#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
AGRN	375790	hgsc.bcm.edu	37	1	957703	957703	+	Silent	SNP	C	C	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:957703C>A	ENST00000379370.2	+	2	374	c.324C>A	c.(322-324)tcC>tcA	p.S108S		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	108	NtA. {ECO:0000255|PROSITE- ProRule:PRU00443}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		ACCAGGTGTCCACTGGGGACA	0.602																																					p.S108S		Atlas-SNP	.											.	AGRN	110	.	0			c.C324A						PASS	.						131.0	137.0	135.0					1																	957703		2203	4300	6503	SO:0001819	synonymous_variant	375790	exon2			GGTGTCCACTGGG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.324C>A	chr1.hg19:g.957703C>A		160.0	0.0	.		216.0	38.0	.	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	hg19	CCDS30551.1																																																																																			.	.	.	none		0.602	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
OTUD3	23252	hgsc.bcm.edu	37	1	20233031	20233031	+	Silent	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:20233031T>C	ENST00000375120.3	+	7	943	c.942T>C	c.(940-942)aaT>aaC	p.N314N		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	314					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGCTTAAATGAAGGCAGGA	0.488																																					p.N314N		Atlas-SNP	.											.	OTUD3	25	.	0			c.T942C						PASS	.						107.0	112.0	110.0					1																	20233031		1980	4166	6146	SO:0001819	synonymous_variant	23252	exon7			CTTAAATGAAGGC	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.942T>C	chr1.hg19:g.20233031T>C		136.0	0.0	.		138.0	23.0	.	NM_015207	O75047	Silent	SNP	ENST00000375120.3	hg19	CCDS41279.1																																																																																			.	.	.	none		0.488	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
KANK4	163782	hgsc.bcm.edu	37	1	62739262	62739262	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:62739262C>T	ENST00000371153.4	-	3	1892	c.1514G>A	c.(1513-1515)gGc>gAc	p.G505D	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	505						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						CTGTTCAGTGCCTGCTTCTTC	0.602																																					p.G505D		Atlas-SNP	.											.	KANK4	135	.	0			c.G1514A						PASS	.						74.0	76.0	75.0					1																	62739262		2203	4300	6503	SO:0001583	missense	163782	exon3			TCAGTGCCTGCTT	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	27263	protein-coding gene	gene with protein product		614612	"""ankyrin repeat domain 38"""	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1514G>A	chr1.hg19:g.62739262C>T	ENSP00000360195:p.Gly505Asp	96.0	0.0	.		133.0	18.0	.	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	C	6.119	0.390267	0.11581	.	.	ENSG00000132854	ENST00000371153	T	0.45668	0.89	5.0	-4.67	0.03319	.	0.629621	0.13219	N	0.404541	T	0.18173	0.0436	N	0.20685	0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	10	0.14656	T	0.56	-0.895	4.4402	0.11570	0.4045:0.2134:0.0:0.382	.	505	Q5T7N3	KANK4_HUMAN	D	505	ENSP00000360195:G505D	ENSP00000360195:G505D	G	-	2	0	KANK4	62511850	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.315000	0.08081	-0.487000	0.06735	-0.880000	0.02959	GGC	.	.	.	none		0.602	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
SYDE2	84144	hgsc.bcm.edu	37	1	85648463	85648463	+	Missense_Mutation	SNP	A	A	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:85648463A>T	ENST00000341460.5	-	3	1911	c.1862T>A	c.(1861-1863)cTt>cAt	p.L621H		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	621					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		TCCATCACTAAGGTAACCACC	0.378																																					p.L621H		Atlas-SNP	.											.	SYDE2	135	.	0			c.T1862A						PASS	.						86.0	80.0	82.0					1																	85648463		1853	4086	5939	SO:0001583	missense	84144	exon3			TCACTAAGGTAAC	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1862T>A	chr1.hg19:g.85648463A>T	ENSP00000340594:p.Leu621His	85.0	0.0	.		84.0	13.0	.	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	hg19	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737544	0.69304	.	.	ENSG00000097096	ENST00000341460	T	0.25749	1.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.46502	0.1396	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.54125	-0.8340	10	0.87932	D	0	.	15.6946	0.77484	1.0:0.0:0.0:0.0	.	621;621	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	H	621	ENSP00000340594:L621H	ENSP00000340594:L621H	L	-	2	0	SYDE2	85421051	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.923000	0.92808	2.116000	0.64780	0.454000	0.30748	CTT	.	.	.	none		0.378	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
NTRK1	4914	hgsc.bcm.edu	37	1	156851384	156851384	+	Silent	SNP	C	C	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:156851384C>T	ENST00000524377.1	+	17	2382	c.2341C>T	c.(2341-2343)Ctg>Ttg	p.L781L	NTRK1_ENST00000368196.3_Silent_p.L775L|NTRK1_ENST00000392302.2_Silent_p.L745L|NTRK1_ENST00000358660.3_Silent_p.L778L|NTRK1_ENST00000531606.1_3'UTR	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	781	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GCACGCCCGGCTGCAAGCCCT	0.697			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)																											p.L781L		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.C2341T						PASS	.						23.0	24.0	24.0					1																	156851384		2202	4297	6499	SO:0001819	synonymous_variant	4914	exon17			GCCCGGCTGCAAG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.2341C>T	chr1.hg19:g.156851384C>T		18.0	0.0	.		19.0	4.0	.	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	hg19	CCDS1161.1																																																																																			.	.	.	none		0.697	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
ERMN	57471	hgsc.bcm.edu	37	2	158178038	158178038	+	Missense_Mutation	SNP	T	T	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:158178038T>A	ENST00000410096.1	-	3	891	c.600A>T	c.(598-600)gaA>gaT	p.E200D	ERMN_ENST00000397283.2_Missense_Mutation_p.E213D|ERMN_ENST00000420719.2_Missense_Mutation_p.E180D|ERMN_ENST00000535935.1_Missense_Mutation_p.E94D	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein	200					actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						TCACTCGAACTtcatcttcat	0.383																																					p.E213D		Atlas-SNP	.											.	ERMN	31	.	0			c.A639T						PASS	.						122.0	118.0	119.0					2																	158178038		1908	4131	6039	SO:0001583	missense	57471	exon4			TCGAACTTCATCT	AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"""juxtanodin"", ""ermin"""	610072	"""KIAA1189"""	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.600A>T	chr2.hg19:g.158178038T>A	ENSP00000387047:p.Glu200Asp	61.0	0.0	.		73.0	12.0	.	NM_001009959	B4DKA6|Q9ULN1	Missense_Mutation	SNP	ENST00000410096.1	hg19	CCDS46431.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290199	0.40494	.	.	ENSG00000136541	ENST00000410096;ENST00000397283;ENST00000535935;ENST00000420719	.	.	.	5.81	4.66	0.58398	.	0.162184	0.43416	D	0.000573	T	0.48021	0.1477	L	0.36672	1.1	0.28039	N	0.933847	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.66602	0.945;0.945;0.945	T	0.37549	-0.9701	9	0.38643	T	0.18	.	8.1808	0.31309	0.0:0.1976:0.0:0.8024	.	180;213;200	B4DIZ1;Q8TAM6-2;Q8TAM6	.;.;ERMIN_HUMAN	D	200;213;94;180	.	ENSP00000380453:E213D	E	-	3	2	ERMN	157886284	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	0.434000	0.21494	1.031000	0.39867	0.533000	0.62120	GAA	.	.	.	none		0.383	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959	
UBR3	130507	hgsc.bcm.edu	37	2	170762609	170762609	+	Missense_Mutation	SNP	T	T	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:170762609T>A	ENST00000272793.5	+	10	1764	c.1714T>A	c.(1714-1716)Ttt>Att	p.F572I	UBR3_ENST00000418381.1_Missense_Mutation_p.F572I			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	572					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CTATGCTGCCTTTGCTGCTGA	0.388																																					p.F572I		Atlas-SNP	.											.	UBR3	182	.	0			c.T1714A						PASS	.						116.0	103.0	107.0					2																	170762609		692	1591	2283	SO:0001583	missense	130507	exon10			GCTGCCTTTGCTG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1714T>A	chr2.hg19:g.170762609T>A	ENSP00000272793:p.Phe572Ile	73.0	0.0	.		101.0	29.0	.	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.	.	.	.	.	.	.	.	.	.	T	34	5.361453	0.95877	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	T;T	0.58060	0.36;0.36	5.58	5.58	0.84498	.	.	.	.	.	T	0.64316	0.2587	L	0.43923	1.385	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.60835	-0.7184	9	0.30854	T	0.27	.	15.7431	0.77918	0.0:0.0:0.0:1.0	.	572	Q6ZT12	UBR3_HUMAN	I	572	ENSP00000272793:F572I;ENSP00000396068:F572I	ENSP00000272793:F572I	F	+	1	0	UBR3	170470855	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.116000	0.64780	0.482000	0.46254	TTT	.	.	.	none		0.388	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
OBSL1	23363	hgsc.bcm.edu	37	2	220416332	220416332	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:220416332G>T	ENST00000404537.1	-	20	5658	c.5602C>A	c.(5602-5604)Cat>Aat	p.H1868N	OBSL1_ENST00000265318.4_3'UTR|OBSL1_ENST00000373876.1_Missense_Mutation_p.H1776N|MIR3132_ENST00000581997.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1868	Ig-like 14.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CGAACGTCATGGATGACCAGG	0.657																																					p.H1868N		Atlas-SNP	.											.	OBSL1	120	.	0			c.C5602A						PASS	.						32.0	37.0	36.0					2																	220416332		2086	4208	6294	SO:0001583	missense	23363	exon20			CGTCATGGATGAC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.5602C>A	chr2.hg19:g.220416332G>T	ENSP00000385636:p.His1868Asn	151.0	0.0	.		209.0	53.0	.	NM_015311	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.174528	0.38413	.	.	ENSG00000124006	ENST00000404537;ENST00000373876	T;T	0.65916	-0.18;-0.18	5.32	3.38	0.38709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53449	0.1797	L	0.28344	0.845	0.80722	D	1	B	0.27192	0.171	B	0.41691	0.364	T	0.43798	-0.9369	9	0.21540	T	0.41	.	9.4425	0.38677	0.0:0.1395:0.5724:0.2881	.	1868	O75147	OBSL1_HUMAN	N	1868;1776	ENSP00000385636:H1868N;ENSP00000362983:H1776N	ENSP00000362983:H1776N	H	-	1	0	OBSL1	220124576	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.056000	0.57448	1.220000	0.43490	0.655000	0.94253	CAT	.	.	.	none		0.657	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
SNED1	25992	hgsc.bcm.edu	37	2	242026825	242026825	+	Silent	SNP	A	A	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:242026825A>T	ENST00000310397.8	+	30	4140	c.4140A>T	c.(4138-4140)cgA>cgT	p.R1380R	SNED1_ENST00000342631.6_Silent_p.R1347R|SNED1_ENST00000405547.3_Intron|MTERFD2_ENST00000464344.2_Intron	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1380					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GAGTCTACCGAGTTCACCAAG	0.488																																					p.R1380R		Atlas-SNP	.											.	SNED1	76	.	0			c.A4140T						PASS	.						50.0	46.0	47.0					2																	242026825		1886	4111	5997	SO:0001819	synonymous_variant	25992	exon30			CTACCGAGTTCAC	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.4140A>T	chr2.hg19:g.242026825A>T		151.0	0.0	.		196.0	70.0	.	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	hg19	CCDS46562.1																																																																																			.	.	.	none		0.488	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
SRGAP3	9901	hgsc.bcm.edu	37	3	9100033	9100033	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:9100033G>T	ENST00000383836.3	-	7	1352	c.925C>A	c.(925-927)Ctg>Atg	p.L309M	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.L309M	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	309	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CGGGAATCCAGGTTGTCCACT	0.552			T	RAF1	pilocytic astrocytoma																																p.L309M		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.C925A						PASS	.						246.0	203.0	218.0					3																	9100033		2203	4300	6503	SO:0001583	missense	9901	exon7			AATCCAGGTTGTC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.925C>A	chr3.hg19:g.9100033G>T	ENSP00000373347:p.Leu309Met	173.0	0.0	.		178.0	29.0	.	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.927507	0.52759	.	.	ENSG00000196220	ENST00000383836;ENST00000360413;ENST00000544908	T;T	0.14893	2.47;2.47	5.54	4.66	0.58398	.	0.000000	0.64402	D	0.000001	T	0.18800	0.0451	M	0.67397	2.05	0.58432	D	0.999993	B;B;B	0.30937	0.074;0.301;0.2	B;B;B	0.27796	0.083;0.083;0.038	T	0.01956	-1.1240	10	0.45353	T	0.12	.	10.889	0.46984	0.1445:0.0:0.8555:0.0	.	178;309;309	Q9ULR4;O43295-2;O43295	.;.;SRGP2_HUMAN	M	309;309;189	ENSP00000373347:L309M;ENSP00000353587:L309M	ENSP00000353587:L309M	L	-	1	2	SRGAP3	9075033	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.275000	0.43399	2.606000	0.88127	0.655000	0.94253	CTG	.	.	.	none		0.552	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
