459000	0.35465	TTG	.	.		0.483	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486	
DIP2C	22982	hgsc.bcm.edu	37	10	436697	436697	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:436697T>A	ENST00000280886.6	-	11	1454	c.1367A>T	c.(1366-1368)gAg>gTg	p.E456V	DIP2C_ENST00000381496.3_Missense_Mutation_p.E349V	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	456						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CTGTGGGATCTCTCCCGTTGG	0.557																																					p.E456V		Atlas-SNP	.											.	DIP2C	195	.	0			c.A1367T						.						210.0	191.0	197.0					10																	436697		2203	4300	6503	SO:0001583	missense	22982	exon11			GGGATCTCTCCCG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.1367A>T	chr10.hg19:g.436697T>A	ENSP00000280886:p.Glu456Val	54.0	0.0		94.0	23.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394392	0.83011	.	.	ENSG00000151240	ENST00000280886;ENST00000381496	T;T	0.44083	0.93;0.93	5.41	5.41	0.78517	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.62441	0.2428	M	0.67953	2.075	0.58432	D	0.999998	D;B	0.64830	0.994;0.319	D;P	0.71656	0.974;0.513	T	0.64943	-0.6288	10	0.56958	D	0.05	-36.63	15.441	0.75181	0.0:0.0:0.0:1.0	.	349;456	E7EPU2;Q9Y2E4	.;DIP2C_HUMAN	V	456;349	ENSP00000280886:E456V;ENSP00000370907:E349V	ENSP00000280886:E456V	E	-	2	0	DIP2C	426697	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.997000	0.88414	2.046000	0.60703	0.254000	0.18369	GAG	.	.		0.557	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
PFKFB3	5209	hgsc.bcm.edu	37	10	6258734	6258734	+	Silent	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:6258734T>C	ENST00000379775.4	+	5	762	c.432T>C	c.(430-432)aaT>aaC	p.N144N	PFKFB3_ENST00000536985.1_Silent_p.N124N|PFKFB3_ENST00000360521.2_Silent_p.N144N|PFKFB3_ENST00000540253.1_Silent_p.N158N|PFKFB3_ENST00000379782.3_Silent_p.N144N|PFKFB3_ENST00000379789.4_Silent_p.N124N|PFKFB3_ENST00000379785.1_Silent_p.N144N|PFKFB3_ENST00000317350.4_Silent_p.N144N	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	144	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CCAAAGAAAATGACTTTAAGG	0.498																																					p.N144N		Atlas-SNP	.											.	PFKFB3	82	.	0			c.T432C						.						197.0	190.0	193.0					10																	6258734		2203	4300	6503	SO:0001819	synonymous_variant	5209	exon5			AGAAAATGACTTT		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.432T>C	chr10.hg19:g.6258734T>C		59.0	0.0		83.0	30.0	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Silent	SNP	ENST00000379775.4	hg19	CCDS7078.1																																																																																			.	.		0.498	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1		
CUBN	8029	hgsc.bcm.edu	37	10	17130262	17130262	+	Silent	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:17130262A>G	ENST00000377833.4	-	15	1913	c.1848T>C	c.(1846-1848)tgT>tgC	p.C616C		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	616	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAATCCAGACACAATCTCTTC	0.458																																					p.C616C		Atlas-SNP	.											.	CUBN	515	.	0			c.T1848C						.						100.0	91.0	94.0					10																	17130262		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon15			CCAGACACAATCT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1848T>C	chr10.hg19:g.17130262A>G		52.0	0.0		140.0	28.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.		0.458	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
RBP3	5949	hgsc.bcm.edu	37	10	48388579	48388579	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:48388579G>A	ENST00000224600.4	-	1	2412	c.2299C>T	c.(2299-2301)Ctg>Ttg	p.L767L	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	767	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	TGCCATACCAGCCGCACCAGC	0.632																																					p.L767L		Atlas-SNP	.											.	RBP3	152	.	0			c.C2299T						.						30.0	29.0	29.0					10																	48388579		2202	4300	6502	SO:0001819	synonymous_variant	5949	exon1			ATACCAGCCGCAC	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2299C>T	chr10.hg19:g.48388579G>A		24.0	0.0		90.0	38.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	hg19	CCDS7218.1																																																																																			.	.		0.632	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
ZWINT	11130	hgsc.bcm.edu	37	10	58118598	58118598	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:58118598C>T	ENST00000373944.3	-	6	629	c.591G>A	c.(589-591)caG>caA	p.Q197Q	ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000318387.2_Silent_p.Q77Q|ZWINT_ENST00000460654.1_5'UTR|ZWINT_ENST00000395405.1_Silent_p.Q197Q			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	197					establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						GTTCTGCCTGCTGCTTCAGGT	0.537																																					p.Q197Q		Atlas-SNP	.											.	ZWINT	39	.	0			c.G591A						.						136.0	133.0	134.0					10																	58118598		2203	4300	6503	SO:0001819	synonymous_variant	11130	exon6			TGCCTGCTGCTTC	AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"""ZW10 interactor"""				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.591G>A	chr10.hg19:g.58118598C>T		120.0	0.0		272.0	49.0	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Silent	SNP	ENST00000373944.3	hg19	CCDS7249.1																																																																																			.	.		0.537	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1		
JMJD1C	221037	hgsc.bcm.edu	37	10	64950774	64950774	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:64950774G>A	ENST00000399262.2	-	17	6389	c.6171C>T	c.(6169-6171)tcC>tcT	p.S2057S	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Silent_p.S1875S|JMJD1C_ENST00000402544.1_Silent_p.S1820S	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2057					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CATTATTCTGGGACACAAGAG	0.433																																					p.S2057S		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C6171T						.						263.0	256.0	258.0					10																	64950774		1907	4116	6023	SO:0001819	synonymous_variant	221037	exon17			ATTCTGGGACACA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.6171C>T	chr10.hg19:g.64950774G>A		151.0	0.0		529.0	161.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	G	8.568	0.879284	0.17467	.	.	ENSG00000171988	ENST00000327520	.	.	.	5.52	-0.906	0.10524	.	.	.	.	.	T	0.57475	0.2056	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53387	-0.8446	4	.	.	.	-1.3648	10.5664	0.45175	0.5247:0.0:0.4753:0.0	.	.	.	.	L	604	.	.	P	-	2	0	JMJD1C	64620780	0.955000	0.32602	0.764000	0.31436	0.855000	0.48748	-0.005000	0.12855	-0.121000	0.11787	0.650000	0.86243	CCC	.	.		0.433	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
JMJD1C	221037	hgsc.bcm.edu	37	10	64966479	64966479	+	Nonsense_Mutation	SNP	G	G	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:64966479G>C	ENST00000399262.2	-	10	5168	c.4950C>G	c.(4948-4950)taC>taG	p.Y1650*	JMJD1C_ENST00000399251.1_Nonsense_Mutation_p.Y1431*|JMJD1C_ENST00000542921.1_Nonsense_Mutation_p.Y1468*|JMJD1C_ENST00000402544.1_Nonsense_Mutation_p.Y1431*	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1650					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					GCTTCTTTTTGTAAGTTGGCT	0.378																																					p.Y1650X		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C4950G						.						173.0	151.0	158.0					10																	64966479		1852	4106	5958	SO:0001587	stop_gained	221037	exon10			CTTTTTGTAAGTT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4950C>G	chr10.hg19:g.64966479G>C	ENSP00000382204:p.Tyr1650*	174.0	0.0		525.0	161.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Nonsense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	49|49	15.123811|15.123811	0.99823|0.99823	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000327520|ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	.|.	.|.	.|.	5.62|5.62	-2.44|-2.44	0.06502|0.06502	.|.	.|0.059320	.|0.64402	.|D	.|0.000001	T|.	0.23572|.	0.0570|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42155|.	-0.9468|.	3|.	.|0.02654	.|T	.|1	-8.1512|-8.1512	13.2443|13.2443	0.60014|0.60014	0.5054:0.0:0.4946:0.0|0.5054:0.0:0.4946:0.0	.|.	.|.	.|.	.|.	R|X	336|1650;1431;1431;1468	.|.	.|ENSP00000382195:Y1431X	T|Y	-|-	2|3	0|2	JMJD1C|JMJD1C	64636485|64636485	0.998000|0.998000	0.40836|0.40836	0.983000|0.983000	0.44433|0.44433	0.986000|0.986000	0.74619|0.74619	0.404000|0.404000	0.20999|0.20999	-0.391000|-0.391000	0.07763|0.07763	-0.225000|-0.225000	0.12378|0.12378	ACA|TAC	.	.		0.378	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
KIF20B	9585	hgsc.bcm.edu	37	10	91474892	91474892	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:91474892A>G	ENST00000371728.3	+	8	958	c.893A>G	c.(892-894)aAg>aGg	p.K298R	KIF20B_ENST00000260753.4_Missense_Mutation_p.K298R|KIF20B_ENST00000394289.2_Missense_Mutation_p.K298R|KIF20B_ENST00000416354.1_Missense_Mutation_p.K298R	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	298	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						CAAAAGAGAAAGATGCTGCGC	0.303																																					p.K298R		Atlas-SNP	.											.	KIF20B	191	.	0			c.A893G						.						44.0	48.0	47.0					10																	91474892		2199	4285	6484	SO:0001583	missense	9585	exon8			AGAGAAAGATGCT	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.893A>G	chr10.hg19:g.91474892A>G	ENSP00000360793:p.Lys298Arg	107.0	0.0		174.0	64.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.39	3.613542	0.66672	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	5.36	5.36	0.76844	Kinesin, motor domain (4);	0.000000	0.49916	D	0.000125	T	0.70509	0.3232	L	0.28649	0.875	0.43313	D	0.995325	B;B	0.32862	0.387;0.055	B;B	0.44163	0.443;0.273	T	0.71695	-0.4515	10	0.51188	T	0.08	-17.2908	11.6171	0.51096	0.9281:0.0:0.0719:0.0	.	298;298	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	R	298	ENSP00000260753:K298R;ENSP00000411545:K298R;ENSP00000377830:K298R;ENSP00000360793:K298R	ENSP00000260753:K298R	K	+	2	0	KIF20B	91464872	0.521000	0.26258	0.999000	0.59377	0.991000	0.79684	1.162000	0.31786	2.160000	0.67779	0.528000	0.53228	AAG	.	.		0.303	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
IDE	3416	hgsc.bcm.edu	37	10	94223595	94223595	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:94223595T>A	ENST00000265986.6	-	21	2710	c.2654A>T	c.(2653-2655)cAc>cTc	p.H885L	IDE_ENST00000371581.5_Missense_Mutation_p.H330L|IDE_ENST00000496903.1_5'UTR	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	885					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""""""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"""	TGCCTGAATGTGTTTTTGGAA	0.413																																					p.H885L		Atlas-SNP	.											.	IDE	77	.	0			c.A2654T						.						234.0	227.0	230.0					10																	94223595		2203	4300	6503	SO:0001583	missense	3416	exon21			TGAATGTGTTTTT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"""insulysin"""	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.2654A>T	chr10.hg19:g.94223595T>A	ENSP00000265986:p.His885Leu	163.0	0.0		521.0	78.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936385	0.73442	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.06768	3.26;3.26	5.61	5.61	0.85477	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.39489	0.1080	M	0.93720	3.45	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79784	0.96;0.993	T	0.50415	-0.8831	10	0.46703	T	0.11	-16.1168	16.0994	0.81158	0.0:0.0:0.0:1.0	.	885;330	P14735;B3KSB8	IDE_HUMAN;.	L	885;330	ENSP00000265986:H885L;ENSP00000360637:H330L	ENSP00000265986:H885L	H	-	2	0	IDE	94213575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.760000	0.85248	2.261000	0.74972	0.533000	0.62120	CAC	.	.		0.413	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969	