TBC1D5	9779	hgsc.bcm.edu	37	3	17550057	17550057	+	Silent	SNP	A	A	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:17550057A>G	ENST00000253692.7	-	3	1670	c.6T>C	c.(4-6)taT>taC	p.Y2Y	TBC1D5_ENST00000414318.2_Intron|TBC1D5_ENST00000429383.4_Silent_p.Y2Y|TBC1D5_ENST00000446818.2_Silent_p.Y2Y	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	2						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						ATAAGGAATGATACATTGTGG	0.403																																					p.Y2Y		Atlas-SNP	.											.	TBC1D5	69	.	0			c.T6C						PASS	.						142.0	122.0	129.0					3																	17550057		2203	4300	6503	SO:0001819	synonymous_variant	9779	exon3			GGAATGATACATT	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.6T>C	chr3.hg19:g.17550057A>G		106.0	0.0	.		109.0	32.0	.	NM_014744	A6NP25|C9JP52	Silent	SNP	ENST00000253692.7	hg19	CCDS33714.1																																																																																			.	.	.	none		0.403	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
STAG1	10274	hgsc.bcm.edu	37	3	136060303	136060303	+	Missense_Mutation	SNP	T	T	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:136060303T>A	ENST00000383202.2	-	31	3793	c.3537A>T	c.(3535-3537)agA>agT	p.R1179S	STAG1_ENST00000536929.1_Missense_Mutation_p.R763S|STAG1_ENST00000434713.2_Missense_Mutation_p.R919S|STAG1_ENST00000236698.5_Intron	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1179					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TCACTCCAGTTCTCACTTTCA	0.423																																					p.R1179S		Atlas-SNP	.											.	STAG1	135	.	0			c.A3537T						PASS	.						273.0	206.0	228.0					3																	136060303		2203	4300	6503	SO:0001583	missense	10274	exon31			TCCAGTTCTCACT	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3537A>T	chr3.hg19:g.136060303T>A	ENSP00000372689:p.Arg1179Ser	77.0	0.0	.		115.0	31.0	.	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970648	0.74246	.	.	ENSG00000118007	ENST00000383202;ENST00000434713;ENST00000536929	T;T;T	0.50277	1.31;0.75;0.97	5.91	3.52	0.40303	.	0.100808	0.64402	D	0.000003	T	0.50633	0.1627	M	0.63843	1.955	0.54753	D	0.999983	D	0.60160	0.987	P	0.54174	0.744	T	0.47724	-0.9095	10	0.13108	T	0.6	.	8.6846	0.34229	0.0:0.2062:0.0:0.7938	.	1179	Q8WVM7	STAG1_HUMAN	S	1179;919;763	ENSP00000372689:R1179S;ENSP00000404396:R919S;ENSP00000445787:R763S	ENSP00000372689:R1179S	R	-	3	2	STAG1	137542993	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.775000	0.26689	0.483000	0.27608	0.528000	0.53228	AGA	.	.	.	none		0.423	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
VWA5B2	90113	hgsc.bcm.edu	37	3	183955086	183955086	+	Missense_Mutation	SNP	A	A	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:183955086A>T	ENST00000426955.2	+	11	1706	c.1606A>T	c.(1606-1608)Act>Tct	p.T536S	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Missense_Mutation_p.T317S	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	547	VWFA.									breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						TGTGCCCGACACTGTGGAGGC	0.612																																					p.T536S		Atlas-SNP	.											.	VWA5B2	47	.	0			c.A1606T						PASS	.						55.0	52.0	53.0					3																	183955086		692	1591	2283	SO:0001583	missense	90113	exon11			CCCGACACTGTGG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.1606A>T	chr3.hg19:g.183955086A>T	ENSP00000398688:p.Thr536Ser	93.0	0.0	.		140.0	22.0	.	NM_138345	B9EGN7	Missense_Mutation	SNP	ENST00000426955.2	hg19	CCDS54686.1	.	.	.	.	.	.	.	.	.	.	A	4.470	0.087175	0.08583	.	.	ENSG00000145198	ENST00000426955;ENST00000273794	T;T	0.16897	2.96;2.31	5.2	-1.1	0.09872	.	0.771688	0.11411	N	0.566836	T	0.08447	0.0210	N	0.16656	0.425	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.002;0.004;0.002	T	0.37267	-0.9713	10	0.25106	T	0.35	.	5.9478	0.19229	0.5205:0.0:0.3502:0.1293	.	317;536;547	E9PF42;B9EGN7;Q8N398	.;.;VW5B2_HUMAN	S	536;317	ENSP00000398688:T536S;ENSP00000273794:T317S	ENSP00000273794:T317S	T	+	1	0	VWA5B2	185437780	0.016000	0.18221	0.000000	0.03702	0.086000	0.17979	1.101000	0.31037	-0.185000	0.10550	-0.366000	0.07423	ACT	.	.	.	none		0.612	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
UBE2K	3093	hgsc.bcm.edu	37	4	39757353	39757353	+	Missense_Mutation	SNP	A	A	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:39757353A>G	ENST00000261427.5	+	4	577	c.293A>G	c.(292-294)gAt>gGt	p.D98G	UBE2K_ENST00000438068.2_3'UTR|UBE2K_ENST00000503368.1_Missense_Mutation_p.D47G|UBE2K_ENST00000295963.6_Intron|UBE2K_ENST00000445950.2_Missense_Mutation_p.D98G	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	98					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						ATCCTGAAAGATCAATGGTAA	0.343																																					p.D98G	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.A293G						PASS	.						152.0	150.0	151.0					4																	39757353		2203	4300	6503	SO:0001583	missense	3093	exon4			TGAAAGATCAATG	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"""Ubiquitin-conjugating enzymes E2"""	4914	protein-coding gene	gene with protein product		602846	"""huntingtin interacting protein 2"", ""ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"""	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.293A>G	chr4.hg19:g.39757353A>G	ENSP00000261427:p.Asp98Gly	43.0	0.0	.		57.0	8.0	.	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	hg19	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885370	0.91814	.	.	ENSG00000078140	ENST00000261427;ENST00000503368;ENST00000445950	T;T;T	0.72835	-0.69;-0.69;-0.69	5.98	5.98	0.97165	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	D	0.82935	0.5145	M	0.74467	2.265	0.80722	D	1	D;D;B	0.61697	0.97;0.99;0.034	D;D;B	0.66497	0.925;0.944;0.131	D	0.84525	0.0630	10	0.62326	D	0.03	-22.3267	15.4553	0.75308	1.0:0.0:0.0:0.0	.	98;47;98	P61086;P61086-2;C9JGP1	UBE2K_HUMAN;.;.	G	98;47;98	ENSP00000261427:D98G;ENSP00000421203:D47G;ENSP00000390483:D98G	ENSP00000261427:D98G	D	+	2	0	UBE2K	39433748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.872000	0.92352	2.296000	0.77279	0.482000	0.46254	GAT	.	.	.	none		0.343	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339	
OCIAD2	132299	hgsc.bcm.edu	37	4	48887522	48887522	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:48887522G>T	ENST00000508632.1	-	7	676	c.444C>A	c.(442-444)gaC>gaA	p.D148E	OCIAD2_ENST00000273860.4_3'UTR|OCIAD2_ENST00000508069.2_5'UTR	NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2	148						endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						AAGGCTGAGAGTCTCCCTTCT	0.368																																					p.D148E		Atlas-SNP	.											.	OCIAD2	16	.	0			c.C444A						PASS	.						185.0	180.0	182.0					4																	48887522		2203	4300	6503	SO:0001583	missense	132299	exon7			CTGAGAGTCTCCC	BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247			28685	protein-coding gene	gene with protein product						17054434	Standard	NM_001286774		Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.444C>A	chr4.hg19:g.48887522G>T	ENSP00000423014:p.Asp148Glu	158.0	0.0	.		195.0	42.0	.	NM_001014446	B4DPE7|Q8N544	Missense_Mutation	SNP	ENST00000508632.1	hg19	CCDS33981.1	.	.	.	.	.	.	.	.	.	.	G	5.308	0.242112	0.10077	.	.	ENSG00000145247	ENST00000508632	T	0.41758	0.99	5.25	-4.51	0.03483	.	0.562361	0.17338	N	0.177837	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18178	-1.0345	9	.	.	.	1.3177	6.0446	0.19752	0.3698:0.2579:0.3723:0.0	.	148	Q56VL3	OCAD2_HUMAN	E	148	ENSP00000423014:D148E	.	D	-	3	2	OCIAD2	48582279	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	-0.089000	0.11180	-1.031000	0.03308	-0.302000	0.09304	GAC	.	.	.	none		0.368	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361984.5	NM_152398	
ADH1B	125	hgsc.bcm.edu	37	4	100231924	100231924	+	Silent	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:100231924T>C	ENST00000305046.8	-	8	1168	c.1101A>G	c.(1099-1101)aaA>aaG	p.K367K	ADH1B_ENST00000394887.3_Silent_p.K327K			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	367					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	AAATCTACCTTTTCCCAGAGT	0.333																																					p.K367K		Atlas-SNP	.											.	ADH1B	68	.	0			c.A1101G						PASS	.						72.0	72.0	72.0					4																	100231924		2202	4300	6502	SO:0001819	synonymous_variant	125	exon8			CTACCTTTTCCCA	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.1101A>G	chr4.hg19:g.100231924T>C		100.0	0.0	.		90.0	13.0	.	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	hg19	CCDS34033.1																																																																																			.	.	.	none		0.333	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668	
SLC6A3	6531	hgsc.bcm.edu	37	5	1394869	1394869	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:1394869C>T	ENST00000270349.9	-	15	1971	c.1844G>A	c.(1843-1845)cGc>cAc	p.R615H	SLC6A3_ENST00000453492.2_Missense_Mutation_p.R615H	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	615					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)	p.R615P(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GAGCCAGTGGCGGAGCTGGAA	0.522																																					p.R615H		Atlas-SNP	.											SLC6A3,NS,carcinoma,0,1	SLC6A3	102	.	1	Substitution - Missense(1)	lung(1)	c.G1844A						PASS	.						101.0	100.0	100.0					5																	1394869		2203	4300	6503	SO:0001583	missense	6531	exon15			CAGTGGCGGAGCT		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1844G>A	chr5.hg19:g.1394869C>T	ENSP00000270349:p.Arg615His	66.0	0.0	.		83.0	5.0	.	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627534	0.28978	.	.	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.74632	-0.86;-0.86	4.79	2.97	0.34412	.	0.585459	0.14305	N	0.328004	T	0.53834	0.1821	N	0.12182	0.205	0.32012	N	0.60198	B	0.16802	0.019	B	0.13407	0.009	T	0.56643	-0.7945	10	0.49607	T	0.09	.	6.8118	0.23809	0.0:0.7896:0.0:0.2104	.	615	Q01959	SC6A3_HUMAN	H	615	ENSP00000270349:R615H;ENSP00000399806:R615H	ENSP00000270349:R615H	R	-	2	0	SLC6A3	1447869	1.000000	0.71417	0.999000	0.59377	0.917000	0.54804	0.574000	0.23714	1.139000	0.42245	0.655000	0.94253	CGC	.	.	.	none		0.522	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
MED10	84246	hgsc.bcm.edu	37	5	6378594	6378594	+	Start_Codon_SNP	SNP	C	C	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:6378594C>A	ENST00000255764.3	-	1	113	c.3G>T	c.(1-3)atG>atT	p.M1I		NM_032286.2	NP_115662.2	Q9BTT4	MED10_HUMAN	mediator complex subunit 10	1					gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	RNA polymerase II transcription cofactor activity (GO:0001104)			kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|urinary_tract(1)	5						ACTTCTCCGCCATCGCCTCGG	0.637																																					p.M1I		Atlas-SNP	.											.	MED10	7	.	0			c.G3T						PASS	.						86.0	74.0	78.0					5																	6378594		2203	4300	6503	SO:0001582	initiator_codon_variant	84246	exon1			CTCCGCCATCGCC		CCDS34134.1	5p15.31	2008-02-05	2007-07-30		ENSG00000133398	ENSG00000133398			28760	protein-coding gene	gene with protein product	"""NUT2 homolog (S. cerevisiae)"""	612382	"""mediator of RNA polymerase II transcription, subunit 10 homolog (NUT2, S. cerevisiae)"""			15657623, 15175163	Standard	NM_032286		Approved	TRG20, L6, MGC5309, NUT2	uc003jdo.3	Q9BTT4	OTTHUMG00000161682	ENST00000255764.3:c.3G>T	chr5.hg19:g.6378594C>A	ENSP00000255764:p.Met1Ile	29.0	0.0	.		47.0	10.0	.	NM_032286	C6G491	Missense_Mutation	SNP	ENST00000255764.3	hg19	CCDS34134.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567880	0.86439	.	.	ENSG00000133398	ENST00000255764	.	.	.	4.87	4.01	0.46588	.	0.000000	0.85682	D	0.000000	T	0.56247	0.1972	.	.	.	0.80722	D	1	P	0.35872	0.525	B	0.42214	0.38	T	0.57447	-0.7810	8	0.45353	T	0.12	-29.2016	12.3741	0.55271	0.0:0.9182:0.0:0.0818	.	1	Q9BTT4	MED10_HUMAN	I	1	.	ENSP00000255764:M1I	M	-	3	0	MED10	6431594	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	4.993000	0.63895	1.283000	0.44513	0.555000	0.69702	ATG	.	.	.	none		0.637	MED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365714.1	NM_032286	Missense_Mutation