MYOF	26509	hgsc.bcm.edu	37	10	95123767	95123767	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr10:95123767C>T	ENST00000359263.4	-	27	2818	c.2819G>A	c.(2818-2820)cGc>cAc	p.R940H	MYOF_ENST00000371502.4_Missense_Mutation_p.R940H|MYOF_ENST00000358334.5_Missense_Mutation_p.R927H|MYOF_ENST00000371501.4_Missense_Mutation_p.R940H	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	940					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CCCGGGGTAGCGGCTCTCGTT	0.607																																					p.R940H		Atlas-SNP	.											.	MYOF	177	.	0			c.G2819A						.						67.0	67.0	67.0					10																	95123767		1953	4146	6099	SO:0001583	missense	26509	exon27			GGGTAGCGGCTCT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.2819G>A	chr10.hg19:g.95123767C>T	ENSP00000352208:p.Arg940His	25.0	0.0		48.0	19.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300298	0.95574	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.87029	-2.19;-2.18;-2.18;-2.2	5.65	5.65	0.86999	Ferlin/Peroxisome membrane (1);	0.049306	0.85682	N	0.000000	D	0.94673	0.8282	M	0.86502	2.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94683	0.7867	10	0.87932	D	0	-14.6837	19.9142	0.97043	0.0:1.0:0.0:0.0	.	927;940	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	H	927;940;940;940	ENSP00000351094:R927H;ENSP00000352208:R940H;ENSP00000360556:R940H;ENSP00000360557:R940H	ENSP00000351094:R927H	R	-	2	0	MYOF	95113757	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.607	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
DENND5A	23258	hgsc.bcm.edu	37	11	9202573	9202573	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:9202573G>T	ENST00000328194.3	-	6	1516	c.1196C>A	c.(1195-1197)cCa>cAa	p.P399Q	DENND5A_ENST00000526523.1_5'Flank|DENND5A_ENST00000530044.1_Missense_Mutation_p.P399Q	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	399					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGGGAACTGTGGCAAGTCCTC	0.468																																					p.P399Q		Atlas-SNP	.											.	DENND5A	84	.	0			c.C1196A						.						67.0	68.0	68.0					11																	9202573		2201	4296	6497	SO:0001583	missense	23258	exon6			AACTGTGGCAAGT	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.1196C>A	chr11.hg19:g.9202573G>T	ENSP00000328524:p.Pro399Gln	82.0	0.0		161.0	35.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.808638	0.90707	.	.	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.05319	3.46;3.46	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.26557	0.0649	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.00740	-1.1586	10	0.87932	D	0	.	18.9552	0.92655	0.0:0.0:1.0:0.0	.	399;399	E9PS91;Q6IQ26	.;DEN5A_HUMAN	Q	399	ENSP00000328524:P399Q;ENSP00000435866:P399Q	ENSP00000328524:P399Q	P	-	2	0	DENND5A	9159149	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.810000	0.99221	2.550000	0.86006	0.563000	0.77884	CCA	.	.		0.468	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
CPT1A	1374	hgsc.bcm.edu	37	11	68530229	68530229	+	Splice_Site	SNP	C	C	A	rs201706909		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:68530229C>A	ENST00000265641.5	-	15	1895	c.1741G>T	c.(1741-1743)Gac>Tac	p.D581Y	CPT1A_ENST00000537756.2_5'UTR|CPT1A_ENST00000539743.1_Splice_Site_p.D581Y|CPT1A_ENST00000376618.2_Splice_Site_p.D581Y|CPT1A_ENST00000540367.1_Splice_Site_p.D581Y	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	581					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	TTGCCCATGTCCTGGGGAAAG	0.547																																					p.D581Y		Atlas-SNP	.											.	CPT1A	89	.	0			c.G1741T						.						67.0	59.0	62.0					11																	68530229		2200	4294	6494	SO:0001630	splice_region_variant	1374	exon15			CCATGTCCTGGGG	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.1741-1G>T	chr11.hg19:g.68530229C>A		20.0	0.0		39.0	24.0	NM_001876	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862602	0.71949	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.89785	3.06	0.80722	D	1	D;D	0.76494	0.977;0.999	D;D	0.70716	0.918;0.97	D	0.86645	0.1894	10	0.02654	T	1	.	19.912	0.97027	0.0:1.0:0.0:0.0	.	581;581	P50416;P50416-2	CPT1A_HUMAN;.	Y	581	ENSP00000439084:D581Y;ENSP00000365803:D581Y;ENSP00000265641:D581Y;ENSP00000446108:D581Y	ENSP00000265641:D581Y	D	-	1	0	CPT1A	68286805	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	7.364000	0.79526	2.783000	0.95769	0.655000	0.94253	GAC	.	C|0.999;T|0.001		0.547	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	Missense_Mutation
ARHGAP42	143872	hgsc.bcm.edu	37	11	100792230	100792230	+	Silent	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:100792230T>C	ENST00000298815.8	+	6	495	c.492T>C	c.(490-492)gaT>gaC	p.D164D	ARHGAP42_ENST00000524892.2_Silent_p.D130D	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	164	BAR.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTTAGGCAGATACACAAATTG	0.348																																					p.D164D		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.T492C						.						106.0	88.0	93.0					11																	100792230		692	1591	2283	SO:0001819	synonymous_variant	143872	exon6			GGCAGATACACAA			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.492T>C	chr11.hg19:g.100792230T>C		76.0	0.0		130.0	45.0	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	hg19																																																																																				.	.		0.348	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
FDXACB1	91893	hgsc.bcm.edu	37	11	111746109	111746109	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:111746109A>G	ENST00000260257.4	-	5	1459	c.1412T>C	c.(1411-1413)aTc>aCc	p.I471T	FDXACB1_ENST00000542429.1_Missense_Mutation_p.I322T|ALG9_ENST00000524880.1_Intron|ALG9_ENST00000527377.1_Intron	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	471					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						GGCAGATGTGATAACAGACCC	0.373																																					p.I471T		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T1412C						.						67.0	66.0	66.0					11																	111746109		1897	4120	6017	SO:0001583	missense	91893	exon5			GATGTGATAACAG		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.1412T>C	chr11.hg19:g.111746109A>G	ENSP00000260257:p.Ile471Thr	69.0	0.0		85.0	48.0	NM_138378	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	hg19	CCDS44729.1	.	.	.	.	.	.	.	.	.	.	A	0.024	-1.392498	0.01185	.	.	ENSG00000255561	ENST00000260257;ENST00000542429;ENST00000528274	T;T;T	0.71222	0.45;-0.55;0.99	5.22	-2.09	0.07232	.	1.085210	0.06820	N	0.792008	T	0.45935	0.1367	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	10	0.14252	T	0.57	.	1.1115	0.01705	0.4584:0.176:0.1633:0.2023	.	471	Q9BRP7	FDXA1_HUMAN	T	471;322;382	ENSP00000260257:I471T;ENSP00000441304:I322T;ENSP00000435572:I382T	ENSP00000260257:I471T	I	-	2	0	FDXACB1	111251319	0.003000	0.15002	0.520000	0.27837	0.563000	0.35712	-0.004000	0.12878	0.012000	0.14892	-0.132000	0.14878	ATC	.	.		0.373	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378	
OR6M1	390261	hgsc.bcm.edu	37	11	123676275	123676275	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:123676275C>T	ENST00000309154.2	-	1	820	c.783G>A	c.(781-783)caG>caA	p.Q261Q		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GTGAGGAGTTCTGATTGGGTC	0.502																																					p.Q261Q		Atlas-SNP	.											OR6M1,NS,carcinoma,0,1	OR6M1	60	.	0			c.G783A						.						110.0	101.0	104.0					11																	123676275		2202	4299	6501	SO:0001819	synonymous_variant	390261	exon1			GGAGTTCTGATTG	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"""GPCR / Class A : Olfactory receptors"""	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.783G>A	chr11.hg19:g.123676275C>T		84.0	0.0		161.0	81.0	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Silent	SNP	ENST00000309154.2	hg19	CCDS31696.1																																																																																			.	.		0.502	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
PKNOX2	63876	hgsc.bcm.edu	37	11	125237764	125237764	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:125237764C>T	ENST00000298282.9	+	5	381	c.110C>T	c.(109-111)cCc>cTc	p.P37L	PKNOX2_ENST00000542175.1_Intron|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	37					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		GCCCAGCCACCCTCCAAGGCC	0.662																																					p.P37L		Atlas-SNP	.											.	PKNOX2	60	.	0			c.C110T						.						53.0	65.0	61.0					11																	125237764		2090	4202	6292	SO:0001583	missense	63876	exon5			AGCCACCCTCCAA	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"""Homeoboxes / TALE class"""	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.110C>T	chr11.hg19:g.125237764C>T	ENSP00000298282:p.Pro37Leu	59.0	0.0		93.0	20.0	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	hg19	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448842	0.63178	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000527238;ENST00000531212;ENST00000535518	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	5.49	5.49	0.81192	.	0.130686	0.52532	D	0.000062	T	0.52141	0.1716	N	0.08118	0	0.80722	D	1	B	0.16603	0.018	B	0.14578	0.011	T	0.48479	-0.9032	10	0.16896	T	0.51	-18.5915	18.1483	0.89665	0.0:1.0:0.0:0.0	.	37	Q96KN3	PKNX2_HUMAN	L	8;8;37;37;37;25	ENSP00000434732:P8L;ENSP00000433971:P8L;ENSP00000298282:P37L;ENSP00000434255:P37L	ENSP00000298282:P37L	P	+	2	0	PKNOX2	124742974	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.210000	0.58500	2.564000	0.86499	0.563000	0.77884	CCC	.	.		0.662	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3		
ANO2	57101	hgsc.bcm.edu	37	12	5936960	5936960	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:5936960G>A	ENST00000356134.5	-	8	929	c.858C>T	c.(856-858)gcC>gcT	p.A286A	ANO2_ENST00000546188.1_Silent_p.A286A|ANO2_ENST00000327087.8_Silent_p.A285A	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	290					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CTCGGGAGCAGGCTGTGCGCT	0.662																																					p.A285A		Atlas-SNP	.											.	ANO2	309	.	0			c.C855T						.						33.0	39.0	37.0					12																	5936960		2026	4194	6220	SO:0001819	synonymous_variant	57101	exon7			GGAGCAGGCTGTG	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.858C>T	chr12.hg19:g.5936960G>A		33.0	0.0		80.0	31.0	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	hg19																																																																																				.	.		0.662	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
OR6C74	254783	hgsc.bcm.edu	37	12	55641327	55641327	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:55641327G>A	ENST00000343870.4	+	1	346	c.256G>A	c.(256-258)Ggt>Agt	p.G86S		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	86			G -> D (in dbSNP:rs6581025).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						TATGGCAACAGGTGATAAGAC	0.393																																					p.G86S		Atlas-SNP	.											.	OR6C74	52	.	0			c.G256A						.						197.0	199.0	198.0					12																	55641327		2203	4300	6503	SO:0001583	missense	254783	exon1			GCAACAGGTGATA		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"""GPCR / Class A : Olfactory receptors"""	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.256G>A	chr12.hg19:g.55641327G>A	ENSP00000342836:p.Gly86Ser	108.0	0.0		260.0	70.0	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	hg19	CCDS31816.1	.	.	.	.	.	.	.	.	.	.	g	15.46	2.841617	0.51057	.	.	ENSG00000197706	ENST00000343870	T	0.02916	4.11	5.36	3.5	0.40072	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000062	T	0.04634	0.0126	L	0.51422	1.61	0.09310	N	1	P	0.39759	0.687	B	0.44133	0.442	T	0.22417	-1.0217	10	0.87932	D	0	.	6.9684	0.24635	0.1567:0.2468:0.5965:0.0	.	86	A6NCV1	O6C74_HUMAN	S	86	ENSP00000342836:G86S	ENSP00000342836:G86S	G	+	1	0	OR6C74	53927594	0.000000	0.05858	0.217000	0.23759	0.954000	0.61252	0.637000	0.24659	1.371000	0.46172	0.551000	0.68910	GGT	.	.		0.393	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
ANO4	121601	hgsc.bcm.edu	37	12	101365128	101365128	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:101365128C>T	ENST00000392977.3	+	6	711	c.501C>T	c.(499-501)gcC>gcT	p.A167A	ANO4_ENST00000538618.1_Silent_p.A333A|ANO4_ENST00000392979.3_Silent_p.A132A|ANO4_ENST00000299222.9_5'UTR			Q32M45	ANO4_HUMAN	anoctamin 4	167					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AGTTGCATGCCCCATGGGAAG	0.368										HNSCC(74;0.22)																											p.A132A		Atlas-SNP	.											.	ANO4	183	.	0			c.C396T						.						145.0	140.0	142.0					12																	101365128		2203	4300	6503	SO:0001819	synonymous_variant	121601	exon5			GCATGCCCCATGG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.501C>T	chr12.hg19:g.101365128C>T		80.0	0.0		152.0	30.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	hg19																																																																																				.	.		0.368	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
C12orf42	374470	hgsc.bcm.edu	37	12	103696092	103696092	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:103696092G>A	ENST00000378113.2	-	6	1102	c.877C>T	c.(877-879)Cgg>Tgg	p.R293W	C12orf42_ENST00000548048.1_Missense_Mutation_p.R226W|C12orf42_ENST00000548883.1_Missense_Mutation_p.R293W|C12orf42_ENST00000315192.8_Intron	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	293										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						CTCCTGTCCCGCGGGGTATGA	0.652																																					p.R293W		Atlas-SNP	.											.	C12orf42	50	.	0			c.C877T						.						33.0	38.0	37.0					12																	103696092		1946	4154	6100	SO:0001583	missense	374470	exon6			TGTCCCGCGGGGT	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.877C>T	chr12.hg19:g.103696092G>A	ENSP00000367353:p.Arg293Trp	45.0	0.0		75.0	10.0	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	hg19	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.920532	0.52653	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113	T;T;T	0.49432	0.78;0.78;0.78	4.75	-4.14	0.03892	.	1.597520	0.04173	N	0.325091	T	0.26955	0.0660	N	0.24115	0.695	0.09310	N	1	B	0.27166	0.17	B	0.20184	0.028	T	0.23332	-1.0191	10	0.66056	D	0.02	-0.607	0.4303	0.00470	0.2949:0.1302:0.2716:0.3033	.	293	Q96LP6	CL042_HUMAN	W	293;226;293	ENSP00000447908:R293W;ENSP00000449362:R226W;ENSP00000367353:R293W	ENSP00000367353:R293W	R	-	1	2	C12orf42	102220222	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.312000	0.08113	-0.207000	0.10187	-0.211000	0.12701	CGG	.	.		0.652	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521	
NOS1	4842	hgsc.bcm.edu	37	12	117710212	117710212	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:117710212T>C	ENST00000338101.4	-	9	1821	c.1817A>G	c.(1816-1818)aAc>aGc	p.N606S	NOS1_ENST00000317775.6_Missense_Mutation_p.N606S|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTAGCGGGAGTTGTCACAGTA	0.587																																					p.N606S	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.A1817G						.						78.0	87.0	84.0					12																	117710212		2193	4296	6489	SO:0001583	missense	4842	exon10			CGGGAGTTGTCAC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1817A>G	chr12.hg19:g.117710212T>C	ENSP00000337459:p.Asn606Ser	51.0	0.0		96.0	8.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	6.547	0.469221	0.12461	.	.	ENSG00000089250	ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.20598	2.06;2.06	4.7	2.36	0.29203	Nitric oxide synthase, oxygenase domain (2);	0.224065	0.52532	N	0.000067	T	0.04407	0.0121	N	0.00268	-1.735	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27673	-1.0067	10	0.18276	T	0.48	-19.7626	8.3814	0.32474	0.0:0.2441:0.0:0.7559	.	606	P29475	NOS1_HUMAN	S	606	ENSP00000320758:N606S;ENSP00000337459:N606S	ENSP00000320758:N606S	N	-	2	0	NOS1	116194595	0.990000	0.36364	0.988000	0.46212	0.990000	0.78478	0.231000	0.17872	0.324000	0.23333	0.533000	0.62120	AAC	.	.		0.587	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
MTMR6	9107	hgsc.bcm.edu	37	13	25823570	25823570	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr13:25823570A>C	ENST00000381801.5	-	14	2427	c.1666T>G	c.(1666-1668)Tca>Gca	p.S556A	MTMR6_ENST00000540661.1_Intron|AL590787.1_ENST00000408397.1_RNA	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	556					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GGATGAACTGAATGTAACAAT	0.368																																					p.S556A		Atlas-SNP	.											.	MTMR6	75	.	0			c.T1666G						.						149.0	142.0	145.0					13																	25823570		2203	4300	6503	SO:0001583	missense	9107	exon14			GAACTGAATGTAA	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1666T>G	chr13.hg19:g.25823570A>C	ENSP00000371221:p.Ser556Ala	141.0	0.0		237.0	58.0	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	hg19	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.711226	0.00712	.	.	ENSG00000139505	ENST00000381801;ENST00000319298	D	0.94046	-3.34	5.87	0.686	0.18015	.	0.861348	0.10383	N	0.681302	D	0.86539	0.5957	L	0.39147	1.195	0.45490	D	0.998459	B	0.02656	0.0	B	0.04013	0.001	T	0.74751	-0.3559	10	0.23302	T	0.38	.	2.6648	0.05041	0.5311:0.2354:0.1255:0.108	.	556	Q9Y217	MTMR6_HUMAN	A	556;124	ENSP00000371221:S556A	ENSP00000317987:S124A	S	-	1	0	MTMR6	24721570	0.096000	0.21769	0.012000	0.15200	0.023000	0.10783	0.591000	0.23969	0.182000	0.20032	0.533000	0.62120	TCA	.	.		0.368	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685	
ERICH6B	220081	hgsc.bcm.edu	37	13	46135603	46135603	+	Silent	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr13:46135603A>G	ENST00000298738.2	-	11	1472	c.1308T>C	c.(1306-1308)ccT>ccC	p.P436P		NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		436										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						CAGGCTTCTCAGGTGTTGGTT	0.383																																					p.P436P		Atlas-SNP	.											.	FAM194B	42	.	0			c.T1308C						.						284.0	230.0	246.0					13																	46135603		692	1591	2283	SO:0001819	synonymous_variant	220081	exon11			CTTCTCAGGTGTT																												ENST00000298738.2:c.1308T>C	chr13.hg19:g.46135603A>G		149.0	0.0		382.0	35.0	NM_182542	Q96MB5	Silent	SNP	ENST00000298738.2	hg19	CCDS45045.1																																																																																			.	.		0.383	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
SLC15A1	6564	hgsc.bcm.edu	37	13	99371494	99371494	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr13:99371494G>A	ENST00000376503.5	-	8	692	c.637C>T	c.(637-639)Ctg>Ttg	p.L213L		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	213					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CACTTACTCAGGGCTACAGCC	0.443																																					p.L213L		Atlas-SNP	.											.	SLC15A1	92	.	0			c.C637T						.						128.0	131.0	130.0					13																	99371494		2203	4300	6503	SO:0001819	synonymous_variant	6564	exon8			TACTCAGGGCTAC	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.637C>T	chr13.hg19:g.99371494G>A		25.0	0.0		53.0	18.0	NM_005073	Q5VW82	Silent	SNP	ENST00000376503.5	hg19	CCDS9489.1																																																																																			.	.		0.443	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72054832	72054832	+	Silent	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr14:72054832A>T	ENST00000555818.1	+	2	591	c.243A>T	c.(241-243)gcA>gcT	p.A81A	SIPA1L1_ENST00000358550.2_Silent_p.A81A|SIPA1L1_ENST00000381232.3_Silent_p.A81A	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	81					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CAAGGATTGCAGATTGGCCCC	0.493																																					p.A81A		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.A243T						.						87.0	95.0	92.0					14																	72054832		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon2			GATTGCAGATTGG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.243A>T	chr14.hg19:g.72054832A>T		63.0	0.0		103.0	46.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.493	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
ATG2B	55102	hgsc.bcm.edu	37	14	96809512	96809512	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr14:96809512A>T	ENST00000359933.4	-	5	1581	c.688T>A	c.(688-690)Tgg>Agg	p.W230R		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	230					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AACTCATCCCAGAAGAGAGAC	0.413																																					p.W230R		Atlas-SNP	.											.	ATG2B	169	.	0			c.T688A						.						99.0	94.0	95.0					14																	96809512		1886	4117	6003	SO:0001583	missense	55102	exon5			CATCCCAGAAGAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.688T>A	chr14.hg19:g.96809512A>T	ENSP00000353010:p.Trp230Arg	106.0	0.0		192.0	14.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032808	0.75504	.	.	ENSG00000066739	ENST00000359933	T	0.09817	2.94	5.31	5.31	0.75309	.	0.265541	0.33515	U	0.004839	T	0.19846	0.0477	N	0.22421	0.69	0.58432	D	0.999997	D	0.76494	0.999	D	0.85130	0.997	T	0.06607	-1.0817	10	0.30078	T	0.28	.	15.2648	0.73651	1.0:0.0:0.0:0.0	.	230	Q96BY7	ATG2B_HUMAN	R	230	ENSP00000353010:W230R	ENSP00000353010:W230R	W	-	1	0	ATG2B	95879265	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.730000	0.91510	2.007000	0.58848	0.482000	0.46254	TGG	.	.		0.413	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
BLOC1S6	26258	hgsc.bcm.edu	37	15	45884374	45884374	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:45884374T>A	ENST00000220531.3	+	2	445	c.124T>A	c.(124-126)Ttg>Atg	p.L42M	BLOC1S6_ENST00000568816.1_5'UTR|BLOC1S6_ENST00000565323.1_Missense_Mutation_p.L47M|BLOC1S6_ENST00000565409.1_5'UTR|Y_RNA_ENST00000363549.1_RNA|BLOC1S6_ENST00000566753.1_Missense_Mutation_p.L42M|BLOC1S6_ENST00000565216.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000562384.1_Intron|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000564765.1_5'UTR|BLOC1S6_ENST00000567461.1_Intron	NM_012388.2	NP_036520.1	Q9UL45	BL1S6_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	42					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|endosome to melanosome transport (GO:0035646)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of pigment cell differentiation (GO:0050942)|post-Golgi vesicle-mediated transport (GO:0006892)|secretion of lysosomal enzymes (GO:0033299)|synaptic vesicle docking involved in exocytosis (GO:0016081)	BLOC-1 complex (GO:0031083)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|transport vesicle (GO:0030133)	actin filament binding (GO:0051015)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)										AATAGAGGACTTGACTATAGA	0.398																																					p.L42M		Atlas-SNP	.											.	.	.	.	0			c.T124A						.						94.0	93.0	93.0					15																	45884374		2198	4298	6496	SO:0001583	missense	26258	exon2			GAGGACTTGACTA	AF080470	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164		"""Biogenesis of lysosomal organelles complex-1 subunits"""	8549	protein-coding gene	gene with protein product		604310	"""pallid (mouse) homolog, pallidin"", ""pallidin homolog (mouse)"""	PA, PLDN		10610180	Standard	NM_012388		Approved	HPS9	uc001zvq.3	Q9UL45	OTTHUMG00000131477	ENST00000220531.3:c.124T>A	chr15.hg19:g.45884374T>A	ENSP00000220531:p.Leu42Met	53.0	0.0		73.0	25.0	NM_012388		Missense_Mutation	SNP	ENST00000220531.3	hg19	CCDS10126.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.467683	0.63625	.	.	ENSG00000104164	ENST00000220531	.	.	.	5.74	0.369	0.16151	.	0.559941	0.20041	N	0.100502	T	0.47563	0.1452	L	0.47716	1.5	0.58432	D	0.999999	P	0.40875	0.731	P	0.47528	0.549	T	0.39781	-0.9597	9	0.59425	D	0.04	1.1294	4.9159	0.13846	0.0:0.1755:0.295:0.5295	.	42	Q9UL45	PLDN_HUMAN	M	42	.	ENSP00000220531:L42M	L	+	1	2	PLDN	43671666	0.159000	0.22864	0.409000	0.26459	0.884000	0.51177	-0.555000	0.05999	0.085000	0.17107	0.460000	0.39030	TTG	.	.		0.398	BLOC1S6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254320.2	NM_012388	
RFX7	64864	hgsc.bcm.edu	37	15	56387953	56387953	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:56387953T>C	ENST00000559447.2	-	9	1953	c.1682A>G	c.(1681-1683)aAa>aGa	p.K561R	RFX7_ENST00000317318.6_Missense_Mutation_p.K658R|RFX7_ENST00000423270.1_Missense_Mutation_p.K658R|RFX7_ENST00000422057.1_Missense_Mutation_p.K561R			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	561					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGACAGTCGTTTTCTTGGGCT	0.448																																					p.K658R		Atlas-SNP	.											.	RFX7	170	.	0			c.A1973G						.						97.0	94.0	95.0					15																	56387953		1901	4113	6014	SO:0001583	missense	64864	exon9			AGTCGTTTTCTTG			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1682A>G	chr15.hg19:g.56387953T>C	ENSP00000453281:p.Lys561Arg	87.0	0.0		151.0	55.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.2	4.119947	0.77323	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.54675	0.56;0.56;0.56	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.54415	0.1857	N	0.24115	0.695	0.58432	D	0.999991	D;D	0.67145	0.996;0.996	P;P	0.60609	0.877;0.877	T	0.51513	-0.8696	10	0.26408	T	0.33	-15.3416	14.6501	0.68792	0.0:0.0:0.0:1.0	.	561;561	Q2KHR2;C9JU50	RFX7_HUMAN;.	R	561;658;658	ENSP00000387504:K561R;ENSP00000313299:K658R;ENSP00000397644:K658R	ENSP00000313299:K658R	K	-	2	0	RFX7	54175245	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.193000	0.77780	2.030000	0.59900	0.533000	0.62120	AAA	.	.		0.448	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