MEGF10	84466	hgsc.bcm.edu	37	5	126790286	126790286	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:126790286G>T	ENST00000274473.6	+	24	3276	c.3009G>T	c.(3007-3009)atG>atT	p.M1003I	MEGF10_ENST00000510828.1_3'UTR|MEGF10_ENST00000503335.2_Missense_Mutation_p.M1003I	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	1003	Necessary for formation of large intracellular vacuoles.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GAAGCTATATGGGAAAATCCT	0.328																																					p.M1003I		Atlas-SNP	.											.	MEGF10	152	.	0			c.G3009T						PASS	.						71.0	73.0	72.0					5																	126790286		2203	4300	6503	SO:0001583	missense	84466	exon24			CTATATGGGAAAA	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.3009G>T	chr5.hg19:g.126790286G>T	ENSP00000274473:p.Met1003Ile	18.0	0.0	.		26.0	4.0	.	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.130925	0.37630	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	T;T	0.79940	-1.32;-1.32	6.03	5.16	0.70880	.	0.346611	0.28847	N	0.013959	T	0.62925	0.2468	N	0.08118	0	0.37163	D	0.902706	B	0.02656	0.0	B	0.04013	0.001	T	0.61461	-0.7058	10	0.24483	T	0.36	-5.9793	12.4451	0.55647	0.1344:0.0:0.8656:0.0	.	1003	Q96KG7	MEG10_HUMAN	I	1003	ENSP00000423354:M1003I;ENSP00000274473:M1003I	ENSP00000274473:M1003I	M	+	3	0	MEGF10	126818185	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.346000	0.52190	1.558000	0.49541	0.655000	0.94253	ATG	.	.	.	none		0.328	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
ADAM19	8728	hgsc.bcm.edu	37	5	156908922	156908922	+	Missense_Mutation	SNP	C	C	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:156908922C>A	ENST00000517905.1	-	22	2624	c.2580G>T	c.(2578-2580)aaG>aaT	p.K860N	ADAM19_ENST00000394020.1_Missense_Mutation_p.K862N|ADAM19_ENST00000430702.2_Intron|ADAM19_ENST00000257527.4_Missense_Mutation_p.K860N			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	860					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCGGGAGTGCCTTCTGGGGCG	0.622																																					p.K860N		Atlas-SNP	.											.	ADAM19	216	.	0			c.G2580T						PASS	.						12.0	15.0	14.0					5																	156908922		2201	4297	6498	SO:0001583	missense	8728	exon22			GAGTGCCTTCTGG	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.2580G>T	chr5.hg19:g.156908922C>A	ENSP00000428654:p.Lys860Asn	71.0	0.0	.		64.0	16.0	.	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.047583|4.047583	0.75846|0.75846	.|.	.|.	ENSG00000135074|ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905|ENST00000517374	T;T;T|.	0.01854|.	4.61;4.62;4.6|.	5.51|5.51	1.19|1.19	0.21007|0.21007	.|.	0.184073|.	0.37809|.	N|.	0.001925|.	T|T	0.50205|0.50205	0.1602|0.1602	L|L	0.50333|0.50333	1.59|1.59	0.35227|0.35227	D|D	0.776606|0.776606	D;D|.	0.76494|.	0.999;0.997|.	D;P|.	0.69479|.	0.964;0.888|.	T|T	0.54827|0.54827	-0.8235|-0.8235	10|5	0.87932|.	D|.	0|.	.|.	7.8|7.8	0.29168|0.29168	0.0:0.5227:0.0:0.4773|0.0:0.5227:0.0:0.4773	.|.	860;860|.	Q9H013-2;Q9H013|.	.;ADA19_HUMAN|.	N|M	860;862;860|431	ENSP00000257527:K860N;ENSP00000377588:K862N;ENSP00000428654:K860N|.	ENSP00000257527:K860N|.	K|R	-|-	3|2	2|0	ADAM19|ADAM19	156841500|156841500	0.995000|0.995000	0.38212|0.38212	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	0.140000|0.140000	0.16056|0.16056	0.304000|0.304000	0.22809|0.22809	0.561000|0.561000	0.74099|0.74099	AAG|AGG	.	.	.	none		0.622	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
UNC5CL	222643	hgsc.bcm.edu	37	6	41000635	41000635	+	Missense_Mutation	SNP	A	A	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:41000635A>G	ENST00000373164.1	-	3	997	c.937T>C	c.(937-939)Tac>Cac	p.Y313H	UNC5CL_ENST00000244565.3_Missense_Mutation_p.Y313H|UNC5CL_ENST00000470102.1_5'UTR			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	313	Interaction with RELA and NFKB1.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTGAGATGTACGTGAGCTTC	0.632																																					p.Y313H		Atlas-SNP	.											.	UNC5CL	52	.	0			c.T937C						PASS	.						19.0	21.0	20.0					6																	41000635		2201	4299	6500	SO:0001583	missense	222643	exon4			AGATGTACGTGAG	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"""ZU5 and death domain containing"""					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.937T>C	chr6.hg19:g.41000635A>G	ENSP00000362258:p.Tyr313His	77.0	0.0	.		77.0	10.0	.	NM_173561	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	hg19	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	A	7.812	0.716007	0.15306	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	T;T	0.52526	0.66;0.66	5.43	5.43	0.79202	.	0.000000	0.40554	N	0.001066	T	0.16342	0.0393	N	0.24115	0.695	0.33409	D	0.578337	B	0.14438	0.01	B	0.12156	0.007	T	0.08785	-1.0705	10	0.19590	T	0.45	-29.4271	11.8914	0.52630	1.0:0.0:0.0:0.0	.	313	Q8IV45	UN5CL_HUMAN	H	313	ENSP00000244565:Y313H;ENSP00000362258:Y313H	ENSP00000244565:Y313H	Y	-	1	0	UNC5CL	41108613	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	4.569000	0.60865	2.042000	0.60477	0.533000	0.62120	TAC	.	.	.	none		0.632	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561	
DEFB110	245913	hgsc.bcm.edu	37	6	49986835	49986835	+	Missense_Mutation	SNP	T	T	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:49986835T>G	ENST00000371148.2	-	2	104	c.59A>C	c.(58-60)aAa>aCa	p.K20T	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	20					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					ATATTTCTTTTTGGCTGTAAG	0.353																																					p.K20T		Atlas-SNP	.											.	DEFB110	5	.	0			c.A59C						PASS	.						129.0	126.0	127.0					6																	49986835		2203	4300	6503	SO:0001583	missense	245913	exon2			TTCTTTTTGGCTG	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"""Defensins, beta"""	18091	protein-coding gene	gene with protein product			"""defensin, beta 110"""			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.59A>C	chr6.hg19:g.49986835T>G	ENSP00000360190:p.Lys20Thr	70.0	0.0	.		102.0	6.0	.	NM_001037497	Q30KR0	Missense_Mutation	SNP	ENST00000371148.2	hg19	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.622246	0.28889	.	.	ENSG00000203970	ENST00000371148	.	.	.	4.77	-6.13	0.02118	.	0.904575	0.09377	N	0.810521	T	0.07954	0.0199	.	.	.	0.23882	N	0.996572	B	0.12630	0.006	B	0.12837	0.008	T	0.34700	-0.9818	7	.	.	.	-4.2088	9.1953	0.37224	0.0:0.6424:0.1253:0.2323	.	20	Q30KQ9	DB110_HUMAN	T	20	.	.	K	-	2	0	DEFB110	50094794	0.245000	0.23899	0.575000	0.28536	0.857000	0.48899	-1.073000	0.03430	-1.040000	0.03271	-0.408000	0.06270	AAA	.	.	.	none		0.353	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728	
SERINC1	57515	hgsc.bcm.edu	37	6	122766258	122766258	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:122766258C>G	ENST00000339697.4	-	10	1377	c.1293G>C	c.(1291-1293)tgG>tgC	p.W431C		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	431					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		CGATGCCAATCCAACTGGAAG	0.428																																					p.W431C		Atlas-SNP	.											.	SERINC1	39	.	0			c.G1293C						PASS	.						107.0	96.0	99.0					6																	122766258		2203	4300	6503	SO:0001583	missense	57515	exon10			GCCAATCCAACTG	AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"""tumor differentially expressed 2"""	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.1293G>C	chr6.hg19:g.122766258C>G	ENSP00000342962:p.Trp431Cys	68.0	0.0	.		92.0	19.0	.	NM_020755	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Missense_Mutation	SNP	ENST00000339697.4	hg19	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569369	0.86439	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	T;T	0.25579	1.79;1.79	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.62405	0.2425	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75502	-0.3295	10	0.87932	D	0	-7.4299	19.5937	0.95526	0.0:1.0:0.0:0.0	.	431	Q9NRX5	SERC1_HUMAN	C	431	ENSP00000342962:W431C;ENSP00000357439:W431C	ENSP00000342962:W431C	W	-	3	0	SERINC1	122807957	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.798000	0.85924	2.629000	0.89072	0.655000	0.94253	TGG	.	.	.	none		0.428	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755	
DUSP26	78986	hgsc.bcm.edu	37	8	33454873	33454873	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:33454873G>T	ENST00000256261.4	-	2	678	c.161C>A	c.(160-162)aCa>aAa	p.T54K	DUSP26_ENST00000523956.1_Missense_Mutation_p.T54K	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	54					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		TGTCTTGCCTGTGTAGAGGAG	0.572																																					p.T54K		Atlas-SNP	.											.	DUSP26	42	.	0			c.C161A						PASS	.						69.0	52.0	58.0					8																	33454873		2203	4300	6503	SO:0001583	missense	78986	exon2			TTGCCTGTGTAGA	AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.161C>A	chr8.hg19:g.33454873G>T	ENSP00000256261:p.Thr54Lys	94.0	0.0	.		93.0	16.0	.	NM_024025	D3DSV8|Q9BTW0	Missense_Mutation	SNP	ENST00000256261.4	hg19	CCDS6092.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638232	0.47153	.	.	ENSG00000133878	ENST00000256261;ENST00000523956;ENST00000522982	T;T;T	0.60040	0.22;0.22;0.22	5.5	5.5	0.81552	.	0.146976	0.64402	D	0.000010	T	0.43765	0.1262	L	0.27053	0.805	0.54753	D	0.999983	B	0.21520	0.057	B	0.20955	0.032	T	0.40776	-0.9545	10	0.05436	T	0.98	-14.8884	18.9825	0.92760	0.0:0.0:1.0:0.0	.	54	Q9BV47	DUS26_HUMAN	K	54	ENSP00000256261:T54K;ENSP00000429176:T54K;ENSP00000430922:T54K	ENSP00000256261:T54K	T	-	2	0	DUSP26	33574415	1.000000	0.71417	0.962000	0.40283	0.975000	0.68041	7.744000	0.85034	2.590000	0.87494	0.561000	0.74099	ACA	.	.	.	none		0.572	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025	
CA13	377677	hgsc.bcm.edu	37	8	86162972	86162972	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:86162972C>T	ENST00000321764.3	+	2	343	c.41C>T	c.(40-42)cCt>cTt	p.P14L	CA13_ENST00000517298.1_3'UTR|RP11-219B4.6_ENST00000551479.1_5'Flank	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	14					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|myelin sheath (GO:0043209)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)	7					Zonisamide(DB00909)	ATTTAAGGTCCTATTCACTGG	0.338																																					p.P14L		Atlas-SNP	.											.	CA13	26	.	0			c.C41T						PASS	.						62.0	64.0	63.0					8																	86162972		2203	4300	6503	SO:0001583	missense	377677	exon2			AAGGTCCTATTCA	BC052602	CCDS6236.1	8q21	2004-05-10				ENSG00000185015		"""Carbonic anhydrases"""	14914	protein-coding gene	gene with protein product		611436				14600151	Standard	NM_198584		Approved	CAXIII, FLJ37995, MGC59868	uc003ydg.2	Q8N1Q1		ENST00000321764.3:c.41C>T	chr8.hg19:g.86162972C>T	ENSP00000318912:p.Pro14Leu	105.0	0.0	.		91.0	11.0	.	NM_198584		Missense_Mutation	SNP	ENST00000321764.3	hg19	CCDS6236.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887731	0.91814	.	.	ENSG00000185015	ENST00000321764	T	0.68624	-0.34	5.48	5.48	0.80851	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.89361	0.6693	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93109	0.6515	10	0.87932	D	0	-23.2453	19.3527	0.94395	0.0:1.0:0.0:0.0	.	14	Q8N1Q1	CAH13_HUMAN	L	14	ENSP00000318912:P14L	ENSP00000318912:P14L	P	+	2	0	CA13	86350224	1.000000	0.71417	0.973000	0.42090	0.987000	0.75469	7.044000	0.76578	2.567000	0.86603	0.563000	0.77884	CCT	.	.	.	none		0.338	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584	
ADCY8	114	hgsc.bcm.edu	37	8	132002781	132002781	+	Missense_Mutation	SNP	G	G	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:132002781G>A	ENST00000286355.5	-	2	3060	c.968C>T	c.(967-969)gCc>gTc	p.A323V	ADCY8_ENST00000377928.3_Missense_Mutation_p.A323V	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	323					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)			CACTGCCTGGGCCACAACCTA	0.428										HNSCC(32;0.087)																											p.A323V		Atlas-SNP	.											.	ADCY8	291	.	0			c.C968T						PASS	.						96.0	106.0	103.0					8																	132002781		2203	4300	6503	SO:0001583	missense	114	exon2			GCCTGGGCCACAA	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.968C>T	chr8.hg19:g.132002781G>A	ENSP00000286355:p.Ala323Val	70.0	0.0	.		91.0	8.0	.	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767301	0.90020	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.81163	-1.46;-1.45	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.89326	0.6683	M	0.76002	2.32	0.58432	D	0.999991	D;P	0.63880	0.993;0.455	D;B	0.70227	0.968;0.214	D	0.88311	0.2956	10	0.44086	T	0.13	.	18.7877	0.91961	0.0:0.0:1.0:0.0	.	323;323	E7EVL1;P40145	.;ADCY8_HUMAN	V	323	ENSP00000286355:A323V;ENSP00000367161:A323V	ENSP00000286355:A323V	A	-	2	0	ADCY8	132071963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.792000	0.99085	2.751000	0.94390	0.650000	0.86243	GCC	.	.	.	none		0.428	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