ANP32A	8125	hgsc.bcm.edu	37	15	69076893	69076893	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:69076893G>A	ENST00000465139.2	-	4	512	c.369C>T	c.(367-369)tgC>tgT	p.C123C	ANP32A_ENST00000560303.1_Silent_p.C123C|ANP32A_ENST00000483551.2_5'UTR	NM_006305.3	NP_006296.1	P39687	AN32A_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	123	LRRCT.				gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|nucleocytoplasmic transport (GO:0006913)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						TGGTTACCTCGCAATTGAAAA	0.483																																					p.C123C		Atlas-SNP	.											.	ANP32A	15	.	0			c.C369T						.						93.0	98.0	96.0					15																	69076893		2200	4298	6498	SO:0001819	synonymous_variant	8125	exon4			TACCTCGCAATTG	AF025684	CCDS45292.1	15q23	2008-05-14			ENSG00000140350	ENSG00000140350		"""ANP32 acidic nuclear phosphoproteins"""	13233	protein-coding gene	gene with protein product		600832		C15orf1		8970164, 9144194	Standard	NM_006305		Approved	LANP, PP32, I1PP2A, PHAPI, MAPM, mapmodulin	uc002arl.3	P39687	OTTHUMG00000154502	ENST00000465139.2:c.369C>T	chr15.hg19:g.69076893G>A		120.0	0.0		255.0	60.0	NM_006305	B2R6T4|Q53FK4|Q5J8L8|Q7M4N6	Silent	SNP	ENST00000465139.2	hg19	CCDS45292.1																																																																																			.	.		0.483	ANP32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335525.2		
RCN2	5955	hgsc.bcm.edu	37	15	77227917	77227917	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:77227917G>A	ENST00000394885.3	+	3	524	c.301G>A	c.(301-303)Gaa>Aaa	p.E101K	RCN2_ENST00000394883.3_Intron|RCN2_ENST00000320963.5_Missense_Mutation_p.E101K	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	101	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						TGCTATGCAAGAAGCAAAACA	0.348																																					p.E101K		Atlas-SNP	.											.	RCN2	16	.	0			c.G301A						.						165.0	146.0	153.0					15																	77227917		2196	4294	6490	SO:0001583	missense	5955	exon3			ATGCAAGAAGCAA	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"""EF-hand domain containing"""	9935	protein-coding gene	gene with protein product	"""Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"""	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.301G>A	chr15.hg19:g.77227917G>A	ENSP00000378349:p.Glu101Lys	53.0	0.0		74.0	20.0	NM_002902	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408127	0.96051	.	.	ENSG00000117906	ENST00000394885;ENST00000320963	T;T	0.74315	-0.83;-0.83	5.47	5.47	0.80525	EF-hand-like domain (1);	0.048133	0.85682	D	0.000000	T	0.81475	0.4830	M	0.80183	2.485	0.80722	D	1	D;P	0.53462	0.96;0.92	P;P	0.47603	0.497;0.551	D	0.84779	0.0772	10	0.72032	D	0.01	-22.0183	19.328	0.94270	0.0:0.0:1.0:0.0	.	101;101	F8WCY5;Q14257	.;RCN2_HUMAN	K	101	ENSP00000378349:E101K;ENSP00000319739:E101K	ENSP00000319739:E101K	E	+	1	0	RCN2	75014972	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.789000	0.91839	2.559000	0.86315	0.591000	0.81541	GAA	.	.		0.348	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902	
FAM169B	283777	hgsc.bcm.edu	37	15	99023985	99023985	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:99023985C>G	ENST00000558256.1	-	4	277	c.28G>C	c.(28-30)Gtt>Ctt	p.V10L	FAM169B_ENST00000332908.4_Missense_Mutation_p.V10L	NM_182562.2	NP_872368.2	Q8N8A8	F169B_HUMAN	family with sequence similarity 169, member B	10										large_intestine(3)|lung(3)|urinary_tract(1)	7						AAAAGCACAACCCTTTCCCCA	0.373																																					p.V10L		Atlas-SNP	.											.	FAM169B	23	.	0			c.G28C						.						72.0	69.0	70.0					15																	99023985		1864	4095	5959	SO:0001583	missense	283777	exon4			GCACAACCCTTTC		CCDS45360.1	15q26.3	2008-08-08			ENSG00000185087	ENSG00000185087			26835	protein-coding gene	gene with protein product							Standard	NM_182562		Approved	FLJ39743, KIAA0888L	uc002buk.1	Q8N8A8		ENST00000558256.1:c.28G>C	chr15.hg19:g.99023985C>G	ENSP00000453554:p.Val10Leu	63.0	0.0		105.0	29.0	NM_182562	B5MDL8	Missense_Mutation	SNP	ENST00000558256.1	hg19	CCDS45360.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.608089	0.28623	.	.	ENSG00000185087	ENST00000332908	T	0.72282	-0.64	5.27	2.89	0.33648	.	0.290655	0.33110	N	0.005280	T	0.50411	0.1614	N	0.17082	0.46	0.26442	N	0.975758	B	0.02656	0.0	B	0.01281	0.0	T	0.39231	-0.9624	10	0.44086	T	0.13	-9.8168	7.3417	0.26640	0.0:0.0771:0.1438:0.7791	.	10	Q8N8A8	F169B_HUMAN	L	10	ENSP00000332615:V10L	ENSP00000332615:V10L	V	-	1	0	FAM169B	96841508	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.945000	0.40273	0.283000	0.22279	-0.294000	0.09567	GTT	.	.		0.373	FAM169B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415488.1	NM_182562	
KIAA0556	23247	hgsc.bcm.edu	37	16	27761333	27761333	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:27761333A>G	ENST00000261588.4	+	16	3071	c.3052A>G	c.(3052-3054)Atc>Gtc	p.I1018V		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1018						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CCCTCCCGATATCAATATTTT	0.527																																					p.I1018V		Atlas-SNP	.											.	KIAA0556	348	.	0			c.A3052G						.						41.0	40.0	40.0					16																	27761333		2197	4300	6497	SO:0001583	missense	23247	exon16			CCCGATATCAATA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3052A>G	chr16.hg19:g.27761333A>G	ENSP00000261588:p.Ile1018Val	54.0	0.0		83.0	14.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.844112	0.51164	.	.	ENSG00000047578	ENST00000261588	T	0.15834	2.39	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.22975	0.0555	L	0.39147	1.195	0.42620	D	0.993346	P	0.40302	0.712	P	0.47573	0.55	T	0.01617	-1.1311	10	0.34782	T	0.22	-11.2124	15.0765	0.72080	1.0:0.0:0.0:0.0	.	1018	O60303	K0556_HUMAN	V	1018	ENSP00000261588:I1018V	ENSP00000261588:I1018V	I	+	1	0	KIAA0556	27668834	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	7.377000	0.79668	2.085000	0.62840	0.533000	0.62120	ATC	.	.		0.527	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
FUS	2521	hgsc.bcm.edu	37	16	31201608	31201608	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:31201608G>T	ENST00000254108.7	+	12	1286	c.1181G>T	c.(1180-1182)cGt>cTt	p.R394L	FUS_ENST00000474990.1_3'UTR|FUS_ENST00000380244.3_Missense_Mutation_p.R393L|FUS_ENST00000568685.1_Missense_Mutation_p.R395L	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	394	Arg/Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		CCCATGGGCCgtggaggctat	0.567			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																p.R394L		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	.	0			c.G1181T						.						144.0	110.0	121.0					16																	31201608		2197	4300	6497	SO:0001583	missense	2521	exon12			TGGGCCGTGGAGG	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1181G>T	chr16.hg19:g.31201608G>T	ENSP00000254108:p.Arg394Leu	84.0	0.0		168.0	29.0	NM_004960	Q9H4A8	Missense_Mutation	SNP	ENST00000254108.7	hg19	CCDS10707.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726726	0.48833	.	.	ENSG00000089280	ENST00000254108;ENST00000380244;ENST00000394533	D	0.97114	-4.25	5.31	3.35	0.38373	.	0.360924	0.28796	N	0.014116	D	0.93976	0.8071	L	0.50333	1.59	0.58432	D	0.999991	B;P;P;P;P;P	0.44429	0.145;0.835;0.704;0.804;0.835;0.704	B;B;B;B;B;B	0.38985	0.073;0.264;0.149;0.287;0.264;0.149	D	0.90342	0.4360	10	0.24483	T	0.36	-1.1004	11.0266	0.47748	0.155:0.0:0.845:0.0	.	393;394;394;393;168;394	A8K4H1;Q8TBR3;Q6IBQ5;P35637-2;Q59H57;P35637	.;.;.;.;.;FUS_HUMAN	L	394;121;323	ENSP00000254108:R394L	ENSP00000254108:R394L	R	+	2	0	FUS	31109109	1.000000	0.71417	0.993000	0.49108	0.542000	0.35054	8.422000	0.90262	0.622000	0.30249	-0.150000	0.13652	CGT	.	.		0.567	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
FTO	79068	hgsc.bcm.edu	37	16	53878098	53878098	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:53878098T>A	ENST00000471389.1	+	4	1005	c.783T>A	c.(781-783)caT>caA	p.H261Q	FTO_ENST00000394647.3_5'UTR	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	261	Fe2OG dioxygenase domain.				adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						ATGACTCTCATCTCGAAGGCA	0.418																																					p.H261Q		Atlas-SNP	.											.	FTO	51	.	0			c.T783A						.						149.0	137.0	141.0					16																	53878098		2198	4300	6498	SO:0001583	missense	79068	exon4			CTCTCATCTCGAA	BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.783T>A	chr16.hg19:g.53878098T>A	ENSP00000418823:p.His261Gln	107.0	0.0		203.0	34.0	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	hg19	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.814678	0.32053	.	.	ENSG00000140718	ENST00000471389	T	0.62105	0.05	5.81	-8.48	0.00935	Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain (1);	1.011690	0.07895	N	0.971788	T	0.22282	0.0537	N	0.02011	-0.69	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.17561	-1.0365	10	0.11182	T	0.66	-1.814	2.9424	0.05835	0.3523:0.1889:0.3573:0.1014	.	261	Q9C0B1	FTO_HUMAN	Q	261	ENSP00000418823:H261Q	ENSP00000418823:H261Q	H	+	3	2	FTO	52435599	0.000000	0.05858	0.000000	0.03702	0.535000	0.34838	-1.869000	0.01643	-1.627000	0.01550	0.533000	0.62120	CAT	.	.		0.418	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
CES3	23491	hgsc.bcm.edu	37	16	67006590	67006590	+	Silent	SNP	G	G	A	rs377447761		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr16:67006590G>A	ENST00000303334.4	+	12	1532	c.1461G>A	c.(1459-1461)gaG>gaA	p.E487E	CES3_ENST00000394037.1_Silent_p.E484E|CES3_ENST00000543856.1_Silent_p.E126E	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	487						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		AGGCCACAGAGGAGGAGAAGC	0.587																																					p.E487E		Atlas-SNP	.											.	CES3	56	.	0			c.G1461A						.	G	,,	1,4399	2.1+/-5.4	0,1,2199	83.0	76.0	78.0		378,1452,1461	2.0	1.0	16		78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CES3	NM_001185176.1,NM_001185177.1,NM_024922.5	,,	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	,,	126/211,484/569,487/572	67006590	1,12999	2200	4300	6500	SO:0001819	synonymous_variant	23491	exon12			CACAGAGGAGGAG	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1461G>A	chr16.hg19:g.67006590G>A		43.0	0.0		66.0	17.0	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Silent	SNP	ENST00000303334.4	hg19	CCDS10826.1																																																																																			.	.		0.587	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
CLUH	23277	hgsc.bcm.edu	37	17	2604781	2604781	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:2604781C>T	ENST00000570628.2	-	6	769	c.664G>A	c.(664-666)Gga>Aga	p.G222R	CLUH_ENST00000538975.1_Missense_Mutation_p.G222R|CLUH_ENST00000435359.1_Missense_Mutation_p.G222R			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	222					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GGGTTCCATCCGCTCATGGTG	0.657																																					p.G222R		Atlas-SNP	.											.	.	.	.	0			c.G664A						.						30.0	36.0	34.0					17																	2604781		1981	4154	6135	SO:0001583	missense	23277	exon6			TCCATCCGCTCAT	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.664G>A	chr17.hg19:g.2604781C>T	ENSP00000458986:p.Gly222Arg	23.0	0.0		53.0	18.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.509303	0.85282	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	T;T	0.80738	-1.41;-1.41	4.75	4.75	0.60458	GSKIP/TIF31 domain (1);	0.048785	0.85682	D	0.000000	D	0.86802	0.6020	M	0.77820	2.39	0.80722	D	1	D;D	0.65815	0.988;0.995	P;P	0.54346	0.749;0.749	D	0.88515	0.3092	10	0.59425	D	0.04	.	16.898	0.86106	0.0:1.0:0.0:0.0	.	222;222	O75153;C9J6D7	K0664_HUMAN;.	R	222	ENSP00000388872:G222R;ENSP00000439628:G222R	ENSP00000320468:G222R	G	-	1	0	KIAA0664	2551531	1.000000	0.71417	0.994000	0.49952	0.833000	0.47200	5.862000	0.69560	2.476000	0.83614	0.591000	0.81541	GGA	.	.		0.657	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
TMEM102	284114	hgsc.bcm.edu	37	17	7339378	7339378	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:7339378C>T	ENST00000323206.1	+	2	461	c.188C>T	c.(187-189)gCc>gTc	p.A63V	TMEM102_ENST00000396568.1_Missense_Mutation_p.A63V|FGF11_ENST00000293829.4_5'Flank|RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000575235.1_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	63					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				CTCCTCCGGGCCAAGGACTTT	0.632																																					p.A63V		Atlas-SNP	.											.	TMEM102	11	.	0			c.C188T						.						88.0	114.0	105.0					17																	7339378		2203	4299	6502	SO:0001583	missense	284114	exon2			TCCGGGCCAAGGA	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.188C>T	chr17.hg19:g.7339378C>T	ENSP00000315387:p.Ala63Val	46.0	0.0		132.0	46.0	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	hg19	CCDS11104.1	.	.	.	.	.	.	.	.	.	.	C	33	5.232363	0.95207	.	.	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.54479	0.57;0.57	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000039	T	0.72087	0.3417	M	0.72894	2.215	0.51012	D	0.999909	D	0.89917	1.0	D	0.74674	0.984	T	0.74237	-0.3730	10	0.72032	D	0.01	-8.6371	17.2341	0.86994	0.0:1.0:0.0:0.0	.	63	Q8N9M5	TM102_HUMAN	V	63	ENSP00000315387:A63V;ENSP00000379815:A63V	ENSP00000315387:A63V	A	+	2	0	TMEM102	7280102	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.801000	0.62532	2.652000	0.90054	0.655000	0.94253	GCC	.	.		0.632	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518	
MYH1	4619	hgsc.bcm.edu	37	17	10404577	10404577	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:10404577C>T	ENST00000226207.5	-	27	3682	c.3588G>A	c.(3586-3588)ctG>ctA	p.L1196L	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1196					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GCTTCTTCCTCAGGGTGGCCG	0.562																																					p.L1196L		Atlas-SNP	.											.	MYH1	403	.	0			c.G3588A						.						88.0	86.0	87.0					17																	10404577		2203	4300	6503	SO:0001819	synonymous_variant	4619	exon27			CTTCCTCAGGGTG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3588G>A	chr17.hg19:g.10404577C>T		103.0	0.0		183.0	51.0	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	hg19	CCDS11155.1																																																																																			.	.		0.562	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
DNAH9	1770	hgsc.bcm.edu	37	17	11786904	11786904	+	Splice_Site	SNP	C	C	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:11786904C>A	ENST00000262442.4	+	56	10876	c.10808C>A	c.(10807-10809)tCc>tAc	p.S3603Y	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Splice_Site_p.S3603Y|DNAH9_ENST00000608377.1_5'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3603	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TATTTGCAGTCCGATCTCACA	0.498																																					p.S3603Y		Atlas-SNP	.											.	DNAH9	695	.	0			c.C10808A						.						112.0	99.0	103.0					17																	11786904		2203	4300	6503	SO:0001630	splice_region_variant	1770	exon56			TGCAGTCCGATCT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10807-1C>A	chr17.hg19:g.11786904C>A		52.0	0.0		73.0	15.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197228	0.79015	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.27557	1.66;1.66	4.91	4.91	0.64330	.	0.200493	0.45361	D	0.000376	T	0.58708	0.2141	M	0.84948	2.725	0.80722	D	1	P	0.40211	0.707	P	0.55667	0.781	T	0.63323	-0.6663	10	0.72032	D	0.01	.	18.6493	0.91425	0.0:1.0:0.0:0.0	.	3603	Q9NYC9	DYH9_HUMAN	Y	3603;3603;2185	ENSP00000262442:S3603Y;ENSP00000414874:S3603Y	ENSP00000262442:S3603Y	S	+	2	0	DNAH9	11727629	0.998000	0.40836	0.984000	0.44739	0.961000	0.63080	3.923000	0.56469	2.709000	0.92574	0.655000	0.94253	TCC	.	.		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	Missense_Mutation
ARHGAP44	9912	hgsc.bcm.edu	37	17	12819314	12819314	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:12819314T>A	ENST00000379672.5	+	5	673	c.373T>A	c.(373-375)Ttt>Att	p.F125I	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.F125I|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.F125I|MIR1269B_ENST00000580405.1_RNA	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	125	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						TGAGCCCCTGTTTTTGCTGGC	0.522																																					p.F125I		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.T373A						.						80.0	81.0	80.0					17																	12819314		2080	4207	6287	SO:0001583	missense	9912	exon5			CCCCTGTTTTTGC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.373T>A	chr17.hg19:g.12819314T>A	ENSP00000368994:p.Phe125Ile	61.0	0.0		99.0	29.0	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	hg19	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.667102	0.47677	.	.	ENSG00000006740	ENST00000379672;ENST00000340825	T;T	0.63096	-0.02;-0.02	5.92	5.92	0.95590	BAR (3);	0.182798	0.49916	D	0.000131	T	0.51398	0.1672	N	0.22421	0.69	0.41260	D	0.986773	P;B	0.38677	0.642;0.409	B;B	0.41135	0.316;0.348	T	0.50668	-0.8801	10	0.25106	T	0.35	.	14.3183	0.66468	0.0:0.0:0.0:1.0	.	125;125	A6NCP5;Q17R89	.;RHG44_HUMAN	I	125	ENSP00000368994:F125I;ENSP00000342566:F125I	ENSP00000342566:F125I	F	+	1	0	ARHGAP44	12760039	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	5.166000	0.64965	2.274000	0.75844	0.533000	0.62120	TTT	.	.		0.522	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
PTRF	284119	hgsc.bcm.edu	37	17	40574856	40574856	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:40574856T>A	ENST00000357037.5	-	1	679	c.260A>T	c.(259-261)cAg>cTg	p.Q87L		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		CTGGATGCTCTGCACTGCGCC	0.627																																					p.Q87L		Atlas-SNP	.											.	PTRF	48	.	0			c.A260T						.						54.0	37.0	43.0					17																	40574856		2203	4300	6503	SO:0001583	missense	284119	exon1			ATGCTCTGCACTG	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.260A>T	chr17.hg19:g.40574856T>A	ENSP00000349541:p.Gln87Leu	44.0	0.0		98.0	24.0	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.667526	0.47677	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.58940	0.3	5.12	5.12	0.69794	.	0.749618	0.13072	N	0.416048	T	0.39200	0.1069	N	0.22421	0.69	0.27481	N	0.952569	B;B	0.12013	0.005;0.003	B;B	0.14023	0.01;0.01	T	0.21930	-1.0231	10	0.49607	T	0.09	-42.1904	2.4995	0.04630	0.1369:0.082:0.2341:0.547	.	87;87	B4DNU9;Q6NZI2	.;PTRF_HUMAN	L	87;42	ENSP00000349541:Q87L	ENSP00000349541:Q87L	Q	-	2	0	PTRF	37828382	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.907000	0.39897	1.917000	0.55516	0.454000	0.30748	CAG	.	.		0.627	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232	
GPATCH8	23131	hgsc.bcm.edu	37	17	42475346	42475346	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:42475346C>T	ENST00000591680.1	-	8	4129	c.4099G>A	c.(4099-4101)Gcc>Acc	p.A1367T	GPATCH8_ENST00000434000.1_Missense_Mutation_p.A1289T	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1367							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GTGGCAGAGGCTGTAGCTGGC	0.607																																					p.A1367T		Atlas-SNP	.											.	GPATCH8	114	.	0			c.G4099A						.						88.0	64.0	72.0					17																	42475346		2203	4300	6503	SO:0001583	missense	23131	exon8			CAGAGGCTGTAGC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.4099G>A	chr17.hg19:g.42475346C>T	ENSP00000467556:p.Ala1367Thr	80.0	0.0		206.0	12.0	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.730358	0.69074	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.14391	2.51	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.01198	-1.1421	10	0.46703	T	0.11	-12.7618	18.199	0.89832	0.0:1.0:0.0:0.0	.	1367	Q9UKJ3	GPTC8_HUMAN	T	1367;1289	ENSP00000395016:A1289T	ENSP00000335486:A1367T	A	-	1	0	GPATCH8	39830872	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.327000	0.79147	2.391000	0.81399	0.305000	0.20034	GCC	.	.		0.607	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552916	43552916	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr17:43552916G>T	ENST00000430334.3	-	4	606	c.473C>A	c.(472-474)gCt>gAt	p.A158D	PLEKHM1_ENST00000421073.2_Missense_Mutation_p.A69D	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	158	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GCCCTCCTCAGCATCCCGGAG	0.597																																					p.A158D		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C473A						.						45.0	43.0	44.0					17																	43552916		2202	4300	6502	SO:0001583	missense	9842	exon4			TCCTCAGCATCCC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.473C>A	chr17.hg19:g.43552916G>T	ENSP00000389913:p.Ala158Asp	71.0	0.0		114.0	8.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782605	0.31502	.	.	ENSG00000225190	ENST00000430334;ENST00000446609;ENST00000421073	T;T	0.10477	2.87;2.87	5.03	5.03	0.67393	RUN (3);	0.123631	0.53938	D	0.000054	T	0.19565	0.0470	L	0.28504	0.86	0.50813	D	0.999891	D;D	0.69078	0.993;0.997	P;D	0.69824	0.854;0.966	T	0.05818	-1.0862	10	0.11794	T	0.64	.	17.1001	0.86647	0.0:0.0:1.0:0.0	.	69;158	F8W648;Q9Y4G2	.;PKHM1_HUMAN	D	158;107;69	ENSP00000389913:A158D;ENSP00000414352:A69D	ENSP00000414352:A69D	A	-	2	0	PLEKHM1	40908699	0.983000	0.35010	0.671000	0.29857	0.293000	0.27360	6.217000	0.72218	2.608000	0.88229	0.655000	0.94253	GCT	.	.		0.597	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
SMCHD1	23347	hgsc.bcm.edu	37	18	2795979	2795979	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:2795979A>T	ENST00000320876.6	+	46	6090	c.5752A>T	c.(5752-5754)Aaa>Taa	p.K1918*	RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1918					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TGCTGTGTGCAAACTAGACAG	0.358																																					p.K1918X		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A5752T						.						49.0	44.0	46.0					18																	2795979		1881	4109	5990	SO:0001587	stop_gained	23347	exon46			GTGTGCAAACTAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5752A>T	chr18.hg19:g.2795979A>T	ENSP00000326603:p.Lys1918*	130.0	0.0		281.0	80.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Nonsense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	47	13.308776	0.99733	.	.	ENSG00000101596	ENST00000320876	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6976	14.5973	0.68415	1.0:0.0:0.0:0.0	.	.	.	.	X	1918	.	ENSP00000326603:K1918X	K	+	1	0	SMCHD1	2785979	0.996000	0.38824	0.185000	0.23176	0.281000	0.26958	6.053000	0.71089	2.174000	0.68829	0.533000	0.62120	AAA	.	.		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
LPIN2	9663	hgsc.bcm.edu	37	18	2925247	2925247	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:2925247G>C	ENST00000261596.4	-	14	2151	c.1913C>G	c.(1912-1914)tCt>tGt	p.S638C		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	638	C-LIP.				cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		GAGGCGGAGAGACTTCTTATA	0.493																																					p.S638C		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1913G						.						98.0	95.0	96.0					18																	2925247		2203	4300	6503	SO:0001583	missense	9663	exon14			CGGAGAGACTTCT	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.1913C>G	chr18.hg19:g.2925247G>C	ENSP00000261596:p.Ser638Cys	88.0	0.0		186.0	53.0	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.998856	0.54147	.	.	ENSG00000101577	ENST00000261596	D	0.82433	-1.61	4.41	4.41	0.53225	.	0.117372	0.64402	D	0.000012	D	0.91690	0.7373	M	0.88775	2.98	0.80722	D	1	D	0.67145	0.996	P	0.62813	0.907	D	0.93294	0.6671	10	0.62326	D	0.03	-17.4867	17.9017	0.88906	0.0:0.0:1.0:0.0	.	638	Q92539	LPIN2_HUMAN	C	638	ENSP00000261596:S638C	ENSP00000261596:S638C	S	-	2	0	LPIN2	2915247	1.000000	0.71417	0.997000	0.53966	0.084000	0.17831	9.214000	0.95140	2.366000	0.80165	0.563000	0.77884	TCT	.	.		0.493	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646	
ZNF519	162655	hgsc.bcm.edu	37	18	14105690	14105690	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:14105690C>T	ENST00000590202.1	-	3	1001	c.849G>A	c.(847-849)caG>caA	p.Q283Q	ZNF519_ENST00000589498.1_Intron|ZNF519_ENST00000589203.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	283					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						TATGAATTTTCTGATGTCCAA	0.368																																					p.Q283Q		Atlas-SNP	.											.	ZNF519	53	.	0			c.G849A						.						49.0	54.0	52.0					18																	14105690		2203	4299	6502	SO:0001819	synonymous_variant	162655	exon3			AATTTTCTGATGT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.849G>A	chr18.hg19:g.14105690C>T		52.0	0.0		42.0	7.0	NM_145287		Silent	SNP	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.		0.368	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
DSG4	147409	hgsc.bcm.edu	37	18	28956907	28956907	+	Silent	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:28956907T>C	ENST00000308128.4	+	1	168	c.33T>C	c.(31-33)ctT>ctC	p.L11L	RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Silent_p.L11L|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	11					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACATTTGCCTTTTGATCATTC	0.428																																					p.L11L		Atlas-SNP	.											.	DSG4	343	.	0			c.T33C						.						108.0	93.0	98.0					18																	28956907		2203	4300	6503	SO:0001819	synonymous_variant	147409	exon1			TTGCCTTTTGATC	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.33T>C	chr18.hg19:g.28956907T>C		84.0	0.0		142.0	53.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.		0.428	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