RMI1	80010	hgsc.bcm.edu	37	9	86617525	86617525	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:86617525G>T	ENST00000325875.3	+	3	1956	c.1624G>T	c.(1624-1626)Gat>Tat	p.D542Y		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	542					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)				biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						TGCATATCTAGATGTAGACTT	0.368																																					p.D542Y		Atlas-SNP	.											.	RMI1	50	.	0			c.G1624T						PASS	.						197.0	193.0	194.0					9																	86617525		2203	4300	6503	SO:0001583	missense	80010	exon3			TATCTAGATGTAG	AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"""BLM-Associated Polypeptide, 75 kDa"""	610404	"""chromosome 9 open reading frame 76"", ""RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"""	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.1624G>T	chr9.hg19:g.86617525G>T	ENSP00000317039:p.Asp542Tyr	110.0	0.0	.		97.0	19.0	.	NM_024945	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	hg19	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935730	0.52972	.	.	ENSG00000178966	ENST00000325875	T	0.47177	0.85	5.29	5.29	0.74685	.	0.104013	0.64402	D	0.000005	T	0.61198	0.2328	L	0.55481	1.735	0.47659	D	0.999484	D	0.89917	1.0	D	0.70487	0.969	T	0.58702	-0.7590	9	.	.	.	-9.5894	12.6452	0.56731	0.0762:0.0:0.9238:0.0	.	542	Q9H9A7	RMI1_HUMAN	Y	542	ENSP00000317039:D542Y	.	D	+	1	0	RMI1	85807345	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.827000	0.75303	2.620000	0.88729	0.563000	0.77884	GAT	.	.	.	none		0.368	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945	
LPAR1	1902	hgsc.bcm.edu	37	9	113704022	113704022	+	Missense_Mutation	SNP	G	G	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:113704022G>A	ENST00000374431.3	-	4	855	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	LPAR1_ENST00000374430.2_Missense_Mutation_p.R158W|LPAR1_ENST00000541779.1_Missense_Mutation_p.R159W|LPAR1_ENST00000538760.1_Missense_Mutation_p.R159W|LPAR1_ENST00000358883.4_Missense_Mutation_p.R158W	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	158					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.R158W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						TTGCTCATCCGTGTGTGGAGC	0.542																																					p.R158W	NSCLC(115;661 2323 9836 34256)	Atlas-SNP	.											LPAR1,colon,carcinoma,0,1	LPAR1	48	.	1	Substitution - Missense(1)	large_intestine(1)	c.C472T						PASS	.						117.0	104.0	109.0					9																	113704022		2203	4300	6503	SO:0001583	missense	1902	exon3			TCATCCGTGTGTG	U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3166	protein-coding gene	gene with protein product		602282	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"""	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.472C>T	chr9.hg19:g.113704022G>A	ENSP00000363553:p.Arg158Trp	154.0	0.0	.		180.0	28.0	.	NM_001401	B4DK36|O00656|O00722|P78351	Missense_Mutation	SNP	ENST00000374431.3	hg19	CCDS6777.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017060	0.75161	.	.	ENSG00000198121	ENST00000374431;ENST00000541779;ENST00000374430;ENST00000358883;ENST00000449490;ENST00000538760;ENST00000441240	T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07	5.53	4.64	0.57946	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60301	0.2258	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.983;0.983	T	0.63189	-0.6693	10	0.72032	D	0.01	.	8.4744	0.33005	0.0771:0.0:0.7707:0.1522	.	159;159;158	B4DQ18;B4DK36;Q92633	.;.;LPAR1_HUMAN	W	158;159;158;158;140;159;158	ENSP00000363553:R158W;ENSP00000445697:R159W;ENSP00000363552:R158W;ENSP00000351755:R158W;ENSP00000440201:R159W;ENSP00000401810:R158W	ENSP00000351755:R158W	R	-	1	2	LPAR1	112743843	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.528000	0.73807	1.357000	0.45904	0.655000	0.94253	CGG	.	.	.	none		0.542	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159	
SPTAN1	6709	hgsc.bcm.edu	37	9	131362363	131362363	+	Missense_Mutation	SNP	A	A	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:131362363A>T	ENST00000372731.4	+	27	3658	c.3548A>T	c.(3547-3549)gAa>gTa	p.E1183V	SPTAN1_ENST00000372739.3_Missense_Mutation_p.E1183V|SPTAN1_ENST00000358161.5_Missense_Mutation_p.E1183V	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1183					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GAATAGGATGAAACTGATTCC	0.433																																					p.E1183V	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A3548T						PASS	.						125.0	114.0	118.0					9																	131362363		2203	4300	6503	SO:0001583	missense	6709	exon27			AGGATGAAACTGA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3548A>T	chr9.hg19:g.131362363A>T	ENSP00000361816:p.Glu1183Val	108.0	0.0	.		94.0	9.0	.	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.305120	0.60305	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.51574	0.7;0.72;0.7	6.08	6.08	0.98989	.	0.142496	0.64402	D	0.000006	T	0.40398	0.1115	N	0.19112	0.55	0.80722	D	1	P;B;B;B	0.36733	0.567;0.384;0.384;0.265	B;B;B;B	0.39840	0.18;0.311;0.311;0.165	T	0.42103	-0.9471	10	0.87932	D	0	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	1183;1163;1183;1183	A6NG51;Q13813-3;Q13813-2;Q13813	.;.;.;SPTA2_HUMAN	V	1183;1183;1183;1163	ENSP00000350882:E1183V;ENSP00000361816:E1183V;ENSP00000361824:E1183V	ENSP00000350882:E1183V	E	+	2	0	SPTAN1	130402184	1.000000	0.71417	0.945000	0.38365	0.557000	0.35523	8.593000	0.90832	2.333000	0.79357	0.533000	0.62120	GAA	.	.	.	none		0.433	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
LCN10	414332	hgsc.bcm.edu	37	9	139633991	139633991	+	Missense_Mutation	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:139633991T>C	ENST00000474369.1	-	5	549	c.550A>G	c.(550-552)Acc>Gcc	p.T184A	LCN10_ENST00000497771.1_Missense_Mutation_p.T197A|LCN10_ENST00000527229.1_Missense_Mutation_p.T161A|LCN6_ENST00000480584.1_5'Flank|LCN6_ENST00000435202.1_3'UTR			Q6JVE6	LCN10_HUMAN	lipocalin 10	184					transport (GO:0006810)	extracellular region (GO:0005576)				breast(2)|cervix(1)|large_intestine(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		GGCAGGATGGTGTGTGTACGG	0.617																																					p.T197A		Atlas-SNP	.											.	LCN10	21	.	0			c.A589G						PASS	.						92.0	76.0	81.0					9																	139633991		2199	4295	6494	SO:0001583	missense	414332	exon6			GGATGGTGTGTGT	AY301271	CCDS35182.2	9q34.3	2011-10-24			ENSG00000187922	ENSG00000187922		"""Lipocalins"""	20892	protein-coding gene	gene with protein product		612904				15363845	Standard	NM_001001712		Approved		uc004civ.3	Q6JVE6	OTTHUMG00000150428	ENST00000474369.1:c.550A>G	chr9.hg19:g.139633991T>C	ENSP00000420564:p.Thr184Ala	140.0	0.0	.		196.0	24.0	.	NM_001001712	A2RUU3|B0QZ79	Missense_Mutation	SNP	ENST00000474369.1	hg19	CCDS35182.2	.	.	.	.	.	.	.	.	.	.	T	13.52	2.260996	0.39995	.	.	ENSG00000187922	ENST00000527229;ENST00000497771;ENST00000474369	T;T	0.33865	1.39;1.41	3.17	2.04	0.26737	.	0.000000	0.36002	U	0.002855	T	0.39655	0.1086	.	.	.	0.27101	N	0.962612	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.63957	0.92;0.92;0.92	T	0.17410	-1.0370	9	0.19147	T	0.46	-7.4152	4.3041	0.10938	0.0:0.1588:0.0:0.8412	.	161;184;197	E9PK15;Q6JVE6;Q6JVE6-2	.;LCN10_HUMAN;.	A	161;197;184	ENSP00000418491:T197A;ENSP00000420564:T184A	ENSP00000420564:T184A	T	-	1	0	LCN10	138753812	0.530000	0.26330	1.000000	0.80357	0.718000	0.41266	1.557000	0.36299	1.410000	0.46936	0.451000	0.29950	ACC	.	.	.	none		0.617	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712	
CUBN	8029	hgsc.bcm.edu	37	10	16941145	16941145	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:16941145G>C	ENST00000377833.4	-	54	8513	c.8448C>G	c.(8446-8448)atC>atG	p.I2816M		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2816	CUB 21. {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)	GAGGGGATCTGATTGTACCAT	0.403																																					p.I2816M		Atlas-SNP	.											.	CUBN	515	.	0			c.C8448G						PASS	.						118.0	112.0	114.0					10																	16941145		2203	4300	6503	SO:0001583	missense	8029	exon54			GGATCTGATTGTA	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.8448C>G	chr10.hg19:g.16941145G>C	ENSP00000367064:p.Ile2816Met	92.0	0.0	.		100.0	4.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.139005	0.21123	.	.	ENSG00000107611	ENST00000377833	T	0.40476	1.03	5.63	0.557	0.17260	CUB (5);	0.137522	0.33057	N	0.005332	T	0.64494	0.2603	M	0.93150	3.385	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.64782	-0.6326	10	0.66056	D	0.02	.	7.5405	0.27735	0.1201:0.0:0.4925:0.3874	.	2816	O60494	CUBN_HUMAN	M	2816	ENSP00000367064:I2816M	ENSP00000367064:I2816M	I	-	3	3	CUBN	16981151	1.000000	0.71417	0.001000	0.08648	0.014000	0.08584	3.071000	0.50041	-0.070000	0.12908	-0.940000	0.02684	ATC	.	.	.	none		0.403	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
NUDT13	25961	hgsc.bcm.edu	37	10	74879794	74879794	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:74879794G>T	ENST00000357321.4	+	3	220	c.102G>T	c.(100-102)aaG>aaT	p.K34N	NUDT13_ENST00000372997.3_Missense_Mutation_p.K34N|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000544879.1_5'UTR|NUDT13_ENST00000537969.1_5'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.K34N	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					TTGAACTGAAGGAAGATGATG	0.403																																					p.K34N		Atlas-SNP	.											.	NUDT13	16	.	0			c.G102T						PASS	.						134.0	144.0	141.0					10																	74879794		2203	4300	6503	SO:0001583	missense	25961	exon3			ACTGAAGGAAGAT	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"""Nudix motif containing"""	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.102G>T	chr10.hg19:g.74879794G>T	ENSP00000349874:p.Lys34Asn	51.0	0.0	.		43.0	15.0	.	NM_015901		Missense_Mutation	SNP	ENST00000357321.4	hg19	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.736917	0.69304	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.58797	1.36;0.36;0.31	5.18	-2.34	0.06704	.	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.992;0.993	T	0.59862	-0.7374	10	0.72032	D	0.01	-2.5729	12.2089	0.54369	0.6313:0.0:0.3687:0.0	.	34;34;34	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	N	34	ENSP00000349874:K34N;ENSP00000335326:K34N;ENSP00000362088:K34N	ENSP00000335326:K34N	K	+	3	2	NUDT13	74549800	0.999000	0.42202	0.977000	0.42913	0.998000	0.95712	0.456000	0.21859	-0.547000	0.06207	0.655000	0.94253	AAG	.	.	.	none		0.403	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901	
LZTS2	84445	hgsc.bcm.edu	37	10	102763858	102763858	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:102763858G>C	ENST00000370220.1	+	2	4066	c.1003G>C	c.(1003-1005)Gac>Cac	p.D335H	LZTS2_ENST00000370223.3_Missense_Mutation_p.D335H					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		AAAGCTCCGAGACCGGGAGGC	0.637																																					p.D335H	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	LZTS2	57	.	0			c.G1003C						PASS	.						43.0	47.0	46.0					10																	102763858		2202	4297	6499	SO:0001583	missense	84445	exon3			CTCCGAGACCGGG	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.1003G>C	chr10.hg19:g.102763858G>C	ENSP00000359240:p.Asp335His	122.0	0.0	.		156.0	33.0	.	NM_032429		Missense_Mutation	SNP	ENST00000370220.1	hg19	CCDS7507.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123472	0.56613	.	.	ENSG00000107816	ENST00000370223;ENST00000315797;ENST00000370220	T;T	0.41065	1.01;1.01	5.12	4.19	0.49359	.	0.157325	0.56097	D	0.000028	T	0.42494	0.1205	L	0.39898	1.24	0.43222	D	0.995102	P	0.40398	0.716	P	0.45946	0.498	T	0.20405	-1.0276	9	.	.	.	-23.6803	15.3201	0.74115	0.0:0.1408:0.8592:0.0	.	335	Q9BRK4	LZTS2_HUMAN	H	335	ENSP00000359243:D335H;ENSP00000359240:D335H	.	D	+	1	0	LZTS2	102753848	1.000000	0.71417	0.732000	0.30844	0.655000	0.38815	7.542000	0.82095	1.243000	0.43853	0.561000	0.74099	GAC	.	.	.	none		0.637	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
TIAL1	7073	hgsc.bcm.edu	37	10	121338280	121338280	+	Missense_Mutation	SNP	A	A	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:121338280A>C	ENST00000436547.2	-	7	558	c.514T>G	c.(514-516)Tgg>Ggg	p.W172G	TIAL1_ENST00000369092.4_Missense_Mutation_p.W49G|TIAL1_ENST00000463089.2_5'Flank|TIAL1_ENST00000369093.2_Missense_Mutation_p.W189G	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	172	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		CGAGTGGCCCAATTGGTTCGG	0.398																																					p.W189G		Atlas-SNP	.											.	TIAL1	47	.	0			c.T565G						PASS	.						160.0	141.0	147.0					10																	121338280		2203	4300	6503	SO:0001583	missense	7073	exon7			TGGCCCAATTGGT	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"""RNA binding motif (RRM) containing"""	11804	protein-coding gene	gene with protein product		603413	"""TIA1 cytotoxic granule-associated RNA-binding protein-like 1"""			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.514T>G	chr10.hg19:g.121338280A>C	ENSP00000394902:p.Trp172Gly	173.0	0.0	.		183.0	39.0	.	NM_001033925	A8K3T0|A8K4L9	Missense_Mutation	SNP	ENST00000436547.2	hg19	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385753	0.82792	.	.	ENSG00000151923	ENST00000369093;ENST00000369092;ENST00000436547	T;T;T	0.75367	3.33;-0.93;-0.93	5.61	5.61	0.85477	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	D	0.85008	0.5599	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	0.993;1.0;1.0;0.999	D;D;D;D	0.91635	0.968;0.999;0.994;0.966	D	0.86674	0.1912	10	0.87932	D	0	-1.9553	15.8113	0.78568	1.0:0.0:0.0:0.0	.	49;49;189;172	B4DHS3;Q49AS9;A8K4L9;Q01085	.;.;.;TIAR_HUMAN	G	189;49;172	ENSP00000358089:W189G;ENSP00000358088:W49G;ENSP00000394902:W172G	ENSP00000358088:W49G	W	-	1	0	TIAL1	121328270	1.000000	0.71417	0.993000	0.49108	0.863000	0.49368	9.125000	0.94402	2.137000	0.66172	0.482000	0.46254	TGG	.	.	.	none		0.398	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252	