ASXL3	80816	hgsc.bcm.edu	37	18	31314285	31314285	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:31314285C>T	ENST00000269197.5	+	10	988	c.988C>T	c.(988-990)Cca>Tca	p.P330S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	330					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(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AGAGTTTACCCCAGAAATGCA	0.308																																					p.P330S		Atlas-SNP	.											.	ASXL3	405	.	0			c.C988T						.						51.0	50.0	50.0					18																	31314285		1798	4059	5857	SO:0001583	missense	80816	exon10			TTTACCCCAGAAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.988C>T	chr18.hg19:g.31314285C>T	ENSP00000269197:p.Pro330Ser	126.0	0.0		211.0	56.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566279	0.86439	.	.	ENSG00000141431	ENST00000269197	T	0.25250	1.81	5.71	5.71	0.89125	.	0.227351	0.38492	N	0.001663	T	0.50735	0.1633	M	0.61703	1.905	0.54753	D	0.999986	D	0.89917	1.0	D	0.81914	0.995	T	0.34428	-0.9829	10	0.41790	T	0.15	.	19.8549	0.96755	0.0:1.0:0.0:0.0	.	330	Q9C0F0	ASXL3_HUMAN	S	330	ENSP00000269197:P330S	ENSP00000269197:P330S	P	+	1	0	ASXL3	29568283	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.365000	0.79537	2.699000	0.92147	0.460000	0.39030	CCA	.	.		0.308	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
DSEL	92126	hgsc.bcm.edu	37	18	65180960	65180960	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr18:65180960G>A	ENST00000310045.7	-	2	2389	c.916C>T	c.(916-918)Cgc>Tgc	p.R306C	CTD-2541J13.2_ENST00000581951.1_RNA|RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	296					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TTAAAATGGCGCTGGGCCAGA	0.398																																					p.R306C		Atlas-SNP	.											DSEL,NS,carcinoma,+1,1	DSEL	196	.	0			c.C916T						.						72.0	77.0	75.0					18																	65180960		2203	4300	6503	SO:0001583	missense	92126	exon2			AATGGCGCTGGGC	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.916C>T	chr18.hg19:g.65180960G>A	ENSP00000310565:p.Arg306Cys	71.0	0.0		103.0	36.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474135	0.63737	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.27720	1.65	4.62	3.75	0.43078	.	0.000000	0.85682	U	0.000000	T	0.36248	0.0960	M	0.78049	2.395	0.80722	D	1	B	0.13594	0.008	B	0.04013	0.001	T	0.34625	-0.9821	10	0.87932	D	0	.	12.9458	0.58371	0.0796:0.0:0.9204:0.0	.	296	Q8IZU8	DSEL_HUMAN	C	306;296	ENSP00000310565:R306C	ENSP00000310565:R306C	R	-	1	0	DSEL	63331940	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.761000	0.85260	1.093000	0.41377	0.462000	0.41574	CGC	.	.		0.398	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
CHAF1A	10036	hgsc.bcm.edu	37	19	4408946	4408946	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:4408946C>T	ENST00000301280.5	+	3	251	c.150C>T	c.(148-150)gcC>gcT	p.A50A		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	50	Binds to CBX1 chromo shadow domain.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGGAAAGCCGATGACATGT	0.473								Chromatin Structure																													p.A50A		Atlas-SNP	.											.	CHAF1A	69	.	0			c.C150T						.						126.0	127.0	126.0					19																	4408946		2203	4300	6503	SO:0001819	synonymous_variant	10036	exon3			GAAAGCCGATGAC	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.150C>T	chr19.hg19:g.4408946C>T		58.0	0.0		129.0	16.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	hg19	CCDS32875.1																																																																																			.	.		0.473	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	
SMARCA4	6597	hgsc.bcm.edu	37	19	11141502	11141502	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:11141502G>A	ENST00000429416.3	+	26	3760	c.3479G>A	c.(3478-3480)gGg>gAg	p.G1160E	SMARCA4_ENST00000589677.1_Missense_Mutation_p.G1160E|SMARCA4_ENST00000450717.3_Missense_Mutation_p.G1160E|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G1160E|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G1160E|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G1160E|SMARCA4_ENST00000444061.3_Missense_Mutation_p.G1160E|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G1160E|SMARCA4_ENST00000541122.2_Missense_Mutation_p.G1160E	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1160	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGGGCTGGGGGGCTCGGCCTG	0.607			"""F, N, Mis"""		NSCLC																																p.G1160E		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G3479A						.						25.0	26.0	26.0					19																	11141502		2197	4298	6495	SO:0001583	missense	6597	exon25			CTGGGGGGCTCGG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3479G>A	chr19.hg19:g.11141502G>A	ENSP00000395654:p.Gly1160Glu	28.0	0.0		54.0	31.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785160	0.90282	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18;-1.18;-1.18	4.59	4.59	0.56863	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93458	0.7913	H	0.99425	4.56	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.96329	0.9242	10	0.87932	D	0	-48.5831	16.3247	0.82975	0.0:0.0:1.0:0.0	.	1160;1160;1160;1160;1160;380;1160;1160	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	E	1160;1160;1224;1160;1160;1160;1160;1160	ENSP00000395654:G1160E;ENSP00000350720:G1160E;ENSP00000343896:G1160E;ENSP00000445036:G1160E;ENSP00000392837:G1160E;ENSP00000397783:G1160E;ENSP00000414727:G1160E	ENSP00000343896:G1160E	G	+	2	0	SMARCA4	11002502	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.356000	0.97091	2.389000	0.81357	0.563000	0.77884	GGG	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
SLC1A6	6511	hgsc.bcm.edu	37	19	15063807	15063807	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:15063807T>C	ENST00000221742.3	-	8	1439	c.1432A>G	c.(1432-1434)Att>Gtt	p.I478V	SLC1A6_ENST00000600144.1_Missense_Mutation_p.I400V|SLC1A6_ENST00000430939.2_Missense_Mutation_p.I414V	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	478					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GTAAGCACAATGACCATGGTG	0.617																																					p.I478V		Atlas-SNP	.											.	SLC1A6	111	.	0			c.A1432G						.						161.0	133.0	143.0					19																	15063807		2203	4300	6503	SO:0001583	missense	6511	exon8			GCACAATGACCAT		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1432A>G	chr19.hg19:g.15063807T>C	ENSP00000221742:p.Ile478Val	55.0	0.0		217.0	42.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	-	23.9	4.469352	0.84533	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.57907	0.37;0.37	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.50480	0.1618	L	0.50333	1.59	0.80722	D	1	P;P	0.47350	0.865;0.894	B;P	0.44647	0.196;0.456	T	0.57306	-0.7834	10	0.87932	D	0	-20.4835	11.9112	0.52739	0.0:0.0:0.0:1.0	.	414;478	E7EV13;P48664	.;EAA4_HUMAN	V	414;478	ENSP00000409386:I414V;ENSP00000221742:I478V	ENSP00000221742:I478V	I	-	1	0	SLC1A6	14924807	1.000000	0.71417	0.990000	0.47175	0.943000	0.58893	5.943000	0.70211	1.983000	0.57843	0.366000	0.22137	ATT	.	.		0.617	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
ZNF100	163227	hgsc.bcm.edu	37	19	21910792	21910792	+	Splice_Site	SNP	C	C	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:21910792C>G	ENST00000358296.6	-	5	521		c.e5-1		ZNF100_ENST00000305570.6_Splice_Site	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						GAACATATAACTGAAAGAAAT	0.303																																					.		Atlas-SNP	.											.	ZNF100	62	.	0			c.323-1G>C						.						20.0	19.0	19.0					19																	21910792		1852	4082	5934	SO:0001630	splice_region_variant	163227	exon6			ATATAACTGAAAG	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.323-1G>C	chr19.hg19:g.21910792C>G		55.0	0.0		77.0	8.0	NM_173531	Q7M4M0	Splice_Site	SNP	ENST00000358296.6	hg19	CCDS42538.1	.	.	.	.	.	.	.	.	.	.	C	4.678	0.126049	0.08931	.	.	ENSG00000197020	ENST00000358296	.	.	.	0.131	0.131	0.14755	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.741	0.28841	0.0:0.9999:0.0:1.0E-4	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF100	21702632	0.000000	0.05858	0.220000	0.23810	0.218000	0.24690	-0.194000	0.09559	0.171000	0.19730	0.174000	0.16983	.	.	.		0.303	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	Intron
ZNF728	388523	hgsc.bcm.edu	37	19	23159320	23159320	+	Silent	SNP	T	T	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:23159320T>C	ENST00000594710.1	-	4	964	c.819A>G	c.(817-819)gaA>gaG	p.E273E		NM_001267716.1	NP_001254645.1	P0DKX0	ZN728_HUMAN	zinc finger protein 728	273					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										TTCTCTTATGTTCAATAAGGC	0.408																																					p.E273E		Atlas-SNP	.											.	.	.	.	0			c.A819G						.																																			SO:0001819	synonymous_variant	388523	exon4			CTTATGTTCAATA	BC128130	CCDS59370.1	19p12	2014-02-14			ENSG00000269067	ENSG00000269067		"""Zinc fingers, C2H2-type"", ""-"""	32463	protein-coding gene	gene with protein product							Standard	NM_001267716		Approved		uc002nqz.2	P0DKX0	OTTHUMG00000183124	ENST00000594710.1:c.819A>G	chr19.hg19:g.23159320T>C		23.0	0.0		32.0	18.0	NM_001267716		Silent	SNP	ENST00000594710.1	hg19	CCDS59370.1																																																																																			.	.		0.408	ZNF728-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465176.1	NM_001267716	
ZNF681	148213	hgsc.bcm.edu	37	19	23926971	23926971	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:23926971G>C	ENST00000402377.3	-	4	1522	c.1381C>G	c.(1381-1383)Cag>Gag	p.Q461E	ZNF681_ENST00000395385.3_Missense_Mutation_p.Q392E	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	461					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTGAGAACTGGTTAAAGGCT	0.368																																					p.Q461E		Atlas-SNP	.											.	ZNF681	76	.	0			c.C1381G						.						51.0	54.0	53.0					19																	23926971		2203	4299	6502	SO:0001583	missense	148213	exon4			AGAACTGGTTAAA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1381C>G	chr19.hg19:g.23926971G>C	ENSP00000384000:p.Gln461Glu	35.0	0.0		69.0	10.0	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	2.531	-0.308544	0.05458	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07327	3.2;3.2	1.51	-2.25	0.06888	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04907	0.0132	L	0.42744	1.35	0.09310	N	1	B	0.32753	0.383	B	0.18561	0.022	T	0.37572	-0.9700	9	0.33141	T	0.24	.	2.0035	0.03472	0.4171:0.0:0.3248:0.2581	.	461	Q96N22	ZN681_HUMAN	E	461;392	ENSP00000384000:Q461E;ENSP00000378783:Q392E	ENSP00000378783:Q392E	Q	-	1	0	ZNF681	23718811	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.382000	0.02546	-0.077000	0.12752	0.313000	0.20887	CAG	.	.		0.368	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
ZNF681	148213	hgsc.bcm.edu	37	19	23927977	23927977	+	Silent	SNP	T	T	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:23927977T>A	ENST00000402377.3	-	4	516	c.375A>T	c.(373-375)ggA>ggT	p.G125G	ZNF681_ENST00000395385.3_Silent_p.G56G	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CATTATAACCTCCTTTTTGCA	0.299																																					p.G125G		Atlas-SNP	.											.	ZNF681	76	.	0			c.A375T						.						59.0	57.0	58.0					19																	23927977		2202	4300	6502	SO:0001819	synonymous_variant	148213	exon4			ATAACCTCCTTTT	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.375A>T	chr19.hg19:g.23927977T>A		74.0	0.0		118.0	48.0	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.		0.299	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
PSG1	5669	hgsc.bcm.edu	37	19	43382236	43382236	+	Missense_Mutation	SNP	C	C	G	rs1058661	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:43382236C>G	ENST00000436291.2	-	2	375	c.259G>C	c.(259-261)Gaa>Caa	p.E87Q	PSG1_ENST00000595356.1_Missense_Mutation_p.E87Q|PSG1_ENST00000403380.3_Missense_Mutation_p.E87Q|PSG1_ENST00000595124.1_Missense_Mutation_p.E87Q|PSG1_ENST00000312439.6_Missense_Mutation_p.E87Q|PSG1_ENST00000244296.2_Missense_Mutation_p.E87Q|PSG1_ENST00000601073.1_5'UTR	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	87	Ig-like V-type.		E -> Q (in dbSNP:rs1058661).		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				ATAATTATTTCACCGTCTACT	0.453																																					p.E87Q		Atlas-SNP	.											.	PSG1	196	.	0			c.G259C						.						262.0	255.0	258.0					19																	43382236		2202	4299	6501	SO:0001583	missense	5669	exon2			TTATTTCACCGTC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.259G>C	chr19.hg19:g.43382236C>G	ENSP00000413041:p.Glu87Gln	99.0	0.0		189.0	36.0	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	hg19	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.001	-3.014542	0.00042	.	.	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.01538	4.79;4.79;4.79;4.79	1.64	-3.28	0.05033	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01029	0.0034	N	0.17082	0.46	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.12013	0.005;0.0;0.0;0.0;0.0;0.0;0.001;0.003;0.0	B;B;B;B;B;B;B;B;B	0.16722	0.016;0.001;0.001;0.001;0.002;0.001;0.002;0.012;0.002	T	0.46541	-0.9184	9	0.02654	T	1	.	6.1783	0.20457	0.0:0.1996:0.5902:0.2102	rs1058661;rs3199315;rs17173161	87;87;87;87;87;87;87;87;87	O75238;P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.;.	Q	87	ENSP00000413041:E87Q;ENSP00000385386:E87Q;ENSP00000308970:E87Q;ENSP00000244296:E87Q	ENSP00000244296:E87Q	E	-	1	0	PSG1	48074076	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-3.999000	0.00083	-3.418000	0.00038	GAA	.	C|1.000;|0.000		0.453	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
ZNF284	342909	hgsc.bcm.edu	37	19	44590091	44590091	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:44590091A>C	ENST00000421176.3	+	5	676	c.460A>C	c.(460-462)Aaa>Caa	p.K154Q	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				GAAGTGTAAAAAATTCTTCAG	0.418																																					p.K154Q		Atlas-SNP	.											.	ZNF284	38	.	0			c.A460C						.						60.0	59.0	59.0					19																	44590091		2122	4271	6393	SO:0001583	missense	342909	exon5			TGTAAAAAATTCT	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.460A>C	chr19.hg19:g.44590091A>C	ENSP00000411032:p.Lys154Gln	63.0	0.0		95.0	9.0	NM_001037813	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	hg19	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	A	2.020	-0.424865	0.04734	.	.	ENSG00000186026	ENST00000421176	T	0.35973	1.28	2.29	-4.58	0.03410	.	.	.	.	.	T	0.31513	0.0799	M	0.72576	2.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34576	-0.9823	9	0.56958	D	0.05	.	5.812	0.18471	0.4256:0.1435:0.4309:0.0	.	154	Q2VY69	ZN284_HUMAN	Q	154	ENSP00000411032:K154Q	ENSP00000411032:K154Q	K	+	1	0	ZNF284	49281931	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.270000	0.18607	-1.315000	0.02297	-0.648000	0.03929	AAA	.	.		0.418	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
ZNF285	26974	hgsc.bcm.edu	37	19	44890916	44890916	+	Silent	SNP	T	T	C	rs548413151		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:44890916T>C	ENST00000330997.4	-	4	1555	c.1491A>G	c.(1489-1491)tcA>tcG	p.S497S	ZNF285_ENST00000544719.2_Silent_p.S497S|ZNF285_ENST00000591679.1_Silent_p.S504S|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	497					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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						AGTGAAAATATGAACTGTAAC	0.378													T|||	1	0.000199681	0.0008	0.0	5008	,	,		24359	0.0		0.0	False		,,,				2504	0.0				p.S497S		Atlas-SNP	.											.	ZNF285	86	.	0			c.A1491G						.						84.0	86.0	86.0					19																	44890916		2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			AAAATATGAACTG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1491A>G	chr19.hg19:g.44890916T>C		105.0	0.0		215.0	116.0	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	hg19	CCDS12638.1																																																																																			.	.		0.378	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
PGLYRP1	8993	hgsc.bcm.edu	37	19	46525997	46525997	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:46525997A>T	ENST00000008938.4	-	1	326	c.283T>A	c.(283-285)Tac>Aac	p.Y95N		NM_005091.2	NP_005082.1	O75594	PGRP1_HUMAN	peptidoglycan recognition protein 1	95					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(3)|ovary(2)	10		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)		ACTCACTTGTAGCCCACGTCG	0.657																																					p.Y95N		Atlas-SNP	.											.	PGLYRP1	21	.	0			c.T283A						.						48.0	50.0	50.0					19																	46525997		2203	4298	6501	SO:0001583	missense	8993	exon1			ACTTGTAGCCCAC	AF076483	CCDS12680.1	19q13.2-q13.3	2008-02-05	2004-03-17	2004-03-19		ENSG00000008438			8904	protein-coding gene	gene with protein product		604963	"""peptidoglycan recognition protein"""	TNFSF3L, PGLYRP		9707603, 12669421	Standard	NM_005091		Approved	TAG7, PGRP, PGRP-S, PGRPS	uc002pdx.2	O75594		ENST00000008938.4:c.283T>A	chr19.hg19:g.46525997A>T	ENSP00000008938:p.Tyr95Asn	85.0	0.0		278.0	20.0	NM_005091	Q4VB36	Missense_Mutation	SNP	ENST00000008938.4	hg19	CCDS12680.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902747	0.72754	.	.	ENSG00000008438	ENST00000008938	T	0.58060	0.36	4.38	4.38	0.52667	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.113326	0.38492	N	0.001671	T	0.76898	0.4052	M	0.93720	3.45	0.40078	D	0.976098	D	0.89917	1.0	D	0.97110	1.0	T	0.82309	-0.0521	10	0.87932	D	0	.	9.9415	0.41583	1.0:0.0:0.0:0.0	.	95	O75594	PGRP1_HUMAN	N	95	ENSP00000008938:Y95N	ENSP00000008938:Y95N	Y	-	1	0	PGLYRP1	51217837	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.748000	0.62148	1.849000	0.53698	0.472000	0.43445	TAC	.	.		0.657	PGLYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461695.1	NM_005091	
HRC	3270	hgsc.bcm.edu	37	19	49657916	49657916	+	Silent	SNP	T	T	C	rs7409255		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119.0	95.0	103.0					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		96.0	0.0		201.0	18.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
LILRA1	11024	hgsc.bcm.edu	37	19	55106781	55106781	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr19:55106781G>A	ENST00000251372.3	+	5	757	c.575G>A	c.(574-576)aGg>aAg	p.R192K	LILRA1_ENST00000453777.1_Missense_Mutation_p.R192K|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	192	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCGAGTCGCAGGTGGTCGTAC	0.572																																					p.R192K		Atlas-SNP	.											LILRA1,NS,carcinoma,0,2	LILRA1	105	.	0			c.G575A						.						157.0	162.0	160.0					19																	55106781		2203	4300	6503	SO:0001583	missense	11024	exon5			GTCGCAGGTGGTC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.575G>A	chr19.hg19:g.55106781G>A	ENSP00000251372:p.Arg192Lys	120.0	0.0		376.0	65.0	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	hg19	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.045528	0.36085	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.03181	4.02;4.02	2.24	-4.48	0.03515	Immunoglobulin-like fold (1);	0.777662	0.11613	N	0.546521	T	0.07503	0.0189	M	0.84082	2.675	0.09310	N	1	P;P	0.45715	0.865;0.512	P;P	0.48270	0.572;0.569	T	0.05257	-1.0896	10	0.54805	T	0.06	.	3.8719	0.09041	0.2278:0.4018:0.3704:0.0	.	192;192	O75019-2;O75019	.;LIRA1_HUMAN	K	192	ENSP00000251372:R192K;ENSP00000413715:R192K	ENSP00000251372:R192K	R	+	2	0	LILRA1	59798593	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-0.310000	0.08135	-0.489000	0.06716	0.194000	0.17425	AGG	.	.		0.572	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
ASXL1	171023	hgsc.bcm.edu	37	20	31016044	31016044	+	Silent	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr20:31016044A>G	ENST00000375687.4	+	5	790	c.366A>G	c.(364-366)gaA>gaG	p.E122E	ASXL1_ENST00000542461.1_3'UTR|ASXL1_ENST00000306058.5_Silent_p.E117E|ASXL1_ENST00000470145.1_3'UTR	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	122					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TGAGTGGTGAAAACGATGGTA	0.517			"""F, N, Mis"""		"""MDS, CMML"""																																p.E122E		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.A366G						.						186.0	170.0	175.0					20																	31016044		2203	4300	6503	SO:0001819	synonymous_variant	171023	exon4			TGGTGAAAACGAT	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.366A>G	chr20.hg19:g.31016044A>G		73.0	0.0		142.0	17.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	hg19	CCDS13201.1																																																																																			.	.		0.517	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
ATP9A	10079	hgsc.bcm.edu	37	20	50287725	50287725	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr20:50287725C>T	ENST00000338821.5	-	12	1373	c.1109G>A	c.(1108-1110)gGg>gAg	p.G370E	ATP9A_ENST00000311637.5_Missense_Mutation_p.G234E|ATP9A_ENST00000402822.1_Missense_Mutation_p.G249E	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	370					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						AACCACGGTCCCGGGGATTTT	0.547																																					p.G370E		Atlas-SNP	.											.,1	ATP9A	135	.	0			c.G1109A						.						94.0	80.0	85.0					20																	50287725		2203	4300	6503	SO:0001583	missense	10079	exon12			ACGGTCCCGGGGA	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1109G>A	chr20.hg19:g.50287725C>T	ENSP00000342481:p.Gly370Glu	47.0	0.0		107.0	30.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.301899	0.40694	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.89485	-2.52;-2.52;-2.52	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.95108	0.8415	M	0.86028	2.79	0.80722	D	1	D;P	0.89917	1.0;0.691	D;B	0.87578	0.998;0.259	D	0.95410	0.8497	10	0.59425	D	0.04	-38.0659	18.6624	0.91475	0.0:1.0:0.0:0.0	.	249;370	O75110-2;O75110	.;ATP9A_HUMAN	E	234;370;249	ENSP00000309086:G234E;ENSP00000342481:G370E;ENSP00000385875:G249E	ENSP00000309086:G234E	G	-	2	0	ATP9A	49721132	1.000000	0.71417	0.988000	0.46212	0.105000	0.19272	5.704000	0.68347	2.397000	0.81536	0.313000	0.20887	GGG	.	.		0.547	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
TPTE	7179	hgsc.bcm.edu	37	21	10921977	10921977	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr21:10921977A>G	ENST00000361285.4	-	18	1375	c.1046T>C	c.(1045-1047)gTt>gCt	p.V349A	TPTE_ENST00000298232.7_Missense_Mutation_p.V331A|TPTE_ENST00000342420.5_Missense_Mutation_p.V311A|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	349	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAGGCACAAACCATAGTTCC	0.333																																					p.V349A		Atlas-SNP	.											.	TPTE	513	.	0			c.T1046C						.						137.0	117.0	124.0					21																	10921977		2203	4299	6502	SO:0001583	missense	7179	exon18			GCACAAACCATAG	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1046T>C	chr21.hg19:g.10921977A>G	ENSP00000355208:p.Val349Ala	149.0	0.0		321.0	14.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	8.949	0.967657	0.18659	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.98947	-5.26;-5.26;-5.26	2.26	2.26	0.28386	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.203904	0.40554	N	0.001072	D	0.96941	0.9001	L	0.53617	1.68	0.31777	N	0.631393	B;P;B	0.37101	0.378;0.582;0.31	B;B;B	0.42163	0.169;0.251;0.378	D	0.96828	0.9609	10	0.87932	D	0	-17.2387	6.5011	0.22170	1.0:0.0:0.0:0.0	.	311;331;349	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	A	331;349;311	ENSP00000298232:V331A;ENSP00000355208:V349A;ENSP00000344441:V311A	ENSP00000298232:V331A	V	-	2	0	TPTE	9943848	0.582000	0.26749	0.967000	0.41034	0.031000	0.12232	1.270000	0.33086	1.075000	0.40932	0.102000	0.15555	GTT	.	.		0.333	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
TENM1	10178	hgsc.bcm.edu	37	X	123517526	123517526	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrX:123517526A>T	ENST00000371130.3	-	29	7297	c.7234T>A	c.(7234-7236)Tac>Aac	p.Y2412N	TENM1_ENST00000422452.2_Missense_Mutation_p.Y2419N|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2412					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCAACTGGGTAGTTATTTTCA	0.358																																					p.Y2419N		Atlas-SNP	.											.	.	.	.	0			c.T7255A						.						116.0	113.0	114.0					X																	123517526		2203	4300	6503	SO:0001583	missense	10178	exon30			CTGGGTAGTTATT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7234T>A	chrX.hg19:g.123517526A>T	ENSP00000360171:p.Tyr2412Asn	97.0	0.0		133.0	28.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	3.347	-0.133446	0.06711	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.83992	-1.79;-1.76	5.97	5.97	0.96955	.	0.058909	0.64402	D	0.000001	T	0.61862	0.2381	N	0.00329	-1.635	0.53688	D	0.999979	D;D;B	0.62365	0.991;0.991;0.012	P;P;B	0.52109	0.69;0.69;0.003	T	0.71307	-0.4632	10	0.06236	T	0.91	.	15.388	0.74718	1.0:0.0:0.0:0.0	.	2418;2419;2412	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	N	2412;2419	ENSP00000360171:Y2412N;ENSP00000403954:Y2419N	ENSP00000360171:Y2412N	Y	-	1	0	ODZ1	123345207	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.750000	0.62162	2.018000	0.59344	0.486000	0.48141	TAC	.	.		0.358	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