WDR11	55717	hgsc.bcm.edu	37	10	122664157	122664157	+	Splice_Site	SNP	G	G	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:122664157G>A	ENST00000263461.6	+	25	3273		c.e25-1		WDR11_ENST00000604509.1_Intron	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11						cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TCTCTTACTAGACAGACAGAG	0.358																																					.		Atlas-SNP	.											.	WDR11	95	.	0			c.3028-1G>A						PASS	.						93.0	89.0	90.0					10																	122664157		2203	4300	6503	SO:0001630	splice_region_variant	55717	exon25			TTACTAGACAGAC	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3028-1G>A	chr10.hg19:g.122664157G>A		93.0	0.0	.		98.0	15.0	.	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Splice_Site	SNP	ENST00000263461.6	hg19	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566439	0.86439	.	.	ENSG00000120008	ENST00000263461	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR11	122654147	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.434000	0.97515	2.836000	0.97738	0.655000	0.94253	.	.	.	.	none		0.358	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		Intron
C11orf40	143501	hgsc.bcm.edu	37	11	4592781	4592781	+	Missense_Mutation	SNP	G	G	C	rs573632085	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:4592781G>C	ENST00000307616.1	-	4	525	c.526C>G	c.(526-528)Cgc>Ggc	p.R176G		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	176										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		taatcagtgcggtccaattca	0.433																																					p.R176G		Atlas-SNP	.											.	C11orf40	37	.	0			c.C526G						PASS	.						81.0	73.0	76.0					11																	4592781		2201	4298	6499	SO:0001583	missense	143501	exon4			CAGTGCGGTCCAA		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.526C>G	chr11.hg19:g.4592781G>C	ENSP00000302918:p.Arg176Gly	67.0	0.0	.		86.0	14.0	.	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.039801	0.00402	.	.	ENSG00000171987	ENST00000307616	T	0.55930	0.49	0.832	-1.66	0.08265	.	.	.	.	.	T	0.26774	0.0655	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.08743	-1.0707	9	0.87932	D	0	.	3.0485	0.06161	0.2412:0.0:0.4837:0.275	.	176	Q8WZ69	CK040_HUMAN	G	176	ENSP00000302918:R176G	ENSP00000302918:R176G	R	-	1	0	C11orf40	4549357	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.923000	0.04000	-1.894000	0.01105	-1.561000	0.00884	CGC	.	.	.	none		0.433	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
DCHS1	8642	hgsc.bcm.edu	37	11	6646473	6646473	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:6646473C>G	ENST00000299441.3	-	19	7513	c.7102G>C	c.(7102-7104)Gat>Cat	p.D2368H	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2368	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATTGACATCCTCCACAAGC	0.587																																					p.D2368H		Atlas-SNP	.											.	DCHS1	277	.	0			c.G7102C						PASS	.						101.0	92.0	95.0					11																	6646473		2201	4296	6497	SO:0001583	missense	8642	exon19			TGACATCCTCCAC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.7102G>C	chr11.hg19:g.6646473C>G	ENSP00000299441:p.Asp2368His	97.0	0.0	.		136.0	20.0	.	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	c	22.9	4.351321	0.82132	.	.	ENSG00000166341	ENST00000299441	T	0.76186	-1.0	4.94	4.94	0.65067	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.43747	D	0.000525	D	0.91202	0.7228	H	0.97682	4.055	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94164	0.7417	10	0.87932	D	0	.	16.9335	0.86197	0.0:1.0:0.0:0.0	.	2368	Q96JQ0	PCD16_HUMAN	H	2368	ENSP00000299441:D2368H	ENSP00000299441:D2368H	D	-	1	0	DCHS1	6603049	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.632000	0.83247	2.560000	0.86352	0.651000	0.88453	GAT	.	.	.	none		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
LRP4	4038	hgsc.bcm.edu	37	11	46898795	46898795	+	Missense_Mutation	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:46898795T>C	ENST00000378623.1	-	23	3474	c.3232A>G	c.(3232-3234)Att>Gtt	p.I1078V	LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1078					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TTCATGGTAATGTTGATTGGT	0.507																																					p.I1078V		Atlas-SNP	.											.	LRP4	160	.	0			c.A3232G						PASS	.						250.0	187.0	208.0					11																	46898795		2201	4299	6500	SO:0001583	missense	4038	exon23			TGGTAATGTTGAT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3232A>G	chr11.hg19:g.46898795T>C	ENSP00000367888:p.Ile1078Val	183.0	0.0	.		176.0	25.0	.	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.991485	0.35131	.	.	ENSG00000134569	ENST00000378623	D	0.90955	-2.76	6.17	-1.45	0.08828	Six-bladed beta-propeller, TolB-like (1);	0.729507	0.14357	N	0.324711	T	0.70850	0.3271	N	0.00926	-1.1	0.20926	N	0.999826	B	0.02656	0.0	B	0.01281	0.0	T	0.58440	-0.7636	10	0.14656	T	0.56	.	13.3945	0.60843	0.0:0.5812:0.0:0.4188	.	1078	O75096	LRP4_HUMAN	V	1078	ENSP00000367888:I1078V	ENSP00000367888:I1078V	I	-	1	0	LRP4	46855371	1.000000	0.71417	0.959000	0.39883	0.998000	0.95712	0.814000	0.27239	-0.251000	0.09542	0.533000	0.62120	ATT	.	.	.	none		0.507	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
AMOTL1	154810	hgsc.bcm.edu	37	11	94533391	94533391	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:94533391G>T	ENST00000433060.2	+	3	1176	c.1035G>T	c.(1033-1035)atG>atT	p.M345I	AMOTL1_ENST00000317837.9_Missense_Mutation_p.M345I|AMOTL1_ENST00000317829.8_Missense_Mutation_p.M295I	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	345					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				TCCACGAGATGGTCAAGCCCT	0.562																																					p.M345I		Atlas-SNP	.											.	AMOTL1	95	.	0			c.G1035T						PASS	.						115.0	116.0	116.0					11																	94533391		2016	4172	6188	SO:0001583	missense	154810	exon3			CGAGATGGTCAAG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1035G>T	chr11.hg19:g.94533391G>T	ENSP00000387739:p.Met345Ile	121.0	0.0	.		127.0	22.0	.	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471025	0.43942	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000317837;ENST00000433060	T;T;T	0.13307	2.6;2.6;2.6	5.13	4.15	0.48705	.	0.155049	0.44688	D	0.000423	T	0.10380	0.0254	L	0.40543	1.245	0.30008	N	0.815444	B;B	0.16802	0.013;0.019	B;B	0.13407	0.009;0.006	T	0.06127	-1.0844	9	.	.	.	-21.0972	7.6609	0.28402	0.0937:0.2865:0.6198:0.0	.	295;345	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	I	295;351;345;345	ENSP00000320968:M295I;ENSP00000323474:M345I;ENSP00000387739:M345I	.	M	+	3	0	AMOTL1	94173039	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.997000	0.29731	2.395000	0.81488	0.555000	0.69702	ATG	.	.	.	none		0.562	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
TMBIM4	51643	hgsc.bcm.edu	37	12	66546147	66546147	+	Silent	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:66546147T>C	ENST00000358230.3	-	3	336	c.216A>G	c.(214-216)ttA>ttG	p.L72L	TMBIM4_ENST00000544599.1_5'UTR|TMBIM4_ENST00000556010.1_Silent_p.L72L|TMBIM4_ENST00000286424.7_Silent_p.L119L|TMBIM4_ENST00000398033.4_Silent_p.L72L|TMBIM4_ENST00000539652.1_Silent_p.L72L|TMBIM4_ENST00000542724.1_Silent_p.L41L	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	72					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		ACAGCAAAATTAAGGCAGGAC	0.303																																					p.L72L		Atlas-SNP	.											.	TMBIM4	47	.	0			c.A216G						PASS	.						79.0	75.0	76.0					12																	66546147		1821	4077	5898	SO:0001819	synonymous_variant	51643	exon3			CAAAATTAAGGCA	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.216A>G	chr12.hg19:g.66546147T>C		114.0	0.0	.		123.0	20.0	.	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Silent	SNP	ENST00000358230.3	hg19	CCDS41805.1																																																																																			.	.	.	none		0.303	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056	
ZNF140	7699	hgsc.bcm.edu	37	12	133683062	133683062	+	Missense_Mutation	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:133683062T>C	ENST00000355557.2	+	5	2482	c.1199T>C	c.(1198-1200)cTc>cCc	p.L400P	ZNF140_ENST00000440550.2_3'UTR|ZNF140_ENST00000544426.1_Missense_Mutation_p.L297P	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	400					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)			NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AGCTTTTCCCTCATTCTACAT	0.448																																					p.L400P		Atlas-SNP	.											.	ZNF140	18	.	0			c.T1199C						PASS	.						90.0	91.0	91.0					12																	133683062		2203	4300	6503	SO:0001583	missense	7699	exon5			TTTCCCTCATTCT	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"""Zinc fingers, C2H2-type"", ""-"""	12925	protein-coding gene	gene with protein product		604082	"""zinc finger protein 140 (clone pHZ-39)"""			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1199T>C	chr12.hg19:g.133683062T>C	ENSP00000347755:p.Leu400Pro	21.0	0.0	.		47.0	7.0	.	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	hg19	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.296703	0.60086	.	.	ENSG00000196387	ENST00000355557;ENST00000544426;ENST00000433577	T;T	0.14266	2.52;2.52	3.85	3.85	0.44370	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31859	N	0.006952	T	0.39627	0.1085	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36672	-0.9738	10	0.87932	D	0	.	7.0829	0.25241	0.0:0.1065:0.0:0.8935	.	400	P52738	ZN140_HUMAN	P	400;297;191	ENSP00000347755:L400P;ENSP00000445411:L297P	ENSP00000347755:L400P	L	+	2	0	ZNF140	132193135	0.996000	0.38824	0.998000	0.56505	0.958000	0.62258	5.435000	0.66532	1.736000	0.51660	0.460000	0.39030	CTC	.	.	.	none		0.448	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440	
KCTD12	115207	hgsc.bcm.edu	37	13	77460122	77460122	+	Silent	SNP	C	C	G	rs371800969		TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr13:77460122C>G	ENST00000377474.2	-	1	403	c.162G>C	c.(160-162)tcG>tcC	p.S54S	AC000403.1_ENST00000579275.1_RNA|KCTD12_ENST00000317765.2_Silent_p.S54S	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	54					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		AGTCGGGCACCGACACCACCG	0.692																																					p.S54S		Atlas-SNP	.											.	KCTD12	11	.	0			c.G162C						PASS	.	C		0,4356		0,0,2178	16.0	15.0	15.0		162	0.4	1.0	13		15	2,8550		0,2,4274	no	coding-synonymous	KCTD12	NM_138444.3		0,2,6452	GG,GC,CC		0.0234,0.0,0.0155		54/326	77460122	2,12906	2178	4276	6454	SO:0001819	synonymous_variant	115207	exon1			GGGCACCGACACC	AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"""predominantly fetal expressed T1 domain"""	610521	"""chromosome 13 open reading frame 2"", ""potassium channel tetramerisation domain containing 12"""	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.162G>C	chr13.hg19:g.77460122C>G		2.0	0.0	.		6.0	4.0	.	NM_138444		Silent	SNP	ENST00000377474.2	hg19	CCDS9455.1																																																																																			.	.	.	weak		0.692	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444	
TEP1	7011	hgsc.bcm.edu	37	14	20845648	20845648	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:20845648G>T	ENST00000262715.5	-	41	5919	c.5879C>A	c.(5878-5880)tCc>tAc	p.S1960Y	TEP1_ENST00000545983.1_Missense_Mutation_p.S298Y|TEP1_ENST00000556935.1_Missense_Mutation_p.S1852Y	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1960					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGCCCCCTGGGAACCTAGAGA	0.582																																					p.S1960Y		Atlas-SNP	.											.	TEP1	224	.	0			c.C5879A						PASS	.						53.0	54.0	54.0					14																	20845648		2203	4300	6503	SO:0001583	missense	7011	exon41			CCCTGGGAACCTA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5879C>A	chr14.hg19:g.20845648G>T	ENSP00000262715:p.Ser1960Tyr	79.0	0.0	.		76.0	17.0	.	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164956	0.78339	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.71461	0.73;-0.57;1.23	5.33	5.33	0.75918	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.606102	0.17469	N	0.173149	T	0.80639	0.4661	M	0.71036	2.16	0.38057	D	0.935966	D;D;D;D	0.59767	0.976;0.983;0.986;0.971	P;P;P;P	0.57152	0.556;0.804;0.814;0.641	D	0.83486	0.0067	10	0.59425	D	0.04	-4.4509	15.9418	0.79758	0.0:0.0:1.0:0.0	.	298;1852;1303;1960	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	Y	1960;1960;1852;298	ENSP00000262715:S1960Y;ENSP00000452574:S1852Y;ENSP00000438849:S298Y	ENSP00000262715:S1960Y	S	-	2	0	TEP1	19915488	0.983000	0.35010	0.894000	0.35097	0.940000	0.58332	4.982000	0.63825	2.502000	0.84385	0.563000	0.77884	TCC	.	.	.	none		0.582	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