GPR112	139378	hgsc.bcm.edu	37	X	135453612	135453612	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrX:135453612A>G	ENST00000394143.1	+	14	7813	c.7522A>G	c.(7522-7524)Atg>Gtg	p.M2508V	GPR112_ENST00000394141.1_Missense_Mutation_p.M2303V|GPR112_ENST00000287534.4_Missense_Mutation_p.M2306V|GPR112_ENST00000412101.1_Missense_Mutation_p.M2303V|GPR112_ENST00000370652.1_Missense_Mutation_p.M2508V	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2508					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TGAGATAAGTATGAACCTAAC	0.313																																					p.M2508V		Atlas-SNP	.											.	GPR112	459	.	0			c.A7522G						.						65.0	59.0	61.0					X																	135453612		2203	4296	6499	SO:0001583	missense	139378	exon14			ATAAGTATGAACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7522A>G	chrX.hg19:g.135453612A>G	ENSP00000377699:p.Met2508Val	138.0	0.0		191.0	86.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	8.194	0.796709	0.16327	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.27557	1.7;1.7;1.66;1.92;1.66	5.14	2.52	0.30459	.	.	.	.	.	T	0.14787	0.0357	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.17667	0.023;0.002	B;B	0.14023	0.01;0.008	T	0.32375	-0.9909	9	0.14252	T	0.57	.	5.4056	0.16320	0.7028:0.1896:0.1076:0.0	.	2303;2508	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	V	2508;2508;2303;2306;2303	ENSP00000377699:M2508V;ENSP00000359686:M2508V;ENSP00000416526:M2303V;ENSP00000287534:M2306V;ENSP00000377697:M2303V	ENSP00000287534:M2306V	M	+	1	0	GPR112	135281278	0.986000	0.35501	1.000000	0.80357	0.981000	0.71138	0.168000	0.16622	0.612000	0.30071	0.483000	0.47432	ATG	.	.		0.313	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
HCFC1	3054	hgsc.bcm.edu	37	X	153222832	153222832	+	Silent	SNP	C	C	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrX:153222832C>T	ENST00000310441.7	-	13	3252	c.2286G>A	c.(2284-2286)aaG>aaA	p.K762K	HCFC1_ENST00000369984.4_Silent_p.K762K|HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000354233.3_Silent_p.K693K	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	762	Interaction with ZBTB17.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCGTGCCGGGCTTGGTGGTAC	0.642																																					p.K762K		Atlas-SNP	.											.	HCFC1	284	.	0			c.G2286A						.						116.0	127.0	123.0					X																	153222832		2147	4204	6351	SO:0001819	synonymous_variant	3054	exon13			GCCGGGCTTGGTG		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.2286G>A	chrX.hg19:g.153222832C>T		111.0	0.0		212.0	89.0	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	hg19	CCDS44020.1																																																																																			.	.		0.642	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
MT-ATP6	4508	hgsc.bcm.edu	37	M	8865	8865	+	Silent	SNP	G	G	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chrM:8865G>A	ENST00000361899.2	+	1	339	c.339G>A	c.(337-339)gtG>gtA	p.V113V	MT-TG_ENST00000387429.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA			P00846	ATP6_HUMAN	mitochondrially encoded ATP synthase 6	113					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(7)|kidney(8)|prostate(1)	18						GCGGGCGCAGTGATTATAGGC	0.483																																					p.V113V		Atlas-SNP	.											.	.	.	.	0			c.G339A						.																																			SO:0001819	synonymous_variant	0	exon1			CACAGTGATTATA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198899	ENSG00000198899		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7414	protein-coding gene	gene with protein product		516060	"""ATP synthase 6"", ""spicular retinitis pigmentosa with dementia, seizures, ataxia, proximal muscle weakness and sensory deficit"""	MTATP6, RP		7219534	Standard			Approved	ATP6, ATPase-6, Su6m		P00846		ENST00000361899.2:c.339G>A	chrM.hg19:g.8865G>A		4.0	0.0		45.0	39.0	ENST00000361899	Q34772|Q5S8W5|Q5S9E7|Q5S9I6|Q5SA31|Q6RPB7|Q6VHC0|Q6VHE0|Q6WQF4|Q7YCC1|Q7YCF8|Q7YCG1|Q85KU8|Q85KX1|Q85L05|Q8HNQ4|Q8HNQ8|Q8WCX6|Q9B2U5|Q9B2Z2	Silent	SNP	ENST00000361899.2	hg19																																																																																				.	.		0.483	MT-ATP6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024031	
STRAP	11171	hgsc.bcm.edu	37	12	16035698	16035698	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:16035698delT	ENST00000419869.2	+	1	370	c.57delT	c.(55-57)gatfs	p.D19fs	STRAP_ENST00000538352.1_5'UTR|STRAP_ENST00000025399.6_Frame_Shift_Del_p.D19fs	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	19					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				CCGTGGTTGATTTGGCCTTCA	0.617																																					p.D19fs		Atlas-Indel,Pindel	.											.	STRAP	33	.	0			c.56delA						.						62.0	55.0	57.0					12																	16035698		2203	4300	6503	SO:0001589	frameshift_variant	11171	exon1			.	AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"""WD repeat domain containing"""	30796	protein-coding gene	gene with protein product	"""Unr-interacting protein"""	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.57delT	chr12.hg19:g.16035698delT	ENSP00000392270:p.Asp19fs	33.0	0.0		69.0	28.0	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Frame_Shift_Del	DEL	ENST00000419869.2	hg19	CCDS8676.1																																																																																			.	.		0.617	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178	
MARS	4141	hgsc.bcm.edu	37	12	57910075	57910076	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:57910075_57910076insA	ENST00000262027.5	+	20	2645_2646	c.2511_2512insA	c.(2512-2514)aagfs	p.K838fs	MIR616_ENST00000385293.1_RNA|RN7SL312P_ENST00000582079.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	838					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	TTACAACAGCCAAGCCACAGCA	0.455																																					p.A837fs		Atlas-INDEL	.											.	MARS	84	.	0			c.2511_2512insA						.																																			SO:0001589	frameshift_variant	4141	exon20			.	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"""Aminoacyl tRNA synthetases / Class I"""	6898	protein-coding gene	gene with protein product	"""methionine tRNA ligase 1, cytoplasmic"""	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2513dupA	chr12.hg19:g.57910077_57910077dupA	ENSP00000262027:p.Lys838fs	57.0	0.0		275.0	20.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Frame_Shift_Ins	INS	ENST00000262027.5	hg19	CCDS8942.1																																																																																			.	.		0.455	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990	
PTPN9	5780	hgsc.bcm.edu	37	15	75762179	75762180	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr15:75762179_75762180delAG	ENST00000306726.2	-	12	2032_2033	c.1520_1521delCT	c.(1519-1521)cctfs	p.P507fs		NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	507	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGGTGGCTCAGGGCACTGCCC	0.574																																					p.507_508del		Atlas-Indel,Pindel	.											.	PTPN9	53	.	0			c.1521_1522del						.																																			SO:0001589	frameshift_variant	5780	exon12			.		CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.1520_1521delCT	chr15.hg19:g.75762179_75762180delAG	ENSP00000303554:p.Pro507fs	62.0	0.0		123.0	37.0	NM_002833	Q53XR9	Frame_Shift_Del	DEL	ENST00000306726.2	hg19	CCDS10280.1																																																																																			.	.		0.574	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1		
LIPI	149998	hgsc.bcm.edu	37	21	15579205	15579206	+	Intron	INS	-	-	T			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr21:15579205_15579206insT	ENST00000536861.1	-	1	46				LIPI_ENST00000344577.2_Frame_Shift_Ins_p.Y14fs			Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TGAGCACTATATTTTTGGCACA	0.347																																					p.Y14fs		Atlas-INDEL	.											.	LIPI	95	.	0			c.40_41insA						.																																			SO:0001627	intron_variant	149998	exon1			.	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.46+3914->A	chr21.hg19:g.15579210_15579210dupT		60.0	0.0		72.0	10.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Frame_Shift_Ins	INS	ENST00000536861.1	hg19																																																																																				.	.		0.347	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
BAP1	8314	hgsc.bcm.edu	37	3	52440270	52440276	+	Splice_Site	DEL	TGCTGCA	TGCTGCA	-			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	TGCTGCA	TGCTGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr3:52440270_52440276delTGCTGCA	ENST00000460680.1	-	9	1247_1253	c.776_782delTGCAGCA	c.(775-783)ctgcagcag>cg	p.LQQ259fs	BAP1_ENST00000296288.5_Splice_Site_p.LQQ241fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q261*(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGCACCTACCTGCTGCAGAGCCTCTAG	0.57			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															p.259_261del	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,NS,carcinoma,-2,1	BAP1	371	.	1	Substitution - Nonsense(1)	breast(1)	c.777_783del						.																																			SO:0001630	splice_region_variant	8314	exon9			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.783+1TGCAGCA>-	chr3.hg19:g.52440270_52440276delTGCTGCA		60.0	0.0		48.0	14.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.570	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Frame_Shift_Del
ASAP2	8853	hgsc.bcm.edu	37	2	9528642	9528643	+	Frame_Shift_Ins	INS	-	-	C	rs376816649		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr2:9528642_9528643insC	ENST00000281419.3	+	22	2690_2691	c.2350_2351insC	c.(2350-2352)gccfs	p.A784fs	ASAP2_ENST00000315273.4_Frame_Shift_Ins_p.A784fs|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	784	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CACCACCAGCGCCCCCCCGCTT	0.579																																					p.A784fs		Atlas-INDEL	.											.,2	ASAP2	91	.	0			c.2350_2351insC						.		,	9,4257		0,9,2124					,	5.6	1.0			28	12,8240		0,12,4114	no	frameshift,frameshift	ASAP2	NM_003887.2,NM_001135191.1	,	0,21,6238	A1A1,A1R,RR		0.1454,0.211,0.1678	,	,		21,12497				SO:0001589	frameshift_variant	8853	exon22			.	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2357dupC	chr2.hg19:g.9528649_9528649dupC	ENSP00000281419:p.Ala784fs	33.0	0.0		70.0	11.0	NM_001135191	D6W4Y8	Frame_Shift_Ins	INS	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.		0.579	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887	
COL6A2	1292	hgsc.bcm.edu	37	21	47531490	47531492	+	In_Frame_Del	DEL	AAC	AAC	-			TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr21:47531490_47531492delAAC	ENST00000300527.4	+	2	204_206	c.100_102delAAC	c.(100-102)aacdel	p.N36del	COL6A2_ENST00000310645.5_In_Frame_Del_p.N36del|COL6A2_ENST00000357838.4_In_Frame_Del_p.N36del|COL6A2_ENST00000397763.1_In_Frame_Del_p.N36del|COL6A2_ENST00000409416.1_In_Frame_Del_p.N36del	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	36	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TACCGAGAGAAACAACAACTGCC	0.695																																					p.33_34del		Atlas-Indel,Pindel	.											.	COL6A2	351	.	0			c.99_101del						.																																			SO:0001651	inframe_deletion	1292	exon2			.	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.100_102delAAC	chr21.hg19:g.47531496_47531498delAAC	ENSP00000300527:p.Asn36del	52.0	0.0		112.0	22.0	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	In_Frame_Del	DEL	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.		0.695	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
CELA1	1990	hgsc.bcm.edu	37	12	51740405	51740433	+	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs150350903|rs573952082|rs201074609|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs148235680|rs370927847|rs148270827|rs116944010|rs386762976|rs149358345|rs55827519	byFrequency	TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr12:51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	0	30_57					NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATATCCACTTACCATAAAGGACCAGCATGTTGCCGATGGAGTAGACCAC	0.524																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						.																																			SO:0001582	initiator_codon_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523		chr12.hg19:g.51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC		0.0	0.0		25.0	25.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	hg19	CCDS8812.1																																																																																			.	-|0.574;CACCAGGAAGCG|0.426		0.524	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
NCAM1	4684	hgsc.bcm.edu	37	11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A1EF-01A-11D-A12Z-10	TCGA-DD-A1EF-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93e828cc-f42a-438f-a94b-9c2208e1988e	a3a82e8b-83d5-4f74-8f92-4ccb2b2ee0e4	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000500537.2_RNA|RP11-629G13.1_ENST00000532002.1_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		18.0	18.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615	