CDH24	64403	hgsc.bcm.edu	37	14	23524349	23524349	+	Nonsense_Mutation	SNP	T	T	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:23524349T>A	ENST00000267383.5	-	2	507	c.415A>T	c.(415-417)Aaa>Taa	p.K139*	CDH24_ENST00000554034.1_Nonsense_Mutation_p.K139*|CDH24_ENST00000397359.3_Nonsense_Mutation_p.K139*|CDH24_ENST00000487137.2_Nonsense_Mutation_p.K139*			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	139	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TCTTGCACTTTGATGATGAAC	0.587											OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K139X		Atlas-SNP	.											.	CDH24	129	.	0			c.A415T						PASS	.						86.0	90.0	88.0					14																	23524349		2203	4300	6503	SO:0001587	stop_gained	64403	exon3			GCACTTTGATGAT	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.415A>T	chr14.hg19:g.23524349T>A	ENSP00000267383:p.Lys139*	118.0	0.0	.	764	138.0	23.0	.	NM_022478	D3DS44|Q86UP1|Q9NT84	Nonsense_Mutation	SNP	ENST00000267383.5	hg19	CCDS9585.1	.	.	.	.	.	.	.	.	.	.	T	36	5.772834	0.96922	.	.	ENSG00000139880	ENST00000397359;ENST00000487137;ENST00000422751;ENST00000554034;ENST00000267383	.	.	.	3.72	3.72	0.42706	.	0.061985	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8066	0.52158	0.0:0.0:0.0:1.0	.	.	.	.	X	139	.	ENSP00000267383:K139X	K	-	1	0	CDH24	22594189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	1.689000	0.51079	0.459000	0.35465	AAA	.	.	.	none		0.587	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478	
NYNRIN	57523	hgsc.bcm.edu	37	14	24885037	24885037	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:24885037G>T	ENST00000382554.3	+	9	4400	c.4082G>T	c.(4081-4083)gGc>gTc	p.G1361V		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1361					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GTGGCCTGCGGCCTGGAGCGC	0.627																																					p.G1361V		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G4082T						PASS	.						68.0	73.0	71.0					14																	24885037		1961	4143	6104	SO:0001583	missense	57523	exon9			CCTGCGGCCTGGA	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.4082G>T	chr14.hg19:g.24885037G>T	ENSP00000371994:p.Gly1361Val	66.0	0.0	.		85.0	27.0	.	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.597704	0.46318	.	.	ENSG00000205978	ENST00000382554	T	0.10668	2.85	4.93	4.02	0.46733	Ribonuclease H-like (1);	.	.	.	.	T	0.12603	0.0306	N	0.24115	0.695	0.49582	D	0.999804	P	0.50066	0.931	P	0.50860	0.652	T	0.03555	-1.1025	9	0.87932	D	0	.	11.5825	0.50900	0.0:0.3481:0.6519:0.0	.	1361	Q9P2P1	NYNRI_HUMAN	V	1361	ENSP00000371994:G1361V	ENSP00000371994:G1361V	G	+	2	0	NYNRIN	23954877	0.997000	0.39634	0.949000	0.38748	0.982000	0.71751	2.871000	0.48459	1.254000	0.44035	0.655000	0.94253	GGC	.	.	.	none		0.627	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
ATXN3	4287	hgsc.bcm.edu	37	14	92549507	92549507	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:92549507G>C	ENST00000532032.1	-	7	580	c.571C>G	c.(571-573)Ctt>Gtt	p.L191V	ATXN3_ENST00000340660.6_Missense_Mutation_p.L136V|ATXN3_ENST00000503767.1_Missense_Mutation_p.L176V|ATXN3_ENST00000502250.1_Missense_Mutation_p.L12V|ATXN3_ENST00000429774.2_Missense_Mutation_p.L176V|ATXN3_ENST00000393287.5_Missense_Mutation_p.L191V|ATXN3_ENST00000545170.1_Missense_Mutation_p.L191V|ATXN3_ENST00000554491.1_5'UTR			P54252	ATX3_HUMAN	ataxin 3	191					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		TCTCCAATAAGTTTTGGTCGA	0.368																																					p.L191V	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											.	ATXN3	46	.	0			c.C571G						PASS	.						146.0	138.0	141.0					14																	92549507		2203	4300	6503	SO:0001583	missense	4287	exon7			CAATAAGTTTTGG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.571C>G	chr14.hg19:g.92549507G>C	ENSP00000437157:p.Leu191Val	42.0	0.0	.		47.0	7.0	.	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.0	4.587229	0.86851	.	.	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220;ENST00000506466	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.55760	2.13;2.17;2.16;0.72;2.16;1.82;1.81;1.42;0.5;1.85;1.41;1.39;1.38;1.45	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.71592	0.3358	M	0.65498	2.005	0.58432	D	0.999997	D;D;D;D;D	0.71674	0.974;0.993;0.97;0.998;0.996	P;P;P;D;D	0.75484	0.829;0.901;0.804;0.986;0.966	T	0.71866	-0.4463	10	0.46703	T	0.11	.	18.7593	0.91843	0.0:0.0:1.0:0.0	.	191;176;191;136;191	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	V	191;191;191;191;191;191;191;176;190;191;12;176;136;191;121;12;190;93;140;85;125	ENSP00000445618:L191V;ENSP00000389376:L176V;ENSP00000376965:L191V;ENSP00000425322:L12V;ENSP00000426697:L176V;ENSP00000339110:L136V;ENSP00000437157:L191V;ENSP00000451001:L121V;ENSP00000450642:L12V;ENSP00000451385:L190V;ENSP00000451417:L93V;ENSP00000451996:L140V;ENSP00000450641:L85V;ENSP00000435571:L125V	ENSP00000339110:L136V	L	-	1	0	ATXN3	91619260	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.235000	0.51328	2.450000	0.82876	0.478000	0.44815	CTT	.	.	.	none		0.368	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
TLE3	7090	hgsc.bcm.edu	37	15	70368460	70368460	+	Missense_Mutation	SNP	T	T	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:70368460T>A	ENST00000558939.1	-	5	1649	c.272A>T	c.(271-273)cAg>cTg	p.Q91L	TLE3_ENST00000560939.1_Missense_Mutation_p.Q97L|TLE3_ENST00000442299.2_Missense_Mutation_p.Q91L|TLE3_ENST00000560589.1_Missense_Mutation_p.Q35L|TLE3_ENST00000557997.1_Missense_Mutation_p.Q91L|TLE3_ENST00000539550.1_Missense_Mutation_p.Q25L|TLE3_ENST00000557907.1_Missense_Mutation_p.Q91L|TLE3_ENST00000317509.8_Missense_Mutation_p.Q91L|TLE3_ENST00000559929.1_Missense_Mutation_p.Q91L|TLE3_ENST00000440567.3_Missense_Mutation_p.Q84L|TLE3_ENST00000451782.2_Missense_Mutation_p.Q91L|TLE3_ENST00000559048.1_Missense_Mutation_p.Q97L|TLE3_ENST00000558379.1_Missense_Mutation_p.Q91L|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000558201.1_Missense_Mutation_p.Q97L	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	91	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGGCATGATCTGTGCTAAAAT	0.438																																					p.Q91L		Atlas-SNP	.											.	TLE3	104	.	0			c.A272T						PASS	.						170.0	166.0	167.0					15																	70368460		1956	4138	6094	SO:0001583	missense	7090	exon5			ATGATCTGTGCTA	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.272A>T	chr15.hg19:g.70368460T>A	ENSP00000452871:p.Gln91Leu	56.0	0.0	.		57.0	7.0	.	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	hg19	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	T	33	5.250170	0.95305	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.63913	0.26;0.29;0.34;0.26;-0.07	5.85	5.85	0.93711	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.81635	0.4864	M	0.93854	3.465	0.80722	D	1	P;P;D;P;P;P;P;P	0.54397	0.851;0.927;0.966;0.877;0.748;0.877;0.62;0.911	B;P;P;P;P;P;P;P	0.56216	0.419;0.794;0.783;0.72;0.575;0.72;0.46;0.786	D	0.86775	0.1975	10	0.87932	D	0	-17.3549	16.2303	0.82332	0.0:0.0:0.0:1.0	.	84;91;91;91;91;91;97;25	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	L	91;91;91;84;25	ENSP00000390007:Q91L;ENSP00000394717:Q91L;ENSP00000319233:Q91L;ENSP00000415057:Q84L;ENSP00000442594:Q25L	ENSP00000319233:Q91L	Q	-	2	0	TLE3	68155514	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.924000	0.87555	2.233000	0.73108	0.533000	0.62120	CAG	.	.	.	none		0.438	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
UACA	55075	hgsc.bcm.edu	37	15	70961458	70961458	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:70961458G>C	ENST00000322954.6	-	16	1750	c.1565C>G	c.(1564-1566)gCc>gGc	p.A522G	UACA_ENST00000539319.1_Missense_Mutation_p.A413G|UACA_ENST00000379983.2_Missense_Mutation_p.A509G|UACA_ENST00000560441.1_Missense_Mutation_p.A507G	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	522					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTCTTTAAGGGCAAGAAAATG	0.378																																					p.A522G		Atlas-SNP	.											.	UACA	235	.	0			c.C1565G						PASS	.						226.0	204.0	211.0					15																	70961458		2199	4297	6496	SO:0001583	missense	55075	exon16			TTAAGGGCAAGAA	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.1565C>G	chr15.hg19:g.70961458G>C	ENSP00000314556:p.Ala522Gly	92.0	0.0	.		84.0	4.0	.	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	hg19	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171155	0.78452	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362;ENST00000539319	T;T;T	0.46451	0.87;0.89;1.33	5.68	5.68	0.88126	.	0.000000	0.56097	D	0.000034	T	0.67031	0.2850	M	0.74258	2.255	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.997;0.998	T	0.66060	-0.6017	10	0.48119	T	0.1	-10.6478	19.7842	0.96430	0.0:0.0:1.0:0.0	.	413;522;522;509	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	G	522;509;498;413	ENSP00000314556:A522G;ENSP00000369319:A509G;ENSP00000438667:A413G	ENSP00000314556:A522G	A	-	2	0	UACA	68748512	1.000000	0.71417	0.993000	0.49108	0.473000	0.32948	6.105000	0.71505	2.676000	0.91093	0.591000	0.81541	GCC	.	.	.	none		0.378	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
CYP11A1	1583	hgsc.bcm.edu	37	15	74640247	74640247	+	Missense_Mutation	SNP	A	A	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:74640247A>T	ENST00000268053.6	-	2	573	c.419T>A	c.(418-420)cTg>cAg	p.L140Q	CYP11A1_ENST00000358632.4_5'UTR|CYP11A1_ENST00000419019.2_Intron|CYP11A1_ENST00000541301.1_Missense_Mutation_p.L140Q	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	140					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	TCACTTCAACAGGACTCCTAT	0.622																																					p.L140Q	Esophageal Squamous(87;818 1337 4093 9268 37314)	Atlas-SNP	.											.	CYP11A1	54	.	0			c.T419A						PASS	.						45.0	42.0	43.0					15																	74640247		2197	4296	6493	SO:0001583	missense	1583	exon2			TTCAACAGGACTC	AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"""Cytochrome P450s"""	2590	protein-coding gene	gene with protein product	"""cholesterol monooxygenase (side-chain-cleaving)"""	118485	"""cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"""	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.419T>A	chr15.hg19:g.74640247A>T	ENSP00000268053:p.Leu140Gln	120.0	0.0	.		102.0	15.0	.	NM_000781	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Missense_Mutation	SNP	ENST00000268053.6	hg19	CCDS32291.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040820	0.55003	.	.	ENSG00000140459	ENST00000268053;ENST00000541301;ENST00000450547;ENST00000433240;ENST00000416978	T;T;T	0.71222	-0.55;-0.55;-0.55	4.46	4.46	0.54185	.	0.000000	0.64402	D	0.000001	T	0.81917	0.4924	M	0.71871	2.18	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.79108	0.929;0.992;0.929	T	0.83072	-0.0142	10	0.51188	T	0.08	-0.0287	13.4211	0.60998	1.0:0.0:0.0:0.0	.	140;140;140	E7EPP8;B4DTE5;P05108	.;.;CP11A_HUMAN	Q	140;140;52;140;140	ENSP00000268053:L140Q;ENSP00000439750:L140Q;ENSP00000388018:L140Q	ENSP00000268053:L140Q	L	-	2	0	CYP11A1	72427300	1.000000	0.71417	0.556000	0.28293	0.404000	0.30871	7.439000	0.80444	1.642000	0.50584	0.523000	0.50628	CTG	.	.	.	none		0.622	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1		
E4F1	1877	hgsc.bcm.edu	37	16	2285002	2285002	+	Splice_Site	SNP	G	G	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:2285002G>T	ENST00000301727.4	+	12	1983	c.1935G>T	c.(1933-1935)gaG>gaT	p.E645D	DNASE1L2_ENST00000567494.1_5'Flank|DNASE1L2_ENST00000564065.1_5'Flank|RP11-304L19.12_ENST00000564055.1_lincRNA|E4F1_ENST00000564139.1_Intron|DNASE1L2_ENST00000382437.4_5'Flank|DNASE1L2_ENST00000320700.5_5'Flank|E4F1_ENST00000565090.1_Splice_Site_p.E468D	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	645					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						ATATCATCGAGGTGGGTGTGG	0.662																																					p.E645D		Atlas-SNP	.											.	E4F1	53	.	0			c.G1935T						PASS	.						18.0	19.0	19.0					16																	2285002		2191	4296	6487	SO:0001630	splice_region_variant	1877	exon12			CATCGAGGTGGGT	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"""Zinc fingers, C2H2-type"""	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.1935+1G>T	chr16.hg19:g.2285002G>T		98.0	0.0	.		108.0	5.0	.	NM_004424	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	hg19	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.123776	0.37436	.	.	ENSG00000167967	ENST00000301727	T	0.36699	1.24	5.3	4.34	0.51931	.	0.101702	0.64402	D	0.000002	T	0.31420	0.0796	N	0.24115	0.695	0.80722	D	1	P	0.52842	0.956	P	0.47528	0.549	T	0.13522	-1.0506	10	0.87932	D	0	-29.9183	12.9793	0.58554	0.0806:0.0:0.9194:0.0	.	645	Q66K89	E4F1_HUMAN	D	645	ENSP00000301727:E645D	ENSP00000301727:E645D	E	+	3	2	E4F1	2225003	.	.	1.000000	0.80357	0.453000	0.32348	.	.	2.477000	0.83638	0.561000	0.74099	GAG	.	.	.	none		0.662	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	Missense_Mutation
SRCAP	10847	hgsc.bcm.edu	37	16	30734928	30734928	+	Silent	SNP	T	T	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:30734928T>C	ENST00000262518.4	+	25	4568	c.4183T>C	c.(4183-4185)Ttg>Ctg	p.L1395L	SRCAP_ENST00000395059.2_Silent_p.L1333L|SRCAP_ENST00000344771.4_Silent_p.L1237L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1395	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AGCTGCCCCCTTGACCATCTC	0.567																																					p.L1395L		Atlas-SNP	.											.	SRCAP	298	.	0			c.T4183C						PASS	.						149.0	141.0	144.0					16																	30734928		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon25			GCCCCCTTGACCA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4183T>C	chr16.hg19:g.30734928T>C		109.0	0.0	.		123.0	30.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.567	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
SLC12A3	6559	hgsc.bcm.edu	37	16	56919183	56919183	+	Missense_Mutation	SNP	A	A	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:56919183A>C	ENST00000563236.1	+	15	1857	c.1832A>C	c.(1831-1833)aAt>aCt	p.N611T	SLC12A3_ENST00000566786.1_Missense_Mutation_p.N610T|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N611T|SLC12A3_ENST00000262502.5_Missense_Mutation_p.N610T			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	611					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CCAGAGGTAAATTGGGGCTCC	0.567																																					p.N611T		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A1832C	GRCh37	CM075008	SLC12A3	M		PASS	.						85.0	63.0	70.0					16																	56919183		2156	4234	6390	SO:0001583	missense	6559	exon15			AGGTAAATTGGGG		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1832A>C	chr16.hg19:g.56919183A>C	ENSP00000456149:p.Asn611Thr	68.0	0.0	.		99.0	35.0	.	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386422	0.82902	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.4	5.4	0.78164	Amino acid permease domain (1);	0.088014	0.85682	D	0.000000	T	0.77478	0.4136	M	0.71296	2.17	0.80722	D	1	P;D;D	0.76494	0.735;0.999;0.999	B;D;D	0.74674	0.426;0.984;0.973	T	0.80415	-0.1392	9	0.87932	D	0	.	14.4174	0.67160	1.0:0.0:0.0:0.0	.	610;611;611	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	T	610;611	.	ENSP00000262502:N611T	N	+	2	0	SLC12A3	55476684	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.060000	0.93907	2.048000	0.60808	0.533000	0.62120	AAT	.	.	.	none		0.567	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
KIAA0753	9851	hgsc.bcm.edu	37	17	6526336	6526336	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:6526336G>C	ENST00000361413.3	-	6	1328	c.970C>G	c.(970-972)Cga>Gga	p.R324G	KIAA0753_ENST00000589033.1_5'Flank|KIAA0753_ENST00000542606.1_Missense_Mutation_p.R25G|KIAA0753_ENST00000572370.1_Missense_Mutation_p.R25G	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	324						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TGCTCCCCTCGGTCAGTAAAC	0.517																																					p.R324G		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C970G						PASS	.						62.0	60.0	60.0					17																	6526336		1915	4127	6042	SO:0001583	missense	9851	exon6			CCCCTCGGTCAGT		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.970C>G	chr17.hg19:g.6526336G>C	ENSP00000355250:p.Arg324Gly	178.0	0.0	.		256.0	68.0	.	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	hg19	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533928	0.27387	.	.	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86230	-2.09;-2.09	5.7	-0.0324	0.13905	.	0.841046	0.10770	N	0.636068	T	0.79052	0.4381	L	0.42245	1.32	0.80722	D	1	B	0.18013	0.025	B	0.17098	0.017	T	0.65903	-0.6055	10	0.30078	T	0.28	-0.3706	5.2141	0.15332	0.0698:0.1147:0.3462:0.4694	.	324	Q2KHM9	K0753_HUMAN	G	324;25	ENSP00000355250:R324G;ENSP00000444634:R25G	ENSP00000355250:R324G	R	-	1	2	KIAA0753	6467060	1.000000	0.71417	0.995000	0.50966	0.396000	0.30629	2.647000	0.46639	0.118000	0.18165	-1.035000	0.02400	CGA	.	.	.	none		0.517	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
SHBG	6462	hgsc.bcm.edu	37	17	7534128	7534128	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:7534128C>G	ENST00000380450.4	+	3	365	c.334C>G	c.(334-336)Cac>Gac	p.H112D	SHBG_ENST00000340624.5_Missense_Mutation_p.H54D|SAT2_ENST00000380466.2_5'Flank|SHBG_ENST00000576478.1_Missense_Mutation_p.H54D|SHBG_ENST00000575903.1_Missense_Mutation_p.H112D|SHBG_ENST00000576728.1_Missense_Mutation_p.H54D|SHBG_ENST00000570547.1_Missense_Mutation_p.H54D|SHBG_ENST00000441599.2_Missense_Mutation_p.H112D|SHBG_ENST00000575314.1_Missense_Mutation_p.H54D|SHBG_ENST00000572262.1_Missense_Mutation_p.H54D|SHBG_ENST00000574539.1_Missense_Mutation_p.H54D|SHBG_ENST00000416273.3_Missense_Mutation_p.H112D|SAT2_ENST00000269298.5_5'Flank|SHBG_ENST00000572182.1_Missense_Mutation_p.H54D	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	112	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	ACTGCACAATCACTGGGCCCA	0.567																																					p.H112D		Atlas-SNP	.											.	SHBG	21	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C334G						PASS	.						81.0	77.0	78.0					17																	7534128		2203	4300	6503	SO:0001583	missense	6462	exon3			CACAATCACTGGG		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"""androgen binding protein"""	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.334C>G	chr17.hg19:g.7534128C>G	ENSP00000369816:p.His112Asp	143.0	0.0	.		202.0	59.0	.	NM_001040	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	hg19	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	C	8.055	0.766779	0.15983	.	.	ENSG00000129214	ENST00000340624;ENST00000441599;ENST00000416273;ENST00000441313;ENST00000452698;ENST00000380450	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	5.04	-0.0208	0.13954	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	2.361970	0.01468	N	0.016151	T	0.71592	0.3358	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B;B;B;B;B;B;B	0.25007	0.01;0.045;0.023;0.001;0.013;0.116;0.116;0.03;0.007;0.013;0.013	B;B;B;B;B;B;B;B;B;B;B	0.28011	0.011;0.03;0.044;0.001;0.042;0.085;0.085;0.045;0.038;0.031;0.013	T	0.49194	-0.8965	10	0.12103	T	0.63	2.7497	9.104	0.36687	0.0:0.6418:0.1148:0.2435	.	112;107;85;112;112;112;85;85;85;112;54	F5H5Z8;P04278-2;B0FWH6;E9PH59;E9PGW1;E9PGQ3;B0FWH7;B0FWH5;B0FWH4;P04278;B4DYU0	.;.;.;.;.;.;.;.;.;SHBG_HUMAN;.	D	54;112;112;112;112;112	ENSP00000345675:H54D;ENSP00000393426:H112D;ENSP00000388867:H112D;ENSP00000369816:H112D	ENSP00000345675:H54D	H	+	1	0	SHBG	7474853	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	-0.109000	0.10840	-0.068000	0.12953	-1.134000	0.01955	CAC	.	.	.	none		0.567	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040	
SOCS7	30837	hgsc.bcm.edu	37	17	36508826	36508826	+	Silent	SNP	C	C	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:36508826C>A	ENST00000577233.1	+	1	699	c.699C>A	c.(697-699)acC>acA	p.T233T	SOCS7_ENST00000331159.5_Silent_p.T233T	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	233	Mediates interaction with SORBS3.				fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					GGGATGGGACCGGCAAGAGGC	0.667																																					p.T233T		Atlas-SNP	.											.	SOCS7	22	.	0			c.C699A						PASS	.						7.0	10.0	9.0					17																	36508826		2166	4235	6401	SO:0001819	synonymous_variant	30837	exon1			TGGGACCGGCAAG	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	29846	protein-coding gene	gene with protein product	"""Nck, Ash and phospholipase C binding protein"", ""NCK-associated protein 4"""	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.699C>A	chr17.hg19:g.36508826C>A		18.0	0.0	.		47.0	10.0	.	NM_014598	A2VCU2|Q0IJ63	Silent	SNP	ENST00000577233.1	hg19	CCDS32637.1																																																																																			.	.	.	none		0.667	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C	rs553572799|rs199957151	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:39240796G>C	ENST00000391417.4	+	1	338	c.338G>C	c.(337-339)aGc>aCc	p.S113T		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						tgccgccccagctgctgccgc	0.667																																					p.S113T		Atlas-SNP	.											.	KRTAP4-7	49	.	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						PASS	.																																			SO:0001583	missense	100132476	exon1			GCCCCAGCTGCTG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.338G>C	chr17.hg19:g.39240796G>C	ENSP00000375236:p.Ser113Thr	12.0	0.0	.		14.0	9.0	.	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	hg19	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.047	-1.263726	0.01433	.	.	ENSG00000240871	ENST00000391417	T	0.00627	6.12	2.73	1.66	0.24008	.	2.038930	0.02697	N	0.111300	T	0.00552	0.0018	.	.	.	0.21290	N	0.999731	B	0.13145	0.007	B	0.12837	0.008	T	0.47222	-0.9134	9	0.17832	T	0.49	.	5.1702	0.15107	0.0:0.2319:0.5315:0.2367	.	168	Q9BYR0	KRA47_HUMAN	T	113	ENSP00000375236:S113T	ENSP00000375236:S113T	S	+	2	0	KRTAP4-7	36494322	0.010000	0.17322	0.067000	0.19924	0.024000	0.10985	-0.517000	0.06275	0.191000	0.20236	0.289000	0.19496	AGC	.	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
TOB1	10140	hgsc.bcm.edu	37	17	48940734	48940734	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:48940734G>C	ENST00000268957.3	-	3	1073	c.645C>G	c.(643-645)gaC>gaG	p.D215E	TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Missense_Mutation_p.D215E	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	215					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GCTTCAAGAGGTCATTCACAT	0.527																																					p.D215E	NSCLC(144;643 1919 24513 29423 40686)	Atlas-SNP	.											.	TOB1	40	.	0			c.C645G						PASS	.						98.0	100.0	99.0					17																	48940734		2203	4300	6503	SO:0001583	missense	10140	exon2			CAAGAGGTCATTC	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.645C>G	chr17.hg19:g.48940734G>C	ENSP00000268957:p.Asp215Glu	135.0	0.0	.		230.0	64.0	.	NM_005749	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	hg19	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	G	6.571	0.473717	0.12521	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.39229	1.09;1.09	6.07	6.07	0.98685	.	0.168901	0.51477	D	0.000081	T	0.21550	0.0519	N	0.02539	-0.55	0.38296	D	0.94283	B	0.16396	0.017	B	0.12156	0.007	T	0.14254	-1.0479	10	0.38643	T	0.18	.	14.7663	0.69642	0.0684:0.0:0.9316:0.0	.	215	P50616	TOB1_HUMAN	E	215	ENSP00000427695:D215E;ENSP00000268957:D215E	ENSP00000268957:D215E	D	-	3	2	TOB1	46295733	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.185000	0.32065	2.885000	0.99019	0.655000	0.94253	GAC	.	.	.	none		0.527	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1		
TOMM40	10452	hgsc.bcm.edu	37	19	45397281	45397281	+	Missense_Mutation	SNP	G	G	A			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr19:45397281G>A	ENST00000426677.2	+	5	781	c.601G>A	c.(601-603)Gca>Aca	p.A201T	TOMM40_ENST00000592434.1_Missense_Mutation_p.A201T|TOMM40_ENST00000405636.2_Missense_Mutation_p.A201T|TOMM40_ENST00000252487.5_Missense_Mutation_p.A201T	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	201					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		TGACTTCACAGCAGCCGTCAC	0.617																																					p.A201T		Atlas-SNP	.											.	TOMM40	13	.	0			c.G601A						PASS	.						45.0	44.0	45.0					19																	45397281		2203	4300	6503	SO:0001583	missense	10452	exon5			TTCACAGCAGCCG	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.601G>A	chr19.hg19:g.45397281G>A	ENSP00000410339:p.Ala201Thr	75.0	0.0	.		106.0	12.0	.	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Missense_Mutation	SNP	ENST00000426677.2	hg19	CCDS12646.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176405	0.57692	.	.	ENSG00000130204	ENST00000426677;ENST00000405636;ENST00000252487	T;T;T	0.45668	0.89;0.89;0.89	4.76	4.76	0.60689	.	0.122142	0.53938	D	0.000046	T	0.39145	0.1067	L	0.49571	1.57	0.46701	D	0.999162	B;B	0.26975	0.165;0.037	B;B	0.28139	0.086;0.05	T	0.20306	-1.0279	10	0.28530	T	0.3	1.0773	15.2511	0.73545	0.0:0.0:1.0:0.0	.	201;201	O96008-2;O96008	.;TOM40_HUMAN	T	201	ENSP00000410339:A201T;ENSP00000385184:A201T;ENSP00000252487:A201T	ENSP00000252487:A201T	A	+	1	0	TOMM40	50089121	1.000000	0.71417	0.016000	0.15963	0.939000	0.58152	5.430000	0.66501	2.191000	0.70037	0.561000	0.74099	GCA	.	.	.	none		0.617	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
NKX2-2	4821	hgsc.bcm.edu	37	20	21492814	21492814	+	Missense_Mutation	SNP	T	T	G			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr20:21492814T>G	ENST00000377142.4	-	2	925	c.569A>C	c.(568-570)aAa>aCa	p.K190T	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	190					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						CTCCATACCTTTCTCGGCCCG	0.667																																					p.K190T		Atlas-SNP	.											.	NKX2-2	49	.	0			c.A569C						PASS	.						38.0	40.0	39.0					20																	21492814		2202	4300	6502	SO:0001583	missense	4821	exon2			ATACCTTTCTCGG	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"""Homeoboxes / ANTP class : NKL subclass"""	7835	protein-coding gene	gene with protein product		604612	"""NK-2 (Drosophila) homolog B"", ""NK2 transcription factor related, locus 2 (Drosophila)"""	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.569A>C	chr20.hg19:g.21492814T>G	ENSP00000366347:p.Lys190Thr	29.0	0.0	.		48.0	5.0	.	NM_002509		Missense_Mutation	SNP	ENST00000377142.4	hg19	CCDS13145.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.724176	0.89298	.	.	ENSG00000125820	ENST00000377142	D	0.91996	-2.95	5.35	5.35	0.76521	Homeobox (1);	0.000000	0.85682	D	0.000000	D	0.94499	0.8229	M	0.73217	2.22	0.80722	D	1	D	0.57257	0.979	P	0.57620	0.824	D	0.94718	0.7898	10	0.56958	D	0.05	.	15.3169	0.74089	0.0:0.0:0.0:1.0	.	190	O95096	NKX22_HUMAN	T	190	ENSP00000366347:K190T	ENSP00000366347:K190T	K	-	2	0	NKX2-2	21440814	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.002000	0.88514	2.014000	0.59158	0.379000	0.24179	AAA	.	.	.	none		0.667	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9		
SETD4	54093	hgsc.bcm.edu	37	21	37408418	37408418	+	Silent	SNP	G	G	C			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr21:37408418G>C	ENST00000399215.1	-	10	2692	c.1320C>G	c.(1318-1320)acC>acG	p.T440T	SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000332131.4_Silent_p.T440T|AP000688.1_ENST00000600312.1_Intron|SETD4_ENST00000399212.1_Silent_p.T416T			Q9NVD3	SETD4_HUMAN	SET domain containing 4	440				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GGTGAAATCAGGTAAAAGCTG	0.433																																					p.T440T		Atlas-SNP	.											.	SETD4	37	.	0			c.C1320G						PASS	.						147.0	146.0	146.0					21																	37408418		2203	4300	6503	SO:0001819	synonymous_variant	54093	exon11			AAATCAGGTAAAA	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 27"", ""chromosome 21 open reading frame 18"""	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.1320C>G	chr21.hg19:g.37408418G>C		78.0	0.0	.		65.0	13.0	.	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Silent	SNP	ENST00000399215.1	hg19	CCDS13640.1																																																																																			.	.	.	none		0.433	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	
MCM3AP	8888	hgsc.bcm.edu	37	21	47664760	47664760	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr21:47664760C>T	ENST00000397708.1	-	24	5253	c.4999G>A	c.(4999-5001)Ggg>Agg	p.G1667R	MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.G1667R|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1667	Acetyltransferase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AGCTGGAACCCGAGCACAGCC	0.642																																					p.G1667R		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G4999A						PASS	.						38.0	38.0	38.0					21																	47664760		2203	4300	6503	SO:0001583	missense	8888	exon23			GGAACCCGAGCAC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4999G>A	chr21.hg19:g.47664760C>T	ENSP00000380820:p.Gly1667Arg	152.0	0.0	.		138.0	32.0	.	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146050	0.37923	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03468	3.92;3.92	5.55	2.48	0.30137	.	0.335736	0.36409	N	0.002607	T	0.05456	0.0144	L	0.47716	1.5	0.29780	N	0.834087	B;D	0.59767	0.022;0.986	B;P	0.49421	0.005;0.61	T	0.14699	-1.0463	10	0.56958	D	0.05	-13.7278	5.035	0.14430	0.3494:0.4672:0.0:0.1834	.	1667;162	O60318;B3KT88	MCM3A_HUMAN;.	R	1667;1667;162	ENSP00000380820:G1667R;ENSP00000291688:G1667R	ENSP00000291688:G1667R	G	-	1	0	MCM3AP	46489188	0.922000	0.31269	0.682000	0.30024	0.188000	0.23474	1.789000	0.38724	0.711000	0.32018	-0.136000	0.14681	GGG	.	.	.	none		0.642	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
PI4KA	5297	hgsc.bcm.edu	37	22	21119517	21119517	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr22:21119517C>T	ENST00000572273.1	-	21	2501	c.2271G>A	c.(2269-2271)tgG>tgA	p.W757*	PI4KA_ENST00000466162.1_5'UTR|PI4KA_ENST00000255882.6_Nonsense_Mutation_p.W815*			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	757					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATTCTTCTGGCCAGAGTCCTG	0.493																																					p.W815X	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G2445A						PASS	.						93.0	97.0	96.0					22																	21119517		2203	4300	6503	SO:0001587	stop_gained	5297	exon21			TTCTGGCCAGAGT	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2271G>A	chr22.hg19:g.21119517C>T	ENSP00000458238:p.Trp757*	145.0	0.0	.		145.0	28.0	.	NM_058004	Q7Z625|Q9UPG2	Nonsense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	C	40	8.059858	0.98632	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5831	19.2017	0.93713	0.0:1.0:0.0:0.0	.	.	.	.	X	757	.	ENSP00000255882:W757X	W	-	3	0	PI4KA	19449517	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	7.539000	0.82063	2.770000	0.95276	0.650000	0.86243	TGG	.	.	.	none		0.493	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131801154	131801154	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:131801154delA	ENST00000326016.5	+	11	2116	c.1597delA	c.(1597-1599)aagfs	p.K533fs	ARHGEF4_ENST00000392953.3_Frame_Shift_Del_p.K533fs|ARHGEF4_ENST00000525839.1_Frame_Shift_Del_p.K533fs|ARHGEF4_ENST00000409303.1_Frame_Shift_Del_p.K473fs|ARHGEF4_ENST00000355771.3_Frame_Shift_Del_p.K462fs|ARHGEF4_ENST00000428230.2_Intron	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	533	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CTACTGTAAGAAGGTACCAGA	0.572																																					p.K532fs		Atlas-Indel,Pindel	.											.	ARHGEF4	89	.	0			c.1596delG						PASS	.						97.0	87.0	90.0					2																	131801154		2203	4300	6503	SO:0001589	frameshift_variant	50649	exon11			.	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1597delA	chr2.hg19:g.131801154delA	ENSP00000316845:p.Lys533fs	126.0	0.0	0		202.0	54.0	0.267327	NM_032995	Q9HDC6|Q9UPP0	Frame_Shift_Del	DEL	ENST00000326016.5	hg19	CCDS2165.1																																																																																			.	.	.	none		0.572	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
CTNNA1	1495	hgsc.bcm.edu	37	5	138118896	138118897	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:138118896_138118897delGG	ENST00000302763.7	+	3	226_227	c.136_137delGG	c.(136-138)gggfs	p.G46fs	CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000518825.1_Frame_Shift_Del_p.G46fs	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	46	Involved in homodimerization.				adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CAATAGTAAAGGGCCCTCTAAT	0.356																																					p.45_46del		Atlas-Indel,Pindel	.											.	CTNNA1	114	.	0			c.135_136del						PASS	.																																			SO:0001589	frameshift_variant	1495	exon3			.	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.136_137delGG	chr5.hg19:g.138118896_138118897delGG	ENSP00000304669:p.Gly46fs	72.0	0.0	0		104.0	18.0	0.173077	NM_001903	Q12795|Q8N1C0	Frame_Shift_Del	DEL	ENST00000302763.7	hg19	CCDS34243.1																																																																																			.	.	.	none		0.356	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
AEBP1	165	hgsc.bcm.edu	37	7	44150535	44150535	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr7:44150535delG	ENST00000223357.3	+	13	1814	c.1509delG	c.(1507-1509)aagfs	p.K503fs	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Frame_Shift_Del_p.K46fs	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	503	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						ACGTGGACAAGGACACACCCG	0.627																																					p.K503fs		Atlas-Indel,Pindel	.											.	AEBP1	102	.	0			c.1508delA						PASS	.						88.0	81.0	83.0					7																	44150535		2203	4300	6503	SO:0001589	frameshift_variant	165	exon13			.	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.1509delG	chr7.hg19:g.44150535delG	ENSP00000223357:p.Lys503fs	73.0	0.0	0		105.0	30.0	0.285714	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Frame_Shift_Del	DEL	ENST00000223357.3	hg19	CCDS5476.1																																																																																			.	.	.	none		0.627	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
FAT4	79633	hgsc.bcm.edu	37	4	126408614	126408614	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:126408614delA	ENST00000394329.3	+	16	12944	c.12931delA	c.(12931-12933)aaafs	p.K4311fs	FAT4_ENST00000335110.5_Frame_Shift_Del_p.K2552fs	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4311	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCTAATTGGGAAAAATGGAAC	0.403																																					p.G4310fs		Atlas-Indel,Pindel	.											FAT4_ENST00000394329,right_upper_lobe,carcinoma,0,2	FAT4	1752	.	0			c.12930delG						PASS	.						82.0	83.0	83.0					4																	126408614		2203	4300	6503	SO:0001589	frameshift_variant	79633	exon16			.	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12931delA	chr4.hg19:g.126408614delA	ENSP00000377862:p.Lys4311fs	54.0	0.0	0		65.0	15.0	0.230769	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Frame_Shift_Del	DEL	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
TG	7038	hgsc.bcm.edu	37	8	133899726	133899727	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:133899726_133899727insTA	ENST00000220616.4	+	9	2149_2150	c.2109_2110insTA	c.(2110-2112)tacfs	p.Y704fs	TG_ENST00000377869.1_Frame_Shift_Ins_p.Y704fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	704	Thyroglobulin type-1 6. {ECO:0000255|PROSITE-ProRule:PRU00500}.				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)		ACTCAGAGTGCTACTGTGTTGA	0.515																																					p.C703fs		Atlas-Indel,Pindel	.											.	TG	416	.	0			c.2109_2110insTA						PASS	.																																			SO:0001589	frameshift_variant	7038	exon9			.	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.2110_2111dupTA	chr8.hg19:g.133899727_133899728dupTA	ENSP00000220616:p.Tyr704fs	416.0	0.0	0		497.0	91.0	0.183099	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Frame_Shift_Ins	INS	ENST00000220616.4	hg19	CCDS34944.1																																																																																			.	.	.	none		0.515	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MLH3	27030	hgsc.bcm.edu	37	14	75516201	75516205	+	Frame_Shift_Del	DEL	TGAAC	TGAAC	-			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	TGAAC	TGAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:75516201_75516205delTGAAC	ENST00000556740.1	-	1	189_193	c.154_158delGTTCA	c.(154-159)gttcaafs	p.VQ52fs	MLH3_ENST00000556257.1_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000238662.7_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000544985.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	52					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GTCTATCACTTGAACTTGGAAGGTT	0.444								Mismatch excision repair (MMR)																													p.52_53del		Atlas-Indel,Pindel	.											.	MLH3	200	.	0			c.155_159del						PASS	.																																			SO:0001589	frameshift_variant	27030	exon2			.	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.154_158delGTTCA	chr14.hg19:g.75516201_75516205delTGAAC	ENSP00000452316:p.Val52fs	157.0	0.0	0		172.0	22.0	0.127907	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.	.	none		0.444	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381	
ZW10	9183	hgsc.bcm.edu	37	11	113619115	113619115	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:113619115delT	ENST00000200135.3	-	8	1097	c.953delA	c.(952-954)aatfs	p.N318fs		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	318					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TGTTTTTTCATTTTCCAGGTC	0.373																																					p.N318fs		Pindel	.											.	ZW10	49	.	0			c.954delT						PASS	.						94.0	87.0	90.0					11																	113619115		2201	4296	6497	SO:0001589	frameshift_variant	9183	exon8			.	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"""ZW10 (Drosophila) homolog, centromere/kinetochore protein"", ""ZW10, kinetochore associated, homolog (Drosophila)"""			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.953delA	chr11.hg19:g.113619115delT	ENSP00000200135:p.Asn318fs	62.0	0.0	.		67.0	10.0	0.149	NM_004724	A1A528	Frame_Shift_Del	DEL	ENST00000200135.3	hg19	CCDS8363.1																																																																																			.	.	.	none		0.373	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724	
